bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mineralogical analysis of 14 PHAs from ViNOS data
Authors: Morate D , Popescu M , Licandro J , Tinaut-Ruano F , Tatsumi E , de León J 
Published: December 2022

ABSTRACT
Potentially hazardous asteroids (PHAs) are objects that can have close encounters with Earth and are significantly large to cause significant regional damage in the event of impact. The mitigation strategy requires to understand their physical properties. We aim to investigate the physical nature of PHAs, using data obtained within the framework of the Visible NEOs Observations Survey (ViNOS). We analysed and characterized a sample comprised of 14 of these objects. To conduct this study, we obtained visible spectra of 14 PHAs in the 0.5–0.9-μm region using the 2.5 m Nordic Optical Telescope, located at the El Roque De Los Muchachos Observatory in La Palma (Spain). The resulting spectra were combined with their corresponding near-infrared counterparts, available in the literature from the Small Main-Belt Asteroid Spectroscopic Survey (SMASS). We performed a taxonomical classification, computed several diagnostic spectral parameters (slopes, band centres, and band area ratios), and provide completely new mineralogical information for 10 of these objects. We also compared the data with laboratory spectra of meteorites from the RELAB data base. Among the studied sample of PHAs, approximately 90 per cent of the objects (13 out of 14) were classified as silicaceous (S-types and subclasses). Only one object, 489 486, was classified as carbonaceous. Five of the studied PHAs did not have previous taxonomic classifications. The comparisons of the silicaceous PHAs with meteoritic spectra yielded, in all cases, ordinary chondrites as the best match for meteoritic analogues. The computed mineralogy of all of our targets is also consistent with this results.
Imprint of f(R) gravity in the cosmic magnification
Authors: Duniya Didam G A , Abebe Amare , de la Cruz-Dombriz Álvaro , Dunsby Peter K S 
Published: December 2022

ABSTRACT
f(R) gravity is one of the simplest viable modifications to General Relativity: it passes local astrophysical tests, predicts both the early-time cosmic inflation and the late-time cosmic acceleration, and describes dark matter. In this paper, we probe cosmic magnification on large scales in f(R) gravity, using the well-known Hu-Sawicki model as an example. Our results indicate that at redshifts $z \, {\lt }\, 3$, values of the model exponent $n \, {\gt }\, 1$ lead to inconsistent behaviour in the evolution of the scalar perturbations. Moreover, when relativistic effects are taken into account in the large-scale analysis, our results show that as z increases, large-scale changes in the cosmic magnification angular power spectrum owing to integral values of n tend to share a similar pattern, while those of decimal values tend to share another. This feature could be searched for in the experimental data, as a potential ‘smoking gun’ for the given class of gravity models. Furthermore, we found that at $z \, {=}\, 1$ and lower, relativistic effects lead to a suppression of the cosmic magnification on large scales in f(R) gravity, relative to the concordance model; whereas, at $z \, {\gt }\, 1$, relativistic effects lead to a relative boost of the cosmic magnification. In general, relativistic effects enhance the potential of the cosmic magnification as a cosmological probe.
Cosmological constraint precision of photometric and spectroscopic multi-probe surveys of China Space Station Telescope (CSST)
Authors: Miao Haitao , Gong Yan , Chen Xuelei , Huang Zhiqi , Li Xiao-Dong , Zhan Hu 
Published: December 2022

ABSTRACT
As a Stage IV space-based telescope, the China Space Station Telescope (CSST) can perform photometric and spectroscopic surveys simultaneously to explore the Universe efficiently in extreme precision. In this work, we investigate several powerful CSST cosmological probes, including cosmic shear, galaxy–galaxy lensing, photometric and spectroscopic galaxy clustering, and number counts of galaxy clusters, and study the capability of these probes by forecasting the results of joint constraints on the cosmological parameters. By referring to real observational results, we generate mock data and estimate the measured errors based on CSST observational and instrumental designs. To study systematic effects on the results, we also consider a number of systematics in CSST photometric and spectroscopic surveys, such as the intrinsic alignment, shear calibration uncertainties, photometric redshift uncertainties, galaxy bias, non-linear effects, instrumental effects, etc. The Fisher matrix method is used to derive the constraint results on the cosmological and systematic parameters from individual or joint surveys. We find that the joint constraints achieved by including all these CSST cosmological probes can significantly improve the results from current observations by one order of magnitude at least, which gives Ωm and σ8 &lt;1 per cent accuracy and w0 and wa &lt;5 and 20 per cent accuracy, respectively. This indicates that CSST photometric and spectroscopic multi-probe surveys could provide powerful tools with which to explore the Universe and greatly improve the studies of relevant cosmological problems.
Gene nceA encodes a Ni/Co-sensing transcription factor to regulate metal efflux in Corynebacterium glutamicum
Authors: Choi Won-Woo , Jeong Haeri , Kim Younhee , Lee Heung-Shick 
Published: December 2022

Abstract
The function of Corynebacterium glutamicum open reading frame (ORF) NCgl2684 (named nceA in this study), which was annotated to encode a metalloregulator, was assessed using physiological, genetic, and biochemical approaches. Cells with deleted-nceA (ΔnceA) showed a resistant phenotype to NiSO4 and CoSO4 and showed faster growth in minimal medium containing 20 μM NiSO4 or 10 μM CoSO4 than both the wild-type and nceA-overexpressing (P180-nceA) cells. In the ΔnceA strain, the transcription of the downstream-located ORF NCgl2685 (nceB), annotated to encode efflux protein, was increased approximately 4-fold, whereas gene transcription decreased down to 30% level in the P180–nceA strain. The transcriptions of the nceA and nceB genes were stimulated, even when as little as 5 nM NiSO4 was added to the growth medium. Protein NceA was able to bind DNA comprising the promoter region (from −14 to + 18) of the nceA––nceB operon. The protein–DNA interaction was abolished in the presence of 20 μM NiSO4, 50 μM CoSO4, or 50 μM CdSO4. Although manganese induced the transcription of the nceA and nceB genes, it failed to interrupt protein–DNA interaction. Simultaneously, the P180–nceA cells showed increased sensitivity to oxidants such as menadione, hydrogen peroxide, and cumene hydroperoxide, but not diamide. Collectively, our data show that NceA is a nickel- and cobalt-sensing transcriptional regulator that controls the transcription of the probable efflux protein-encoding nceB. The genes are able to suppress intracellular levels of nickel to prevent reactions, which can cause oxidative damage to cellular components.
Calcium isotope ratio in kidney stones: preliminary exploration of mechanism from the geochemical perspective
Authors: Qu Rui , Han Guilin , Tian Yu , Zhao Ye 
Published: December 2022

Abstract
Stable calcium (Ca) isotope ratios are sensitive and radiation-free biomarkers in monitoring biological processes in human bodies. Recently, the Ca isotope ratios of bone, blood, and urine have been widely reported to study bone mineral balance. However, as a pure Ca crystallization product, there is no report on the Ca isotope ratios of kidney stones, even though the prevalence of kidney stones is currently on the rise. Here, we measured Ca isotope data of 21 kidney stone samples collected in Beijing, China. The δ44/42CaNIST 915a values ranged from 0.25‰ to 2.85‰ for calcium oxalate, and from 0.38‰ to 3.00‰ and 0.61‰ to 0.69‰ for carbonate apatite and uric acid, respectively. Kidney stones have heavier Ca isotope ratios than bone or blood, which is probably because complexed Ca contains more heavy Ca isotopes than free Ca2+. Ca isotope evidence suggests that magnesium (Mg) affects kidney stone formation, as the δ44/42CaNIST 915a value is inversely correlated with the Ca/Mg ratio. This study provides important preliminary reference values on the Ca isotopic composition of kidney stones and proposes a factor influencing Ca isotope fractionation in biological processes for future research.
Biological Magnetic Resonance Data Bank
Authors: Hoch Jeffrey C , Baskaran Kumaran , Burr Harrison , Chin John , Eghbalnia Hamid R , Fujiwara Toshimichi , Gryk Michael R , Iwata Takeshi , Kojima Chojiro , Kurisu Genji , Maziuk Dmitri , Miyanoiri Yohei , Wedell Jonathan R , Wilburn Colin , Yao Hongyang , Yokochi Masashi 
Published: December 2022

Abstract
The Biological Magnetic Resonance Data Bank (BMRB, https://bmrb.io) is the international open data repository for biomolecular nuclear magnetic resonance (NMR) data. Comprised of both empirical and derived data, BMRB has applications in the study of biomacromolecular structure and dynamics, biomolecular interactions, drug discovery, intrinsically disordered proteins, natural products, biomarkers, and metabolomics. Advances including GHz-class NMR instruments, national and trans-national NMR cyberinfrastructure, hybrid structural biology methods and machine learning are driving increases in the amount, type, and applications of NMR data in the biosciences. BMRB is a Core Archive and member of the World-wide Protein Data Bank (wwPDB).
MGnify: the microbiome sequence data analysis resource in 2023
Authors: Richardson Lorna , Allen Ben , Baldi Germana , Beracochea Martin , Bileschi Maxwell L , Burdett Tony , Burgin Josephine , Caballero-Pérez Juan , Cochrane Guy , Colwell Lucy J , Curtis Tom , Escobar-Zepeda Alejandra , Gurbich Tatiana A , Kale Varsha , Korobeynikov Anton , Raj Shriya , Rogers Alexander B , Sakharova Ekaterina , Sanchez Santiago , Wilkinson Darren J , Finn Robert D 
Published: December 2022

AbstractThe MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. The platform provides access to taxonomic assignments and functional annotations for nearly half a million analyses covering metabarcoding, metatranscriptomic, and metagenomic datasets, which are derived from a wide range of different environments. Over the past 3 years, MGnify has not only grown in terms of the number of datasets contained but also increased the breadth of analyses provided, such as the analysis of long-read sequences. The MGnify protein database now exceeds 2.4 billion non-redundant sequences predicted from metagenomic assemblies. This collection is now organised into a relational database making it possible to understand the genomic context of the protein through navigation back to the source assembly and sample metadata, marking a major improvement. To extend beyond the functional annotations already provided in MGnify, we have applied deep learning-based annotation methods. The technology underlying MGnify's Application Programming Interface (API) and website has been upgraded, and we have enabled the ability to perform downstream analysis of the MGnify data through the introduction of a coupled Jupyter Lab environment.
The mechanisms of siRNA selection by plant Argonaute proteins triggering DNA methylation
Authors: Liu Wei , Shoji Keisuke , Naganuma Masahiro , Tomari Yukihide , Iwakawa Hiro-oki 
Published: December 2022

Abstract
The model plant Arabidopsis thaliana encodes as many as ten Argonaute proteins (AGO1–10) with different functions. Each AGO selectively loads a set of small RNAs by recognizing their length and 5′ nucleotide identity to properly regulate target genes. Previous studies showed that AGO4 and AGO6, key factors in DNA methylation, incorporate 24-nt small-interfering RNAs with 5′ adenine (24A siRNAs). However, it has been unclear how these AGOs specifically load 24A siRNAs. Here, we biochemically investigated the siRNA preference of AGO4, AGO6 and their chimeric mutants. We found that AGO4 and AGO6 use distinct mechanisms to preferentially load 24A siRNAs. Moreover, we showed that the 5′ A specificity of AGO4 and AGO6 is not determined by the previously known nucleotide specificity loop in the MID domain but rather by the coordination of the MID and PIWI domains. These findings advance our mechanistic understanding of how small RNAs are accurately sorted into different AGO proteins in plants.
TheEscherichia coliclamp loader rapidly remodels SSB on DNA to load clamps
Authors: Newcomb Elijah S P , Douma Lauren G , Morris Leslie A , Bloom Linda B 
Published: December 2022

AbstractSingle-stranded DNA binding proteins (SSBs) avidly bind ssDNA and yet enzymes that need to act during DNA replication and repair are not generally impeded by SSB, and are often stimulated by SSB. Here, the effects of Escherichia coli SSB on the activities of the DNA polymerase processivity clamp loader were investigated. SSB enhances binding of the clamp loader to DNA by increasing the lifetime on DNA. Clamp loading was measured on DNA substrates that differed in length of ssDNA overhangs to permit SSB binding in different binding modes. Even though SSB binds DNA adjacent to single-stranded/double-stranded DNA junctions where clamps are loaded, the rate of clamp loading on DNA was not affected by SSB on any of the DNA substrates. Direct measurements of the relative timing of DNA-SSB remodeling and enzyme–DNA binding showed that the clamp loader rapidly remodels SSB on DNA such that SSB has little effect on DNA binding rates. However, when SSB was mutated to reduce protein–protein interactions with the clamp loader, clamp loading was inhibited by impeding binding of the clamp loader to DNA. Thus, protein–protein interactions between the clamp loader and SSB facilitate rapid DNA-SSB remodeling to allow rapid clamp loader-DNA binding and clamp loading.
Growth differentiation factor-15 predicts major bleeding, major adverse cardiac events and mortality in patients with end-stage kidney disease on haemodialysis: findings from the VIVALDI study
Authors: Nopp Stephan , Königsbrügge Oliver , Schmaldienst Sabine , Klauser-Braun Renate , Lorenz Matthias , Pabinger Ingrid , Säemann Marcus , Ay Cihan 
Published: December 2022

ABSTRACT

Background
Patients with end-stage kidney disease (ESKD) are at high risk of cardiovascular events and bleeding. Optimizing risk assessment of ESKD patients regarding the risk of thromboembolism and bleeding complications in comorbid conditions, including atrial fibrillation and coronary heart disease, is challenging. To improve risk prediction we investigated growth differentiation factor-15 (GDF-15), a promising cardiovascular biomarker, and its relation to adverse outcomes.

Methods
In this prospective, multicentre, population-based cohort study, GDF-15 was measured in 594 ESKD patients on haemodialysis (median age 66 years, 38% female), who were followed up for a median of 3.5 years. The association of GDF-15 with major bleeding, arterial thromboembolism, major adverse cardiac events (MACE) and death was analysed within a competing risk framework. Further, we evaluated the additive predictive value of GDF-15 to cardiovascular and death risk assessment.

Results
GDF-15 levels were in median 5475 ng/l (25th–75th percentile 3964–7533) and independently associated with major bleeding {subdistribution hazard ratio [SHR] 1.31 per double increase [95% confidence interval (CI) 1.00–1.71]}, MACE [SHR 1.47 (95% CI 1.11–1.94)] and all-cause mortality [SHR 1.58 (95% CI 1.28–1.95)] but not arterial thromboembolism [SHR 0.91 (95% CI 0.61–1.36)]. The addition of GDF-15 to the HAS-BLED score significantly improved discrimination and calibration for predicting major bleeding [C-statistics increased from 0.61 (95% CI 0.52–0.70) to 0.68 (95% CI 0.61–0.78)]. Furthermore, we established an additive predictive value of GDF-15 beyond current risk models for predicting MACE and death.

Conclusion
GDF-15 predicts the risk of major bleeding, cardiovascular events and death in ESKD patients on haemodialysis and might be a valuable marker to guide treatment decisions in this challenging patient population.
Non-steroidal mineralocorticoid receptor antagonists and cardiorenal outcomes in chronic kidney disease
Authors: Lo Kevin Bryan , Rangaswami Janani , Vaduganathan Muthiah 
Published: December 2022

ABSTRACTThe burden of adverse cardiorenal outcomes among patients with the trifecta of diabetes, heart failure (HF) and chronic kidney disease (CKD) remains high. Steroidal mineralocorticoid receptor antagonists (MRAs) have been shown to improve clinical outcomes in patients with HF, however, there is significant underutilization of these agents, especially in patients with advanced CKD. Non-steroidal MRAs are an emerging therapeutic option for patients with diabetic kidney disease and are now guideline-supported in this population. Non-steroidal MRAs have a unique pharmacological profile distinct from their steroidal counterparts that retains the class-specific cardiorenal benefits but may help mitigate adverse effects, especially hyperkalaemia, in patients with CKD. In this review we summarize the current evidence on the use of non-steroidal MRAs for improving cardiorenal outcomes in patients with CKD and diabetes, as well as for combination use alongside other foundational medical therapies used in HF and CKD.
ANGI-1 ASSESSING THE THERAPEUTIC EFFECT OF BEVACIZUMAB USING FMISO-PET IN GBM THERAPY
Authors: Suzuki Tomoya , Tanaka Toshihide , Takei Jun , Miyake Keisuke , Suzuki Kenta , Ogawa Daisuke , Akasaki Yasuharu , Yuichi Murayama 
Published: December 2022

Abstract

Background
Gd-enhanced MRI and T2WI/FLAIR images are used to determine the efficacy of bevacizumab(Bev) in glioblastoma(GBM). FMISO-PET reflects hypoxia in tumor tissue. In this study, we hypothesized that FMISO-PET could detect a series of changes in the hypoxic environment during the Bev effect and at the time of Bev recurrence, and compared images and pathological findings after initial Bev treatment and recurrence.

Subjects and Methods
Seven patients with first-episode GBM, IDH-wild type were included in the study. 3 patients underwent tumor resection after completion of Bev, radiation, and temozolomide treatment, and reoperation was performed at recurrence. FMISO-PET was performed at each time point. Four patients who underwent tumor resection after FMISO-PET in the absence of treatment were also included. The explanted specimens were analyzed for expression of hypoxia (CA9) and stem cell surface marker (FOXM1) by immunohistochemistry (IHC).

Results
All three patients treated with preoperative chemoradiotherapy showed reduced FMISO accumulation. Two of them showed recurrence and increased FMISO accumulation, and IHC showed increased CA9 and FOXM1 positive cells at the time of reoperation. There was a trend toward fewer CA9-positive cells in patients with low FMISO accumulation, including controls.

Conclusion
FMISO-PET was used to visualize the improvement of oxygenation in tumor tissues after preoperative chemoradiotherapy including Bev, and the increased FMISO accumulation at the time of Bev resistance suggested that FMISO-PET may be useful for monitoring the duration of Bev treatment effect by reflecting the oxygenation of tumor tissues. The results suggest that FMISO-PET may be useful for monitoring the duration of response to Bev therapy.
CBMS-1 TARGETING GLUTAMINE METABOLISM IN IDH-MUTANT GLIOMAS
Authors: Ohba Shigeo , Teranishi Takao , Hirayama Akiyoshi , Hitachi Keisuke , Yamaguchi Hisateru , Natsumeda Manabu , Tateishi Kensuke , Mukherjee Joydeep , Pieper Russell , Hirose Yuichi 
Published: December 2022

Abstract
IDH-wildtype and IDH-mutant glioma have different genetical and metabolic background although their histological appearances are similar. To reveal the difference in metabolites between IDH-wildtype and IDH-mutant glioma, two artificial cell lines made from normal human astrocyte, NHAE6E7hTERTRas (IDH-wildtype) and NHAE6E7hTERTIDHmut (IDH-mutant), were investigated. Capillary electrophoresis- and ion chromatography-coupled mass spectrometry revealed the lower amount of glutamine, glutamate and 2-oxoglutarate in NHAE6E7hTERTIDHmut cells than NHAE6E7hTERTRas cells. Pharmacological or genetical inhibition of GLUD1 which converts glutamate to 2-oxoglutarate, suppressed proliferation of the cells by inducing ROS and apoptosis in NHAE6E7hTERTIDHmut cells. ROS inhibitor, NAC suppressed GLUD1 inhibitor-induced ROS, apoptosis, and cytotoxicity in NHAE6E7hTERTIDHmut cells, revealing that cytotoxicity by GLUD1 inhibitor was at least partially due to the inhibitor-induced ROS. Exogeneous dimethyl 2-oxoglutarate rescued the cytotoxicity by GLUD1 inhibitor, suggesting decreased 2-oxoglutarate was associated with GLUD1 inhibitor-induced cytotoxicity. Mutant IDH1 overexpressed glioma cell line showed similar sensitivity to GLUD1 inhibitor to NHAE6E7hTERTIDHmut, which suggested that the difference of sensitivity to GLUD1 inhibitor was due to the status of mutant IDH. In conclusion, GLUD1 inhibitor will be new therapeutic options for IDH-mutant glioma.
CBMS-3 SEARCH FOR COMPOUNDS WITH ANTI-TUMOUR EFFECTS AGAINST GLIOBLASTOMA
Authors: Iwashimizu Sonoka , Ono Masaya , Sunagawa Yoichi , Hamabe Toshihide , Inai Kyoko , Katanasaka Yasufumi , Arakawa Yoshiki , Hasegawa Koji , Morimoto Tatsuya 
Published: December 2022

Abstract

Purpose
Glioblastoma (GBM) has a high risk of recurrence and a poor prognosis due to the difficulty of surgical resection and the resistance to temozolomide, the standard treatment for GBM. Therefore, the development of new therapeutic agents for GBM is desired. We searched our compound library for compounds with anti-tumor activity against GBM and identified Curcumin (Cur) derivatives, Compound A and B. The purpose of this study was to investigate the antitumor activity of Compound A and B against GBM.

Methods and Results
To evaluate the antitumor activity of Compound A and B against GBM, we performed the MTT assay. Human glioblastoma cell lines, U87-MG and U251 cells, were treated with Compound A and B. After 96 hours, cell viability was evaluated using CCK-8, and the IC50 values of Compound A and B were calculated. In U87-MG, the IC50 of Cur was 9.78 μM, whereas the that of Compound A was 2.42 μM and that of Compound B was 1.28 μM. In U251 cells, the IC50 of Cur was 9.50 μM, whereas that of Compound A was 2.27 μM and that of Compound B was 0.64 μM. Next, to examine the effects of Compound A and B on normal cells, we performed the same MTT assay using primary cultured rat astrocytes. At the concentrations at which antitumor effects were observed (Compound A; 3 μM, B; 1.5 μM), there was no reduction in cell viability in primary rat cultured astrocytes.

Discussion
The present study shows that Compound A and B exhibit antitumor activity against human glioblastoma cells at lower concentrations than Cur without affecting normal cells. We will examine the effects of Compound A and B in a mouse model of brain tumor transplanted with U87-RFP cells in the future, which may lead to the development of noble brain tumor therapeutics.