bluuebunny/crossref_metadata_2025_split huggingface dataset:
Residual periodontal ligament in the extraction socket promotes the dentin regeneration potential of DPSCs in the rabbit jaw
Authors: Luo Bin , Luo Yu , He Lin , Cao Yangyang , Jiang Qingsong 
Published: March 2023

Abstract
Background
Because of the low regeneration efficiency and unclear underlying molecular mechanism, tooth regeneration applications are limited. In this study, we explored the influence of residual periodontal ligament on the dentin regeneration potential of dental pulp stem cells (DPSCs) in the jaw.

Methods
To establish a tooth regeneration model, the incisors of New Zealand white rabbits were extracted while preserving residual periodontal ligament, followed by the implantation of DPSCs. After 3 months, micro-computed tomography (micro-CT), stereomicroscopy and scanning electron microscopy (SEM) were used to observe the volume, morphology and microstructure of regenerated tissue. Histological staining and immunostaining analyses were used to observe the morphological characteristics and expression of the dentin-specific proteins DMP1 and DSPP. To explore the mechanism, DPSCs and periodontal ligament stem cells (PDLSCs) were cocultured in vitro, and RNA was collected from the DPSCs for RNA-seq and bioinformatic analysis.

Results
The results of micro-CT and stereomicroscopy showed that the number of sites with regeneration and the volume of regenerated tissue in the DPSCs/PDL group (6/8, 1.07 ± 0.93 cm3) were larger than those in the DPSCs group (3/8, 0.23 ± 0.41 cm3). The results of SEM showed that the regenerated dentin-like tissue in the DPSCs and DPSCs/PDL groups contained dentin tubules. Haematoxylin and eosin staining and immunohistochemical staining indicated that compared with the DPSCs group, the DPSCs/PDL group showed more regular regenerated tissue and higher expression levels of the dentin-specific proteins DMP1 and DSPP (DMP1: P = 0.02, DSPP: P = 0.01). RNA-seq showed that the coculture of DPSCs with PDLSCs resulted in the DPSCs differentially expressing 427 mRNAs (285 upregulated and 142 downregulated), 41 lncRNAs (26 upregulated and 15 downregulated), 411 circRNAs (224 upregulated and 187 downregulated), and 19 miRNAs (13 upregulated and 5 downregulated). Bioinformatic analysis revealed related Gene Ontology function and signalling pathways, including extracellular matrix (ECM), tumour necrosis factor (TNF) signalling and chemokine signalling pathways.

Conclusions
Residual periodontal ligament in the extraction socket promotes the dentin regeneration potential of DPSCs in the jaw. RNA-seq and bioinformatic analysis revealed that ECM, TNF signalling and chemokine signalling pathways may represent the key factors and signalling pathways.
Interpreting vibrational circular dichroism spectra: the Cai•factor for absolute configuration with confidence
Authors: Lam Jonathan , Lewis Richard J. , Goodman Jonathan M. 
Published: March 2023

AbstractVibrational circular dichroism (VCD) spectroscopy can generate the data required for the assignment of absolute configuration, but the spectra are hard to interpret. We have recorded VCD data for thirty pairs of small organic compounds and we use this database to validate a method for the automated analysis of VCD spectra and the assignment of absolute configuration: the Cai•factor (Configuration: absolute information). The analysis of the data demonstrates that the procedure is a reliable and time-efficient method for determination of absolute configuration, which gives both the assignment and a measure of confidence in the outcome, even when the spectra are imperfect. The majority of molecules tested have a high confidence score and all of these have the correct assignment.
Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods
Authors: Lou Chaofeng , Yang Hongbin , Deng Hua , Huang Mengting , Li Weihua , Liu Guixia , Lee Philip W. , Tang Yun 
Published: March 2023

AbstractChemical mutagenicity is a serious issue that needs to be addressed in early drug discovery. Over a long period of time, medicinal chemists have manually summarized a series of empirical rules for the optimization of chemical mutagenicity. However, given the rising amount of data, it is getting more difficult for medicinal chemists to identify more comprehensive chemical rules behind the biochemical data. Herein, we integrated a large Ames mutagenicity data set with 8576 compounds to derive mutagenicity transformation rules for reversing Ames mutagenicity via matched molecular pairs analysis. A well-trained consensus model with a reasonable applicability domain was constructed, which showed favorable performance in the external validation set with an accuracy of 0.815. The model was used to assess the generalizability and validity of these mutagenicity transformation rules. The results demonstrated that these rules were of great value and could provide inspiration for the structural modifications of compounds with potential mutagenic effects. We also found that the local chemical environment of the attachment points of rules was critical for successful transformation. To facilitate the use of these mutagenicity transformation rules, we integrated them into ADMETopt2 (http://lmmd.ecust.edu.cn/admetsar2/admetopt2/), a free web server for optimization of chemical ADMET properties. The above-mentioned approach would be extended to the optimization of other toxicity endpoints.
Graphical Abstract
Comprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine
Authors: Kim Eiseul , Jung Hae-In , Park Si Hong , Kim Hae-Yeong , Kim Soo-Ki 
Published: March 2023

AbstractThe Burkholderia cepacia complex (BCC) is a Gram-negative bacterial, including Burkholderia contaminans species. Although the plain Burkholderia is pervasive from taxonomic and genetic perspectives, a common characteristic is that they may use the quorum-sensing (QS) system. In our previous study, we generated the complete genome sequence of Burkholderia contaminans SK875 isolated from the respiratory tract. To our knowledge, this is the first study to report functional genomic features of B. contaminans SK875 for understanding the pathogenic characteristics. In addition, comparative genomic analysis for five B. contaminans genomes was performed to provide comprehensive information on the disease potential of B. contaminans species. Analysis of average nucleotide identity (ANI) showed that the genome has high similarity (> 96%) with other B. contaminans strains. Five B. contaminans genomes yielded a pangenome of 8832 coding genes, a core genome of 5452 genes, the accessory genome of 2128 genes, and a unique genome of 1252 genes. The 186 genes were specific to B. contaminans SK875, including toxin higB-2, oxygen-dependent choline dehydrogenase, and hypothetical proteins. Genotypic analysis of the antimicrobial resistance of B. contaminans SK875 verified resistance to tetracycline, fluoroquinolone, and aminoglycoside. Compared with the virulence factor database, we identified 79 promising virulence genes such as adhesion system, invasions, antiphagocytic, and secretion systems. Moreover, 45 genes of 57 QS-related genes that were identified in B. contaminans SK875 indicated high sequence homology with other B. contaminans strains. Our results will help to gain insight into virulence, antibiotic resistance, and quorum sensing for B. contaminans species.
Remote ischemic preconditioning protects against spinal cord ischemia–reperfusion injury in mice by activating NMDAR/AMPK/PGC-1α/SIRT3 signaling
Authors: Gu Changjiang , Kong Fanqi , Zeng Junkai , Geng Xiangwu , Sun Yanqing , Chen Xiongsheng 
Published: March 2023

Abstract
Background
To study the protective effects of delayed remote ischemic preconditioning (RIPC) against spinal cord ischemia–reperfusion injury (SCIRI) in mice and determine whether SIRT3 is involved in this protection and portrayed its upstream regulatory mechanisms.

Methods
In vivo, WT or SIRT3 global knockout (KO) mice were exposed to right upper and lower limbs RIPC or sham ischemia. After 24 h, the abdominal aorta was clamped for 20 min, then re-perfused for 3 days. The motor function of mice, number of Nissl bodies, apoptotic rate of neurons, and related indexes of oxidative stress in the spinal cord were measured to evaluate for neuroprotective effects. The expression and correlation of SIRT3 and NMDAR were detected by WB and immunofluorescence. In vitro, primary neurons were exacted and OGD/R was performed to simulate SCIRI in vivo. Neuronal damage was assessed by observing neuron morphology, detecting LDH release ratio, and flow cytometry to analyze the apoptosis. MnSOD and CAT enzyme activities, GSH and ROS level were also measured to assess neuronal antioxidant capacity. NMDAR-AMPK-PGC-1α signaling was detected by WB to portray upstream regulatory mechanisms of RIPC regulating SIRT3.

Results
Compared to the SCIRI mice without RIPC, mice with RIPC displayed improved motor function recovery, a reduced neuronal loss, and enhanced antioxidant capacity. To the contrary, the KO mice did not exhibit any effect of RIPC-induced neuroprotection. Similar results were observed in vitro. Further analyses with spinal cord tissues or primary neurons detected enhanced MnSOD and CAT activities, as well as increased GSH level but decreased MDA or ROS production in the RIPC + I/R mice or NMDA + OGD/R neurons. However, these changes were completely inhibited by the absence of SIRT3. Additionally, NMDAR-AMPK-PGC-1α signaling was activated to upregulate SIRT3 levels, which is essential for RIPC-mediated neuroprotection.

Conclusions
RIPC enhances spinal cord ischemia tolerance in a SIRT3-dependent manner, and its induced elevated SIRT3 levels are mediated by the NMDAR-AMPK-PGC-1α signaling pathway. Combined therapy targeting SIRT3 is a promising direction for treating SCIRI.
Aging aggravates acetaminophen-induced acute liver injury and inflammation through inordinate C/EBPα-BMP9 crosstalk
Authors: Liu Rui , Xu Wentao , Zhu He , Dong Zijian , Dong Huke , Yin Shi 
Published: March 2023

Abstract
Background
Previous studies have shown that bone morphogenetic protein 9 (BMP9) is almost exclusively produced in the liver and reaches tissues throughout the body as a secreted protein. However, the mechanism of BMP9 action and its role in aging-associated liver injury and inflammation are still unclear.

Results
Aging significantly aggravates acetaminophen (APAP)-induced acute liver injury (ALI). Increased expression of CCAAT/enhancer binding protein α (C/EBPα) and BMP9 was identified in aged livers and in hepatocytes and macrophages (MФs) isolated from aged mice. Further analysis revealed that excess BMP9 was directly related to APAP-induced hepatocyte injury and death, as evidenced by activated drosophila mothers against decapentaplegic protein 1/5/9 (SMAD1/5/9) signaling, an increased dead cell/total cell ratio, decreased levels of ATG3 and ATG7, blocked autophagy, increased senescence‐associated beta‐galactosidase (SA‐β‐Gal) activity, and a higher rate of senescence‐associated secretory phenotype (SASP) acquisition. In contrast, Bmp9 knockout (Bmp9−/−) partially alleviated the aforementioned manifestations of BMP9 overexpression. Moreover, BMP9 expression was found to be regulated by C/EBPα in vitro and in vivo. Notably, BMP9 also downregulated autophagy through its effect on autophagy-related genes (ATG3 and ATG7) in MΦs, which was associated with aggravated liver injury and SASP acquisition.

Conclusions
In summary, the present study highlights the crucial roles played by C/EBPα-BMP9 crosstalk and provides insights into the interrelationship between hepatocytes and MΦs during acute liver injury.
Trends and correlated outcomes in population-level prescription opioid and transdermal fentanyl use in Israel
Authors: Shapira Barak , Berkovitz Ronny , Haklai Ziona , Goldberger Nehama , Lipshitz Irena , Rosca Paola 
Published: March 2023

Abstract
Background
In the last twenty years, there was a documented increase in prescription opioid procurement in Israel. However, there is still little evidence of the association between opioid procurement rates, health service utilisation in secondary care, and enrollment rates to substance use disorder treatment programmes. In this study, we show trends in the reports of opioid-related hospitalisations, emergency department visits, enrollment to community-based outpatient treatment for Prescription Opioid Use Disorder and opioid-related mortality rates. Additionally, we examine potential correlations between these health service utilisation rates and prescription opioid procurement rates at the population level, with a focus on transdermal fentanyl.

Methods
A longitudinal study at the population level. We used seven-year data on indicators of opioid-related morbidity, prescription opioid procurement data for 2015–2021, and six-year opioid-related mortality data for 2015–2020. We measure the correlation between procurement rates of prescription opioids in Oral Morphine Equivalent per capita, and aggregated rates obtained from hospital administrative data for hospitalisations, emergency department visits, and patient enrolment in specialised prescription opioid use disorder outpatient treatment in the community setting.

Results
Between 2015 and 2021, procurement rates in primary care per capita for all prescription opioids increased by 85%, while rates of transdermal fentanyl procurement increased by 162%. We found a significant positive correlation at the population level, between annual opioid procurement rates, and rates per population of opioid-related visits to emergency departments (r = 0.96, p value < 0.01, [CI 0.74–0.99]), as well as a positive correlation with the rates per population of patient enrolment in specialised prescription opioid use disorder outpatient treatment (r = 0.93, p value = 0.02, [CI 0.58–0.99]). Opioid-related mortality peaked in 2019 at 0.31 deaths per 100,000 but decreased to 0.20 deaths per 100,000 in 2020.

Conclusion
Data shows that all-opioid and transdermal fentanyl procurement has increased yearly between 2015 and 2021. This increase is positively correlated with a growing demand for community-based Prescription Opioid Use Disorder outpatient treatment. Efforts to reduce opioid-related morbidity may require effective approaches toward appropriate prescribing, monitoring, and further increasing access to prescription opioid outpatient treatment.
Association between body condition score, testicular haemodynamics and echogenicity, nitric oxide levels, and total antioxidant capacity in rams
Authors: El-Sherbiny Hossam R. , El-Shalofy Amr S. , Samir Haney 
Published: March 2023

AbstractHigher body fatness adversely affects metabolic and hormonal homeostasis. The present work aimed to evaluate the association between body condition score (BCS) and haemodynamic pattern and echogenic appearence of the testes as well as nitric oxide (NO) levels and total antioxidant capacity (TAC). For that, fifteen Ossimi rams were blocked according to their BCS into a lower BCS group (L-BCS:2–2.5; n = 5), medium BCS group (M-BCS:3–3.5; n = 5), and higher BCS group (H-BCS:4–4.5; n = 5). Rams were examined for testicular haemodynamics (TH; Doppler ultrasonography), testicular echotexture (TE; B-mode image software analysis), and serum levels of NO and TAC (colorimetric). Results are presented as means ± standard error of the mean. There was a significant (P < 0.05) difference in the resistive index and pulsatility index means among the groups under experimentation, being the least in the L-BCS group (0.43 ± 0.02 and 0.57 ± 0.04, respectively) compared to the M-BCS (0.53 ± 0.03 and 0.77 ± 0.03, respectively) and H-BCS rams (0.57 ± 0.01 and 0.86 ± 0.03, respectively). Among blood flow velocity measurements [peak systolic, end-diastolic (EDV), and time-average maximum], only EDV showed significant (P < 0.05) higher values in the L-BCS group (17.06 ± 1.03 cm/s) compared to M-BCS (12.58 ± 0.67 cm/s) and H-BCS (12.51 ± 0.61 cm/s) groups. Regarding the TE results, there were no significant differences among the examined groups. There were significant differences (P < 0.01) in the concentrations of TAC and NO among the groups under experimentation, in which the L-BCS rams had the highest levels of TAC and NO in their sera (0.90 ± 0.05 mM/L and 62.06 ± 2.72 μM/L, respectively) than the M-BCS (0.058 ± 0.05 mM/L and 47.89 ± 1.49 μM/L, respectively) and H-BCS rams (0.45 ± 0.03 mM/L and 49.93 ± 3.63 μM/L, respectively). In conclusion, body condition score is associated with both testicular hemodynamic and the antioxidant capacity in rams.
ASBL: low-cost, small-sized AUV remote guidance method and experimental verification
Authors: Shi Yang , Han Xiao , Ma Lin , Guo Lin 
Published: March 2023

AbstractThe low-cost, small-sized autonomous underwater vehicle (AUV) is the preferred carrier for seabed operations. As all know, the inertial navigation system (INS) error drifts over time. Three or more seafloor datum signals are required when error-correcting the INS using the long baseline (LBL). Typically, a seafloor datum has an acoustic ranging capability of 15 km. However, the positioning ability of the conventional LBL is limited and cannot play the role of remote guidance when there is only a single datum. The paper proposes the Acoustic Synthetic Baseline (ASBL) positioning technology, which can achieve target positioning through multi-frame acoustic distance estimates between the measured target and the underwater datum. Firstly, the positioning principle of the ASBL is introduced, and the error distribution is analyzed in the paper. Secondly, a small-sized AUV is used to carry out the verification on the lake test, and the result shows that the ASBL positioning technology can play a guiding role. According to the statistics of the positioning results, the detection probability of less than 5% positioning error can reach more than 83%. The ASBL technology can reduce the dependence on the number of seafloor datums that convenience and operation efficiency can improve only by a single datum.
Deep learning-based wave digital modeling of rate-dependent hysteretic nonlinearities for virtual analog applications
Authors: Massi Oliviero , Mezza Alessandro Ilic , Giampiccolo Riccardo , Bernardini Alberto 
Published: March 2023

AbstractElectromagnetic components greatly contribute to the peculiar timbre of analog audio gear. Indeed, distortion effects due to the nonlinear behavior of magnetic materials are known to play an important role in enriching the harmonic content of an audio signal. However, despite the abundant research that has been devoted to the characterization of nonlinearities in the context of virtual analog modeling over the years, the discrete-time simulation of circuits exhibiting rate-dependent hysteretic phenomena remains an open challenge. In this article, we present a novel data-driven approach for the wave digital modeling of rate-dependent hysteresis using recurrent neural networks (RNNs). Thanks to the modularity of wave digital filters, we are able to locally characterize the wave scattering relations of a hysteretic reluctance by encapsulating an RNN-based model into a single one-port wave digital block. Hence, we successfully apply the proposed methodology to the emulation of the output stage of a vacuum-tube guitar amplifier featuring a nonlinear transformer.
Analysis of scalable channel estimation in FDD massive MIMO
Authors: Zhang Xing , Sabharwal Ashutosh 
Published: March 2023

AbstractOne of the key ideas for reducing downlink channel acquisition overhead for FDD massive MIMO systems is to exploit a combination of two assumptions: (i) the dimension of channel models in propagation domain may be much smaller than the next-generation base-station array sizes (e.g., 64 or more antennas), and (ii) uplink and downlink channels may share the same low-dimensional propagation domain. Our channel measurements demonstrate that the two assumptions may not always hold, thereby impacting the predicted performance of methods that rely on the above assumptions. In this paper, we analyze the error in modeling the downlink channel using uplink measurements, caused by the mismatch from the above two assumptions. We investigate how modeling error varies with base-station array size and provide both numerical and experimental results. We observe that modeling error increases with the number of base-station antennas, and channels with larger angular spreads have larger modeling error. Utilizing our modeling error analysis, we then investigate the resulting beamforming performance rate loss. Accordingly, we observe that the rate loss increases with the number of base-station antennas, and channels with larger angular spreads suffer from higher rate loss.
A monopole broadband circularly polarized antenna with coupled disc and folded microstrip stub lines
Authors: Ma Zhonghua , Chen Jiaxiang , Li Chen , Jiang Yanfeng 
Published: March 2023

AbstractA broadband circularly polarized (CP) printed monopole antenna which fed by coplanar waveguide (CPW) is proposed in the paper. The structure of the novel antenna includes a quarter circular disc radiating monopole, a coupled circular patch, and a bent L-shaped microstrip stub line. The L-shaped microstrip stub line is used to widen the impedance bandwidth and generate a horizontal component of the electromagnetic wave. The adoption of the asymmetric ground coplanar waveguide structure with the single-feed technology and the coupled circular patch, simultaneously achieve wide impedance bandwidth and wide axial ratio (AR) bandwidth. The structure parameters and the surface current of the designed antenna are analysed. The simulation and the measurement are conducted, showing good characterizations of the designed antenna. The 10-dB impedance bandwidth is 7.57 GHz, the fractional bandwidth from 6.05 to 13.62 GHz is 76.9%, the 3-dB axial ratio bandwidth is 3.01 GHz, and the fractional bandwidth from 6.05 to 9.06 GHz is 39.8%. The antenna can generate right/left hand circularly polarized waves in the direction of ± z axis. The designed antenna has wide applications in the fields of Internet of Things (IoT), broadband dual-CP communication systems and polarization diversity systems, wireless personal area network and other advanced communication systems.
A flower bud-shaped flexible UWB antenna for healthcare applications
Authors: Karad Kailash V. , Hendre Vaibhav S. 
Published: March 2023

AbstractRemote surveillance of the elderly and others with health difficulties is becoming increasingly important in these epidemic days. To address these issues, low-cost, lightweight, and portable wearable devices are in huge demand. This paper realizes the design and analysis of a flexible ultra-wideband (UWB) antenna for healthcare applications. The proposed hexagonal microstrip antenna encompasses two cuts on the top left and right side of the hexagon which looks like a flower bud. The antenna is fabricated using a flexible foam substrate with a dielectric constant of 1.07 and has a dimension of$$38 \times 30 \times 1.7\,{\text{mm}}^{3}$$38×30×1.7mm3. With a unique patch shape and corner cut in the partial ground, the present design strives to optimize the antenna structure to accommodate UWB (3.1 to 10.6 GHz) operating spectrum from 2.6 to 11.3 GHz. The proposed antenna has achieved an FBW of 125.17% with a total gain of 5.24 dB. The antenna is also evaluated on the line of bending and SAR over a tissue of 1 g and 10 g. The antenna operated admirably, with an average SAR value below the safety limits of 1.6 W/kg and 2 W/kg for the tissues, respectively.