bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spermidine protects against acute kidney injury by modulating macrophage NLRP3 inflammasome activation and mitochondrial respiration in an eIF5A hypusination-related pathway
Authors: Li Xianzhi , Zhou Xiaojun , Liu Xigao , Li Xiaoyun , Jiang Xianzhou , Shi Benkang , Wang Shuo 
Published: September 2022

AbstractBackgroundAcute kidney injury (AKI) is still a critical problem in clinical practice, with a heavy burden for national health system around the world. It is notable that sepsis is the predominant cause of AKI for patients in the intensive care unit and the mortality remains considerably high. The treatment for AKI relies on supportive therapies and almost no specific treatment is currently available. Spermidine is a naturally occurring polyamine with pleiotropic effects. However, the renoprotective effect of spermidine and the underlying mechanism remain elusive.MethodsWe employed mice sepsis-induced AKI model and explored the potential renoprotective effect of spermidine in vivo with different administration time and routes. Macrophage depleting was utilized to probe the role of macrophage. In vitro experiments were conducted to examine the effect of spermidine on macrophage cytokine secretion, NLRP3 inflammasome activation and mitochondrial respiration.ResultsWe confirmed that spermidine improves AKI with different administration time and routes and that macrophages serves as an essential mediator in this protective effect. Meanwhile, spermidine downregulates NOD-like receptor protein 3 (NLRP3) inflammasome activation and IL-1 beta production in macrophages directly. Mechanically, spermidine enhances mitochondrial respiration capacity and maintains mitochondria function which contribute to the NLRP3 inhibition. Importantly, we showed that eukaryotic initiation factor 5A (eIF5A) hypusination plays an important role in regulating macrophage bioactivity.ConclusionsSpermidine administration practically protects against sepsis-induced AKI in mice and macrophages serve as an essential mediator in this protective effect. Our study identifies spermidine as a promising pharmacologic approach to prevent AKI.
Novel eIF4A1 inhibitors with anti‐tumor activity in lymphoma
Authors: Kayastha Forum , Herrington Noah B. , Kapadia Bandish , Roychowdhury Anirban , Nanaji Nahid , Kellogg Glen E. , Gartenhaus Ronald B. 
Published: September 2022

Abstract
Background
Deregulated translation initiation is implicated extensively in cancer initiation and progression. It is actively pursued as a viable target that circumvents the dependency on oncogenic signaling, a significant factor in current strategies. Eukaryotic translation initiation factor (eIF) 4A plays an essential role in translation initiation by unwinding the secondary structure of messenger RNA (mRNA) upstream of the start codon, enabling active ribosomal recruitment on the downstream genes. Several natural product molecules with similar scaffolds, such as Rocaglamide A (RocA), targeting eIF4A have been reported in the last decade. However, their clinical utilization is still elusive due to several pharmacological limitations. In this study we identified new eIF4A1 inhibitors and their possible mechanisms.

Methods
In this report, we conducted a pharmacophore-based virtual screen of RocA complexed with eIF4A and a polypurine RNA strand for novel eIF4A inhibitors from commercially available compounds in the MolPort Database. We performed target-based screening and optimization of active pharmacophores. We assessed the effects of novel compounds on biochemical and cell-based assays for efficacy and mechanistic evaluation.

Results
We validated three new potent eIF4A inhibitors, RBF197, RBF 203, and RBF 208, which decreased diffuse large B-cell lymphoma (DLBCL) cell viability. Biochemical and cellular studies, molecular docking, and functional assays revealed that thosenovel compounds clamp eIF4A into mRNA in an ATP-independent manner. Moreover, we found that RBF197 and RBF208 significantly depressed eIF4A-dependent oncogene expression as well as the colony formation capacity of DLBCL. Interestingly, exposure of these compounds to non-malignant cells had only minimal impact on their growth and viability.

Conclusions
Identified compounds suggest a new strategy for designing novel eIF4A inhibitors.
Variational Wavelet Ensemble Empirical (VWEE) Denoising Method for Electromagnetic Ultrasonic Signal in High-Temperature Environment with Low-Voltage Excitation
Authors: Zhou Jinjie , Zhao Shuaijie , Zheng Yang , Shen Xingquan , Zhang Jitang 
Published: September 2022

AbstractLow excitation voltage for an electromagnetic acoustic transducer (EMAT) is necessary for the petrochemical equipment and facilities inspection, which work at high-temperatures, to avoid potential explosion. However, low excitation voltage causes low signal-to-noise ratio (SNR) signals that are difficult to extract features, especially in a high-temperature environment, which causes high noise. In this study, a denoising method called the variational wavelet ensemble empirical (VWEE) method was proposed by combining the advantages of the variational modal decomposition (VMD), wavelet threshold (WT) denoising, and ensemble empirical mode decomposition (EEMD) methods. To validate the VWEE method, EMAT signals obtained in the temperature range of 25 to 700 °C were analyzed. The results show that, compared with VMD, WT and empirical mode decomposition denoising methods, the SNR of proposed method is improved more than two times. The VWEE method dramatically improved the SNR of a high-temperature EMAT signal and enhanced the accuracy of defect echos extraction.
Osteoporosis pathogenesis and treatment: existing and emerging avenues
Authors: Liang Bo , Burley George , Lin Shu , Shi Yan-Chuan 
Published: September 2022

AbstractOsteoporotic fractures lead to increased disability and mortality in the elderly population. With the rapid increase in the aging population around the globe, more effective treatments for osteoporosis and osteoporotic fractures are urgently required. The underlying molecular mechanisms of osteoporosis are believed to be due to the increased activity of osteoclasts, decreased activity of osteoblasts, or both, which leads to an imbalance in the bone remodeling process with accelerated bone resorption and attenuated bone formation. Currently, the available clinical treatments for osteoporosis have mostly focused on factors influencing bone remodeling; however, they have their own limitations and side effects. Recently, cytokine immunotherapy, gene therapy, and stem cell therapy have become new approaches for the treatment of various diseases. This article reviews the latest research on bone remodeling mechanisms, as well as how this underpins current and potential novel treatments for osteoporosis.
The O-glycosylating enzyme GALNT2 acts as an oncogenic driver in non-small cell lung cancer
Authors: Hu Qing , Tian Tian , Leng Yahui , Tang Yuanhui , Chen Shuang , Lv Yueyao , Liang Jingyin , Liu Yanni , Liu Tianhui , Shen Li , Dong Xiaoxia 
Published: September 2022

Abstract
Background
N-Acetylgalactosaminyltransferases (GALNTs), the enzymes that initiate mucin-type O-glycosylation, are closely associated with tumor occurrence and progression. However, a comprehensive analysis of GALNTs in non-small cell lung cancer (NSCLC) is lacking.

Methods
The expression profiles and prognostic values of the GALNT family members in NSCLC were analyzed using publicly available databases. Gain- and loss-of-function experiments were applied to assess the biological function of GALNT2 in NSCLC. High-throughput sequencing and bioinformatics approaches were employed to uncover the regulatory mechanism of GALNT2.

Results
Among the family members of GALNTs, only GALNT2 was frequently overexpressed in NSCLC tissues and was positively correlated with poor prognosis. In vitro assays showed that GALNT2 knockdown repressed NSCLC cell proliferation, migration, and invasion, but induced apoptosis and cell cycle arrest. Correspondently, GALNT2 overexpression exerted the opposite effects. In vivo experiments demonstrated that knockdown of GALNT2 restrained tumor formation in nude mice. Mechanistic investigations revealed that GALNT2 modified the O-glycosylation of ITGA5 and affected the activation of the PI3K/Akt and MAPK/ERK pathways. Further studies showed that miR-30d was a negative regulator of GALNT2.

Conclusions
These findings suggest that GALNT2 is an oncogene in NSCLC and has the potential as a target for NSCLC therapy.
Double Narrowband Induced Perfect Absorption Photonic Sensor Based on Graphene–Dielectric–Gold Hybrid Metamaterial
Authors: Liu Zhimin , Zhuo Shanshan , Zhou Fengqi , Zhang Xiao , Qin Yipeng , Luo Xin , Ji Cheng , Yang Guangxin 
Published: September 2022

AbstractDouble narrowband induced perfect absorption in the terahertz region is achieved in a graphene–dielectric–gold hybrid metamaterial, whose physical mechanism is analyzed using the coupled-mode theory (CMT), which agreed well with the finite-difference time-domain (FDTD) simulation. This study found that the Fermi level of graphene can be adjusted to improve the absorptivity when the refractive index (RI) nd of the chosen dielectric cannot achieve a good absorption effect. In addition, the blue shift of absorption spectrum can be used in the design of dual-frequency electro-optical switches, of which the modulation degree of amplitude (MDA) can reach as high as 94.05% and 93.41%, indicating that this is a very promising electro-optical switch. Most significantly, the RI sensing performance is investigated, which shows an ultra-high absorption sensitivity SA = 4.4°/RIU, wavelength sensitivity Sλ = 9.8°/RIU, and phase shift sensitivity Sφ = 2691°/RIU. At last, an interesting finding is that the two peaks (R1 and R2) of plasmon-induced absorption (PIA) show different polarization characteristics (insensitive or sensitive) to the incident light angle; this polarization-sensitive is particularly important for the PIT/PIA-based optical polarizers. Undoubtedly, this paper is of great significance to the research and design of terahertz photonic devices and sensors.
Urethral duplication associated with complex chordee: a narrative review of literature and report of a case
Authors: Nnabugwu Ikenna I. , Onoh Wilson C. , Ukekwe Francis I. , Nwosu Ekeoma O. , Iwenofu Chukwunonso A. , Anakebe Ikenna N. , Nnabugwu Chinwe A. , Onuh Augustine C. 
Published: September 2022

AbstractBackgroundUrethral duplication (UD) is reportedly rare. It is rarer in females. Knowledge on this anomaly comes from isolated report of cases. The aim of this review is to summarize information available on this anomaly thereby revealing gaps in knowledge, and to appropriately situate a recently managed case.MethodsPublications on UD in English language from 2001 to 2021 were searched for in the literature. Of importance were age at presentation, class of UD, nature of associated penile deformity and other structural anomalies. Available information was used to synthesize opinions after descriptive analyses using SPSS® version 21 (IBM Co., Armonk, NY, USA). In addition, a recently managed case of UD was reported and appropriately situated in the discourse.ResultIn all, 115 articles met the inclusion criteria. Majority (75.7%) were individual case reports, while the rest were retrospective review of case series. These provided a total of 269 reported cases. Of this lot, 38 cases were excluded because they either had no Effmann’s class or were not described well enough for an Effmann’s class to be assigned. Ultimately, 231 cases formed the basis for this review. Male to female ratio was 12:1. Types III and IIB had more females. Types IIA 2 (26.0%), IIA 2 “Y” (26.4%) and IA (22.5%) were frequently reported. About 61.8% males and 68.4% females had no associated defects. Isolated dorsal chordee was prevalent (7.1%), especially among type IA (16.7%) UD. Reported in 10.4%, vesicoureteric reflux may not be attributable always to high pressure voiding.A boy who presented at the age of 18 years with Effmann type IA UD and an associated complex chordee of the penile shaft was reported. The complex nature of the chordee adds to the challenge of explaining associated penile defects in UD.ConclusionUD is rare, but reported from all parts of the globe. There are a number of associated defects involving the external genitalia and other organs reported in UD in the male. The mechanisms of these defects are yet to be fully understood.
International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight
Authors: Bonifazi Renzo , Calus Mario P. L. , ten Napel Jan , Veerkamp Roel F. , Michenet Alexis , Savoia Simone , Cromie Andrew , Vandenplas Jérémie 
Published: September 2022

Abstract
Background
Compared to national evaluations, international collaboration projects further improve accuracies of estimated breeding values (EBV) by building larger reference populations or performing a joint evaluation using data (or proxy of them) from different countries. Genomic selection is increasingly adopted in beef cattle, but, to date, the benefits of including genomic information in international evaluations have not been explored. Our objective was to develop an international beef cattle single-step genomic evaluation and investigate its impact on the accuracy and bias of genomic evaluations compared to current pedigree-based evaluations.

Methods
Weaning weight records were available for 331,593 animals from seven European countries. The pedigree included 519,740 animals. After imputation and quality control, 17,607 genotypes at a density of 57,899 single nucleotide polymorphisms (SNPs) from four countries were available. We implemented two international scenarios where countries were modelled as different correlated traits: an international genomic single-step SNP best linear unbiased prediction (SNPBLUP) evaluation (ssSNPBLUPINT) and an international pedigree-based BLUP evaluation (PBLUPINT). Two national scenarios were implemented for pedigree and genomic evaluations using only nationally submitted phenotypes and genotypes. Accuracies, level and dispersion bias of EBV of animals born from 2014 onwards, and increases in population accuracies were estimated using the linear regression method.

Results
On average across countries, 39 and 17% of sires and maternal-grand-sires with recorded (grand-)offspring across two countries were genotyped. ssSNPBLUPINT showed the highest accuracies of EBV and, compared to PBLUPINT, led to increases in population accuracy of 13.7% for direct EBV, and 25.8% for maternal EBV, on average across countries. Increases in population accuracies when moving from national scenarios to ssSNPBLUPINT were observed for all countries. Overall, ssSNPBLUPINT level and dispersion bias remained similar or slightly reduced compared to PBLUPINT and national scenarios.

Conclusions
International single-step SNPBLUP evaluations are feasible and lead to higher population accuracies for both large and small countries compared to current international pedigree-based evaluations and national evaluations. These results are likely related to the larger multi-country reference population and the inclusion of phenotypes from relatives recorded in other countries via single-step international evaluations. The proposed international single-step approach can be applied to other traits and breeds.
Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle
Authors: Riggio Valentina , Tijjani Abdulfatai , Callaby Rebecca , Talenti Andrea , Wragg David , Obishakin Emmanuel T. , Ezeasor Chukwunonso , Jongejan Frans , Ogo Ndudim I. , Aboagye-Antwi Fred , Toure Alassane , Nzalawahej Jahashi , Diallo Boubacar , Missohou Ayao , Belem Adrien M. G. , Djikeng Appolinaire , Juleff Nick , Fourie Josephus , Labuschagne Michel , Madder Maxime , Marshall Karen , Prendergast James G. D. , Morrison Liam J. 
Published: September 2022

Abstract
Background
In cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array.

Results
We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS.

Conclusions
Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.
Draft genome of the aardaker (Lathyrus tuberosus L.), a tuberous legume
Authors: Flood Pádraic J. , Nowrousian Minou , Huettel Bruno , Woehle Christian , Becker Kerstin , Wollenweber Tassilo Erik , Begerow Dominik , Grefen Christopher 
Published: September 2022

Abstract
Objectives
Lathyrus tuberosus is a nitrogen-fixing member of the Fabaceae which forms protein-rich tubers. To aid future domestication programs for this legume plant and facilitate evolutionary studies of tuber formation, we have generated a draft genome assembly based on Pacific Biosciences sequence reads.

Data description
Genomic DNA from L. tuberosus was sequenced with PacBio’s HiFi sequencing chemistry generating 12.8 million sequence reads with an average read length of 14 kb (approximately 180 Gb of sequence data). The reads were assembled to give a draft genome of 6.8 Gb in 1353 contigs with an N50 contig length of 11.1 Mb. The GC content of the genome assembly was 38.3%. BUSCO analysis of the genome assembly indicated a genome completeness of at least 96%. The genome sequence will be a valuable resource, for example, in assessing genomic consequences of domestication efforts and developing marker sets for breeding programs. The L. tuberosus genome will also aid in the analysis of the evolutionary history of plants within the nitrogen-fixing Fabaceae family and in understanding the molecular basis of tuber evolution.
Minimally invasive apical cannulation and cannula design for short-term mechanical circulatory support devices
Authors: Székely Marcell , Ruttkay Tamás , Suhai Ferenc Imre , Bóna Áron , Merkely Béla , Székely László 
Published: September 2022

Abstract
Background
Refractory cardiogenic shock is still a major clinical challenge with high mortality rates, although several devices can be used to conquer this event. These devices have different advantages and disadvantages originating from their insertion or cannulation method, therefore many complications can occur during their use. The aim of our study was to develop and create prototypes of a novel minimal invasively insertable, transapical cannula for surgical ventricular assist devices, which uniquely incorporates the inflow and outflow routes for the blood of the patient in itself, therefore it enables the use for only one cannula for patients in cardiogenic shock.

Methods
To define the available space for the planned cannula in the left ventricle and ascending aorta, we analyzed computed tomography scans of 24 heart failure patients, who were indicated to left ventricular assist device therapy. Parallel to these measurements, hydrodynamical calculations were performed to determine the sizes of the cannulas, which were necessary to provide effective cardiac output.

Results
After the designing steps, we produced prototypes of double-lumened, tube-in-tube apically insertable devices for three different patient groups, which included a separated venous and an arterial part using 3D modelling and printing technology. All the created cannulas are able to provide 5 l/min circulatory support.

Conclusion
As a result of our research we created a sizing method based on the specific analysis of computed tomography pictures of end stage heart failure patients and a cannula concept, which can provide effective antegrade flow for patients in cardiogenic shock. We believe the improved version of our tool could have a significant therapeutic role in the future after further development based on animal and in vivo tests.
Gastric lymphangioma: a case report and review of literature
Authors: Bai Kunhao , Dai Yujun , Jiang Chen , Lin Shiyong , Wang Guobao 
Published: September 2022

Abstract
Background
Gastric lymphangioma is one of the highly rare benign tumors characterized by multilocular or unilocular lymphatic spaces. Herein, we report a case of lymphangioma in the gastric antrum.

Case presentation
A 77-year-old male patient who had been experiencing epigastric discomfort for a year was presented to our hospital. A gastric subepithelial lesion was diagnosed by upper endoscopy and was entirely excised via diatal subtotal gastrectomy. Endoscopic ultrasonography revealed an echoless homogenous echo pattern in the third wall layer. A lymphangioma was diagnosed by pathologic investigation of the resected specimen. The PubMed, Embase and Web of Science databases were reviewed for literature in English while using the keywords of “gastric lymphangioma” or “lymphangioma of stomach” or “gastric lymphatic cyst” or “lymphatic cyst of stomach” and the results were discussed.

Conclusion
Gastric lymphangioma is a rarely occurring submucosal tumor that should be considered when diagnosing subepithelial lesions in the stomach.