bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unifying the identification of biomedical entities with the Bioregistry
Authors: Hoyt Charles Tapley , Balk Meghan , Callahan Tiffany J. , Domingo-Fernández Daniel , Haendel Melissa A. , Hegde Harshad B. , Himmelstein Daniel S. , Karis Klas , Kunze John , Lubiana Tiago , Matentzoglu Nicolas , McMurry Julie , Moxon Sierra , Mungall Christopher J. , Rutz Adriano , Unni Deepak R. , Willighagen Egon , Winston Donald , Gyori Benjamin M. 
Published: November 2022

AbstractThe standardized identification of biomedical entities is a cornerstone of interoperability, reuse, and data integration in the life sciences. Several registries have been developed to catalog resources maintaining identifiers for biomedical entities such as small molecules, proteins, cell lines, and clinical trials. However, existing registries have struggled to provide sufficient coverage and metadata standards that meet the evolving needs of modern life sciences researchers. Here, we introduce the Bioregistry, an integrative, open, community-driven metaregistry that synthesizes and substantially expands upon 23 existing registries. The Bioregistry addresses the need for a sustainable registry by leveraging public infrastructure and automation, and employing a progressive governance model centered around open code and open data to foster community contribution. The Bioregistry can be used to support the standardized annotation of data, models, ontologies, and scientific literature, thereby promoting their interoperability and reuse. The Bioregistry can be accessed through https://bioregistry.io and its source code and data are available under the MIT and CC0 Licenses at https://github.com/biopragmatics/bioregistry.
ANGPTL4, IL-6 and TNF-α as regulators of lipid metabolism during a marathon run
Authors: Górecka Monika , Krzemiński Krzysztof , Mikulski Tomasz , Ziemba Andrzej Wojciech 
Published: November 2022

AbstractThe aim of the study was to reveal whether marathon running influences regulators of lipid metabolism i.e. angiopoietin-like protein 4 (ANGPTL4), interleukin 6 (IL-6) and tumor necrosis factor-α (TNF-α). Plasma concentration of ANGPTL4, IL-6, TNF-α and lipids were determined in samples collected from 11 male runners before the marathon, immediately after the run and at 90 min of recovery. Plasma ANGPTL4 increased during exercise from 55.5 ± 13.4 to 78.1 ± 15.0 ng/ml (P < 0.001). This was accompanied by a significant increase in IL-6, TNF-α, free fatty acids (FFA) and glycerol (Gly) and a decrease in triacylglycerols (TG). After 90 min of recovery ANGPTL4 and TG did not differ from the exercise values, while plasma IL-6, TNF-α, FFA and Gly concentration were significantly lower. The exercise-induced increase in plasma concentration of ANGPTL4 correlated positively with the rise in plasma IL-6, TNF-α, FFA and Gly and negatively with the duration of the run. The increase in plasma IL-6 and TNF-α correlated positively with the rise in Gly. Summarizing, marathon running induced an increase in plasma ANGPTL4 and the value was higher in faster runners. The increase in plasma FFA, IL-6 and TNF-α concentration during a marathon run may be involved in plasma ANGPTL4 release, which could be a compensatory mechanism against FFA-induced lipotoxicity and oxidative stress. All of the analyzed cytokines may stimulate lipolysis during exercise.
Direct calculation of the ionic mobility in superionic conductors
Authors: Carvalho Alexandra , Negi Suchit , Neto Antonio H. Castro 
Published: November 2022

AbstractWe describe an approach based on non-equilibrium molecular dynamics (NEMD) simulations to calculate the ionic mobility of solid ion conductors such as solid electrolytes from first-principles. The calculations are carried out in finite slabs of the material, where an electric field is applied and the dynamic response of the mobile ions is measured. We compare our results with those obtained from diffusion calculations, under the non-interacting ion approximation, and with experiment. This method is shown to provide good quantitative estimates for the ionic mobilities of two silver conductors,$$\alpha$$α-AgI and$$\alpha$$α-RbAg$$_4$$4I$$_5$$5. In addition to being convenient and numerically robust, this method accounts for ion-ion correlations at a much lower computational cost than exact approaches.
The diminution and modulation role of water-soluble gallic acid-carboxymethyl chitosan conjugates against the induced nephrotoxicity with cisplatin
Authors: Hafez Hani S. , Kotb Ebtesam S. , El-Khayat Zakaria , Elshaarawy Reda F. M. , Serag Waleed M. 
Published: November 2022

AbstractThe toxicity of cisplatin (CDDP) toward the renal tubules and its severe effects on the proximal tubules limits its further use in cancer therapy. The current study was undertaken to evaluate the protective effects of gallic acid-grafted O-carboxymethyl chitosan (GA@CMCS) against nephrotoxicity induced by CDDP in rats. Renal injury was assessed in the GA@CMCS/CDDP-treated rats using kidney injury molecule-1 (KIM-1). Moreover, the levels of reduced glutathione (GSH), malondialdehyde (MDA), and nitric oxide (NO) were measured. The comet assay was performed to measure the DNA damage. The renoprotective activity of GA@CMCS was supported by histo- and immuno-pathological studies of the kidney. GA@CMCS significantly normalized the increases in kidney homogenate of KIM-1, MDA, and NO-induced by CDDP and significantly increased GSH as compared with the CDDP group. GA@CMCS also significantly protects rat kidneys from CDDP-induced histo- and immuno-pathological changes. Both biochemical findings and histo- and immuno-pathological evidence showed the renoprotective potential of GA@CMCS against CDDP-induced oxidative stress, inflammation, and renal dysfunction in rats. In conclusion, GA@CMCS has been shown to mitigate the nephrotoxicity impact of CDDP in cancer therapy.
A fluorescent photoimmunoconjugate for imaging of cholesteatoma
Authors: Early Samuel , Saad M. Ahsan , Mallidi Srivalleesha , Mansour Amer , Seist Richard , Hasan Tayyaba , Stankovic Konstantina M. 
Published: November 2022

AbstractCholesteatoma is a potentially serious complication of chronic ear infections and requires surgical intervention for definitive management. Long-term complications include a frequent need for repeat surgical intervention for disease recurrence, and techniques to improve efficacy of single-stage surgery are an important area of continued research. This study investigates a novel application of the photosensitizer immune conjugate (PIC) cetuximab-benzoporphyrin derivative (Cet-BPD) for in vitro localization of human cholesteatoma tissue, coupled with an in vivo safety study for middle ear application of Cet-BPD in a murine model. In fresh human cholesteatoma tissues, Cet-BPD demonstrates selective localization to the hyperplastic squamous cell tissue associated with cholesteatoma, without localizing to other tissues such as middle ear mucosa. Applied to the murine middle ear, Cet-BPD does not demonstrate any deleterious effect on murine hearing when assessed by any of auditory brainstem response (ABR) thresholds, distortion product otoacoustic emission thresholds, or ABR wave I amplitudes. These findings demonstrate the technical promise and encouraging safety profile for the use of PICs for intraoperative localization and treatment of cholesteatoma.
Triglyceride-glucose index is significantly associated with the risk of hyperuricemia in patients with diabetic kidney disease
Authors: Li Qiuhong , Shao Xian , Zhou Saijun , Cui Zhuang , Liu Hongyan , Wang Tongdan , Fan Xiaoguang , Yu Pei 
Published: November 2022

AbstractTriglyceride–glucose (TyG) index has been proposed to be a simple, economical, and reliable marker of insulin resistance. We aimed to investigate whether TyG is an independent predictor of hyperuricemia in diabetic kidney disease (DKD) populations by conducting a cross-sectional and longitudinal study. A total of 6,471 patients were enrolled in cross-sectional analysis, and 3,634 patients without hyperuricemia at the baseline were included in longitudinal analysis and were followed up for a median of 23.0 months. Hyperuricemia was categorized as a serum uric acid level ≥ 420 umol/L (7 mg/dL). In this study, 19.58% of participants had hyperuricemia. In the cross-sectional analysis, multivariate logistics regression analysis showed that the ORs (95% CI) for hyperuricemia in the second, third, and fourth TyG quartiles were 1.40 (95% CI 0.73–2.65), 1.69 (95% CI 0.90–3.18), and 4.53 (95% CI 2.39–8.57), respectively, compared with the first quartile. Longitudinally, the Kaplan–Meier survival analysis showed that higher TyG levels predicted higher incidence of hyperuricemia. Multivariate Cox regression model revealed that the hazard ratios for hyperuricemia in the upper quartiles of the TyG index were 1.69 (95% CI 0.97–2.93), 2.23 (95% CI 1.33–3.75), and 2.50 (95% CI 1.46–4.27), respectively, compared with the first quartile. Moreover, the subgroup analyses revealed that the relationship between TyG levels and hyperuricemia was robust in DKD patients. Our findings indicate a significant independent correlation between the TyG index and the risk of hyperuricemia in DKD patients.
Investigating the role of the foveal cortex in peripheral object discrimination
Authors: Contemori Giulio , Oletto Carolina Maria , Cessa Roberta , Marini Elena , Ronconi Luca , Battaglini Luca , Bertamini Marco 
Published: November 2022

AbstractPeripheral object discrimination is hindered by a central dynamic mask presented between 150 and 300 ms after stimulus onset. The mask is thought to interfere with task-relevant feedback coming from higher visual areas to the foveal cortex in V1. Fan et al. (2016) supported this hypothesis by showing that the effect of mask can be further delayed if the task requires mental manipulation of the peripheral target. The main purpose of this study was to better characterize the temporal dynamics of foveal feedback. Specifically, in two experiments we have shown that (1) the effect of foveal noise mask is sufficiently robust to be replicated in an online data collection (2) in addition to a change in sensitivity the mask affects also the criterion, which becomes more conservative; (3) the expected dipper function for sensitivity approximates a quartic with a global minimum at 94 ms, while the best fit for criterion is a quintic with a global maximum at 174 ms; (4) the power spectrum analysis of perceptual oscillations in sensitivity data shows a cyclic effect of mask at 3 and 12 Hz. Overall, our results show that foveal noise affects sensitivity in a cyclic manner, with a global dip emerging earlier than previously found. The noise also affects the response bias, even though with a different temporal profile. We, therefore, suggest that foveal noise acts on two distinct feedback mechanisms, a faster perceptual feedback followed by a slower cognitive feedback.
Tube length of chironomid larvae as an indicator for dissolved oxygen in water bodies
Authors: Podder Rahul , Nath Susanta , Modak Biplob Kumar , Weltje Lennart , Malakar Biswanath 
Published: November 2022

AbstractTube-building larvae of non-biting midges, or chironomids, are considered bioindicators of water pollution. The larvae use benthic particles to make their tubes and create a respiratory current with the movement of their bodies inside the tubes. The tube length of the chironomid larvae varies depending on several physicochemical properties of the aquatic medium. Here we study the role of physicochemical parameters on the tube length from different field sites and in the laboratory. It appears that among different physicochemical factors, dissolved oxygen (DO) has a major role in determining the tube length of the larvae. A quantitative relationship between oxygen concentration and the tube length of larvae is presented here. Our study reveals a longer tube in aquatic media with oxygen deficiency and a shorter tube in those with higher oxygen. This result may help to assess the quality of water bodies and, in particular the status of DO.
Baseline bony erosions and time-averaged DAS28 predict discontinuation of TNF inhibitors in rheumatoid arthritis
Authors: Min Hong Ki , Kim Se Hee , Lee Sang-Heon , Kim Hae-Rim 
Published: November 2022

AbstractThe present study evaluated the predictive role of baseline radiographic change and disease activity on drug retention and clinical response in patients with rheumatoid arthritis (RA) treated with tumor necrosis factor inhibitor (TNFi). Korean Observational Study Network for Arthritis (KORONA) registry was evaluated to identify RA patients treated with a TNFi. Disease activity score-28 (DAS28) was evaluated at baseline and 1 year after TNFi initiation or at termination of TNFi due to inefficacy (within 1 year). The retention rate of TNFi was compared in patients with and without bony erosions. The hazard ratio (HR) for drug retention was evaluated by Cox regression analysis, as was the odds ratio (OR) for achieving remission (DAS28 < 2.6). This study included 109 RA patients, including 97 (89%) women and 30 (27.5%) with erosions, who were treated with a TNFi. Higher baseline DAS28 was negatively associated with achievement of remission (OR = 0.56, 95% CI 0.35–0.88). The TNFi retention rate was significantly lower in RA patients with than in those without erosions (p = 0.04). Factors significantly associated with drug discontinuation included the presence of erosions (HR = 2.45, 95% CI 1.08–5.51) and higher time-averaged DAS28 (HR = 2.17, 95% CI 1.47–3.20), whereas concomitant methotrexate was associated with lack of drug discontinuation (HR = 0.40, 95% CI 0.17–0.95). The presence of erosions and high time-averaged disease activity could predict poor retention of TNFi by RA patients. Higher baseline DAS28 was associated with a reduced clinical response in patients with RA.Trial registration Clinical Research Information Service of South Korea https://cris.nih.go.kr: KCT0000086, registered May 26, 2009.
Profiling mRNA, miRNA and lncRNA expression changes in endothelial cells in response to increasing doses of ionizing radiation
Authors: Chopra Sunita , Shankavaram Uma , Bylicky Michelle , Dalo Juan , Scott Kevin , Aryankalayil Molykutty J. , Coleman C. Norman 
Published: November 2022

AbstractRecent and past research have highlighted the importance of the endothelium in the manifestation of radiation injury. Our primary focus is on medical triage and management following whole body or partial-body irradiation. Here we investigated the usability of endothelial cells’ radiation response for biodosimetry applications. We profiled the transcriptome in cultured human endothelial cells treated with increasing doses of X-rays. mRNA expression changes were useful 24 h and 72 h post-radiation, microRNA and lncRNA expression changes were useful 72 h after radiation. More mRNA expressions were repressed than induced while more miRNA and lncRNA expressions were induced than repressed. These novel observations imply distinct radiation responsive regulatory mechanisms for coding and non-coding transcripts. It also follows how different RNA species should be explored as biomarkers for different time-points. Radiation-responsive markers which could classify no radiation (i.e., ‘0 Gy’) and dose-differentiating markers were also predicted. IPA analysis showed growth arrest-related processes at 24 h but immune response coordination at the 72 h post-radiation. Collectively, these observations suggest that endothelial cells have a precise dose and time-dependent response to radiation. Further studies in the laboratory are examining if these differences could be captured in the extracellular vesicles released by irradiated endothelial cells.
Ultrasound-assisted synthesis of kojic acid-1,2,3-triazole based dihydropyrano[3,2-b]pyran derivatives using Fe3O4@CQD@CuI as a novel nanomagnetic catalyst
Authors: Najafi Zahra , Esmaili Soheila , Khaleseh Behnam , Babaee Saeed , Khoshneviszadeh Mehdi , Chehardoli Gholamabbas , Akbarzadeh Tahmineh 
Published: November 2022

AbstractThe magnetic nanoparticles coated with carbon quantum dot and copper (I) iodide (Fe3O4@CQD@CuI) were used as eco-friendly heterogeneous Lewis / Brønsted acid sites and Cu (I) nanocatalysts. In the first step, it was applied in the synthesis of kojic acid-based dihydropyrano[3,2-b]pyran derivatives in a three-component reaction and in the second step, as a recyclable catalyst for the synthesis of kojic acid-1,2,3-triazole based dihydropyrano[3,2-b]pyran derivatives in the CuI-catalyzed azide/alkyne cycloaddition (CuAAC) reaction. The catalyst was characterized fully by using the different techniques including fourier transform infrared spectroscopy (FT-IR), elemental mapping analysis, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), X-ray spectroscopy (EDX), transmission electron microscopy (TEM), thermal gravimetric (TG) and value-stream mapping (VSM) methods. The final synthesized derivatives were identified by 1H- and 13C-NMR spectroscopy.
Mohawk impedes angiofibrosis by preventing the differentiation of tendon stem/progenitor cells into myofibroblasts
Authors: Mechakra Asma , Lin Junxin , Yang Yuwei , Du Xiaotian , Zhang Jingwei , Ewetse Paul Maswikitu , Zhou Feifei , Alakpa Enateri 
Published: November 2022

AbstractAdult tendons heal via fibrovascular scarring with inferior biomechanical properties. Mohawk (Mkx) emerged as a pivotal actor in tenolineage commitment. However, its precise function in tendinopathy remains poorly understood. This study investigates the cellular and molecular mechanisms underlying Mkx’ role in fibrovascular healing. Human samples were collected to test fibrovascular markers. We then performed RNAseq onMkx−/−mice compared to their wild type littermates to decipher Mkx regulome. We therefore sought to reproduce TSPCs transition to myofibroblasts in-vitro by over-expressing MyoD and followed by phenotypic and experimental cells’ characterization using microscopy, qRT-PCR, flow cytometry sorting, presto-blue cell viability assay and immunofluorescence. Two different in vivo models were used to assess the effect of the MyoD-expressing myofibroblasts: transplantation in the dorsal area of immunodeficient mice and in an adult Achilles tendon injury model. To prevent angiofibrosis, we tested the molecule Xav939 and proceeded with histological stainings, q-RT PCR transcriptional quantification of angifibrotic markers, mechanical tests, and immunofluorescence. Tendinopathy samples showed fibrovascular healing with decreased tenolineage phenotype. Transcriptomic analysis ofMkx−/− tendons revealed myofibroblast-associated biological processes. Over-expression of MyoD in WT tendon stem progenitor cells (TSPCs) gave rise to myofibroblasts reprogramming in-vitro and fibrovascular scarring in-vivo. MKX directly binds to MyoD promoter and underlies global regulative processes related to angiogenesis and Wnt signaling pathway. Blocking Wnt signaling with the small molecule Xav393 resulted in higher histological and biomechanical properties. Taken together, our data provide the first in vivo and in-vitro evidence of tendon stem progenitor cells to myofibroblasts transition and show improved tendon healing via angiofibrosis modulation, thus opening potential therapeutic avenues to treat tendinopathy patients.
Quantum DFT methods to explore the interaction of 1-Adamantylamine with pristine, and P, As, Al, and Ga doped BN nanotubes
Authors: Nemati‐Kande Ebrahim , Pourasadi Amir , Aghababaei Fatemeh , Baranipour Samaneh , Mehdizadeh Ata , Sardroodi Jaber Jahanbin 
Published: November 2022

AbstractNanostructures, nowadays, found growing applications in different scientific and industrial areas. Nano-coins, nanosheets, and nanotubes are used in medical applications as sensors or drug delivery substances. The aim of this study is to explore the adsorption of 1-Adamantylamine drug on the pristine armchair boron nitride nanotubes (BNNTs) with BNNT(5,5), BNNT(6,6), and BNNT(7,7) chirality along with the P, As, Al and Ga-doped BNNTs, using the quantum mechanical density functional methods. Considering the fact that dispersion effects are important in the case of weak Van der Waals interactions, computations have been done using B3LYP hybrid functional with the implementation of the D3(BJ) empirical dispersion correction methods. Quantum theory of atoms in molecules, natural bonding orbitals, and Kohn–Sham orbitals were used to investigate the nature and type of the adsorption process. The results showed that, while the adsorption of 1-Adamantylamine on the outer surface of pristine BNNT is physical in nature, doping can improve the ability of detracted BN to adsorb the drug through chemical bonds. Also, it was found that, by increasing the radius of the BNNT the adsorption energy was decreased. In conclusion, results of the present work suggest that, Ga doped nanotube, due the chemisorption, is not an ideal nanotube in drug delivery of 1-Adamantylamine drug, whereas, the other studied cases physiosorbed the drug, and may not have serious problem in release of the 1-Adamantylamine drug.
Ultrafast switching in synthetic antiferromagnet with bilayer rare-earth transition-metal ferrimagnets
Authors: Ma Chung Ting , Zhou Wei , Poon S. Joseph 
Published: November 2022

AbstractIn spintronics, it is important to be able to manipulate magnetization rapidly and reliably. Several methods can control magnetization, such as by applying current pulses or magnetic fields. An applied current can reverse magnetization with nanosecond speed through the spin torque effect. For faster switching, subpicosecond switching with femtoseconds laser pulse has been achieved in amorphous rare-earth transition-metal ferrimagnets. In this study, we employed atomistic simulations to investigate ultrafast switching in a synthetic antiferromagnet with bilayer amorphous FeGd ferrimagnets. Using a two-temperature model, we demonstrated ultrafast switching in this synthetic antiferromagnet without external magnetic fields. Furthermore, we showed that if we initially stabilize a skyrmion in this heterostructure, the ultrafast laser can switch the skyrmion state using the same mechanism. Furthermore, this bilayer design allows the control of each ferrimagnetic layer individually and opens the possibility for a magnetic tunnel junction.