bluuebunny/crossref_metadata_2025_split huggingface dataset:
A clustering approach to improve our understanding of the genetic and phenotypic complexity of chronic kidney disease
Authors: Eoli Andrea , Ibing Susanne , Schurmann Claudia , Nadkarni Girish N. , Heyne Henrike , Böttinger Erwin 
Published: October 2023

Abstract

Chronic kidney disease (CKD) is a complex disorder that causes a gradual loss of kidney function, affecting approximately 9.1% of the world's population. Here, we use a soft-clustering algorithm to deconstruct its genetic heterogeneity. First, we selected 322 CKD-associated independent genetic variants from published genome-wide association studies (GWAS) and added association results for 229 traits from the GWAS catalog. We then applied nonnegative matrix factorization (NMF) to discover overlapping clusters of related traits and variants. We computed cluster-specific polygenic scores and validated each cluster with a phenome-wide association study (PheWAS) on the BioMe biobank (n=31,701). NMF identified nine clusters that reflect different aspects of CKD, with the top-weighted traits signifying areas such as kidney function, type 2 diabetes (T2D), and body weight. For most clusters, the top-weighted traits were confirmed in the PheWAS analysis. Results were found to be more significant in the cross-ancestry analysis, although significant ancestry-specific associations were also identified. While all alleles were associated with a decreased kidney function, associations with CKD-related diseases (e.g., T2D) were found only for a smaller subset of variants and differed across genetic ancestry groups. Our findings leverage genetics to gain insights into the underlying biology of CKD and investigate population-specific associations.
Paeoniflorin alleviates oxidative stress and apoptosis in heat stress-induced H9c2 cells
Authors: Wang Meng , Liu Ying , Li Hua , Liu Hui , Wang Xinxing , Dong Qingyang 
Published: October 2023

Abstract
Purpose: The increasing annual mean temperature has exacerbated the severity of heat stress (HS) which could increase cardiac burden. Paeoniflorin (PF), the primary bioactive constituent extracted from the Paeonifloraceae, exhibits robust antioxidant properties. However, its protective potential against HS-induced cardiomyocyte injury remains unclear. This study aimed to investigate the protective effects of PF on H9c2 cells subjected to HS-induced injury and elucidate the underlying mechanisms.
Methods: To establish the heat stress model, H9c2 cells were exposed to HS for 2 h at 45 °C in a 5% CO2 incubator. Before HS exposure, H9c2 cells were pretreated with PF (5 µM) for 24 h. Subsequently, we assessed cell viability, oxidative stress, cardiomyocyte apoptosis, and mitochondrial function.
Results: HS treatment significantly increased oxidative stress and apoptosis in H9c2 cells. However, pretreatment with PF for 24 h attenuated the HS-induced damage in H9c2 cells, protecting against thermal injury.
Conclusion: Current studies have not investigated the role of PF on oxidative damage and apoptosis in vitro after HS. Our experiment demonstrated that PF ameliorates HS-induced oxidative stress and apoptosis in H9c2 cells which suggest that PF can potentially be an effective preventive medicine against heat injury to cardiomyocyte.
Association of prevalence rates of infantine social-emotional developmental risks and regional deprivation in Mecklenburg-Western Pomerania: A plea for regional small-scale data
Authors: Ernst Vanessa Sophie , Hoffmann Wolfgang , Franze Marco , Stentzel Ulrike 
Published: October 2023

Abstract

Background: Early childhood is essential for a child’s overall development. Twenty to 30%of children are impaired by a lack of needed social and emotional skills when starting school. Children living in socioeconomic deprivation are particularly affected. Early childhood development is determined by family socioeconomic status (SES) and regional socioeconomic aspects. In a preventive early childhood development support program for preschool children in social hotspots,an annual standardized developmental screening (Dortmunder Entwicklungsscreening für den Kindergarten - DESK 3–6 R) was carried out. This study aimed to investigate the association between the prevalence ofpreschool children at risk of social-emotional problems and socioeconomic deprivation in northeast Germany.
Methods: Screening data from DESK 3–6 R were linked with the German Index of Socioeconomic Deprivation (GISD) for 2019. For the social-emotional domains ‘social behaviour’, ‘social competence’ and ‘social interaction’ as dependent variables and the GISD score as explanatory variable Generalized Linear Regressions (GLR) and to model spatially varying relationships Local Bivariate Relationships (LBR) were performed within ArcGIS pro 3.1.
Results: A total of 147preschools participated, with atotal of 7,836 three- to six-year-old children in 2019. The prevalence of developmental risks for ‘social behavior’ was 14 % (standard deviation (SD) = 13 %), for ‘social competence’ 13 % (SD=12 %) and for ‘social interaction’ 10 % (SD=10 %). For ‘social behavior’ and ‘social interaction’, GLR showed statistically significant coefficients of approximately0.5 but low data fit (explaining only 6.3% of thevariance at max). LBR revealed no relevant association.
Conclusions: Contrary to our expectation, we did not observe consistent significant associations between social-emotional developmental risks (measured with DESK) and regional deprivation (operationalized with GISD) of 3- to 6-year-olds attending preschools in social hotspots in Mecklenburg Western-Pomerania. Although the GISD was available on the level of five-digit postal zip codes, due to the relatively low population density, the relatively large administrative units, and the modifiable area unit problem (MAUP), differences in the degree of deprivation are evened out. To reflect the effect of regional differences on individual children, small-scale data with high geographical resolution are needed.
Sampling of environmental DNA for breeding distribution mapping in an endangered goose species, the lesser white-fronted goose
Authors: Honka Johanna , Kvist Laura , Øien Ingar J. , Aarvak Tomas , Siivonen Stefan , Aspi Jouni 
Published: October 2023

Abstract
Detecting extremely rare and elusive species from vast wilderness areas is highly challenging. The Fennoscandian population of lesser white-fronted goose (LWfG; Anser erythropus) is the most endangered bird in Europe, with only 25–30 breeding pairs remaining in Northern Norway. Its former breeding range, however, covered mountainous parts of the entire Fennoscandia. Targeted conservation efforts during the 21st century has enabled the LWfG to recolonise some of its former breeding areas in Norway and possibly also in Finland. To locate individuals of this elusive species during the breeding season, we used environmental DNA (eDNA) extracted from filtered lake water from selected lakes in the former breeding habitat in northern Finland. We amplified and sequenced a short region of the mitochondrial control region to identify Anser-goose species in the lake water. In addition, we sampled eDNA from the water of a spring staging site of the Fennoscandian LWfG and from a known Norwegian breeding site, from which eDNA of the LWfG was positively found. eDNA of the LWfG was not detected within the former Finnish breeding range. Based on this, the LWfG has not recolonised its former breeding habitats in Finland or alternatively, we may not have sampled the exactly right lakes, or the eDNA concentration was below detection limits. Due to genus-specific primers, we discovered taiga (A. fabalis fabalis) and tundra bean goose (A. fabalis rossicus) eDNA from several lakes in Northern Finland, proving the usefulness of the method.
Evaluation of electrophysiological examinations for the diagnosis of carpal tunnel syndrome
Authors: Chen Xi , Cao JinJin , Lao Jie , Liu AiLin , Rui Jing 
Published: October 2023

Abstract

To investigate the clinical significance of results in electrodiagnostic evaluations for carpal tunnel syndrome(CTS) and analyse the correlation between electrodiagnostic evaluations and physical examinations, 236 CTS patients and 96 healthy volunteers were included to accept electrodiagnostic evaluations. There were significant differences between CTS and control groups, mild and moderate patients, moderate and severe patients in CTS groups respectively, in terms of compound muscle action potential(CMAP), sensory conduction velocity of middle finger(SCV), distal motor latency(DML) difference between median nerve and ulnar nerve on the ring finger(△DML) (p<0.05).△DML has larger area under curve of ROC curve (0.974) than CMAP, SCV and DML(0.748, 0.950, 0.958), then △DML could be included as valuable test for diagnosing and classification of carpal tunnel syndromes. There was low correlation between electrodiagnostic evaluations and physical examinations (rho <0.4),so electrodiagnostic evaluation and physical examination should be combined to diagnose CTS.
Spatio-Temporal Changes in Rook’s Assemblage Revealed by Thousands of Citizen Science Photos
Authors: Yun Jiweon , Shin Wonhyeop , Kim Jihwan , Thorne James , Song Youngkeun 
Published: October 2023

Abstract
Citizen science data are increasingly being used to address ecological challenges. In our study, we utilized these data to analyze the urban invasion of rooks (Corvus frugilegus), which posed sanitary concerns and caused disruptions for residents. Although various strategies exist to contain rook invasions, effective mitigation relies on understanding their habitat preferences and daily movements—information hard to gather over extensive areas. To address this, we collected 4,523 geolocated observations from citizens who were monetarily incentivized to photograph the birds. These observations were categorized based on sunrise and sunset timings and further divided into 3-hour intervals. Our analysis revealed that rooks ventured to agricultural areas for foraging after sunrise but predominantly settled within the city post-sunset. During roosting, rooks displayed a preference for environments mimicking forested habitats, likely seeking protection from predators and adverse environmental elements like wind and extreme temperatures.
Identification of SERTAD1 Oncoprotein as a Novel USP15-interacting Protein Regulated by USP15 and SIAH1 in Ovarian Cancer
Authors: Yaginuma Yuji , Yoshimoto Masafumi 
Published: October 2023

Abstract
Ubiquitin-specific protease 15 (USP15), a member of the deubiquitylating enzyme (DUB) family, reportedly stabilizes several important oncoprotein substrates and is also reportedly up-regulated in ovarian cancers. In this study, we identified SERTA-containing domain 1 (SERTAD1) as a novel interacting protein with USP15 using yeast-two hybrid analysis. SERTAD1 is reportedly overexpressed in ovarian cancer cells and induces chromosome instability, cancer cell survival, and exhibits anti-apoptotic effects. Our study showed that overexpression of USP15 results in increased levels of SERTAD1 protein, and knockdown of USP15 using small interfering RNA decreased SERTAD1 protein levels in ovarian cancer cell lines. The catalytically inactive form of USP15 exhibited a decreased stabilizing effect on SERTAD1. These results suggest that USP15 directly regulates SERTAD1 protein levels via USP15-mediated DUB enzymatic activity in ovarian cancers. Moreover, we found that SERTAD1 expression was decreased by SIAH1, and reduced SIAH1 protein levels are frequently found in ovarian cancers. Our results indicate that USP15 overexpression and reduced SIAH1 levels induce SERTAD1 overexpression to promote carcinogenesis in human ovarian cancer.
Facile synthesis of core-shell magnetic Fe3O4@SiO2-NH2 nanoparticles and their application for rapid boron removal from aqueous solution
Authors: Hu Qinqin , Zhang Manman , Peng Jiaoyu , Dong Yaping , Li Wu , Meng Lingzong 
Published: October 2023

Abstract
Amino-functionalized magnetic particles (Fe3O4@SiO2-NH2) with core-shell structure were synthesized and evaluated for rapid boron removal from aqueous solution. Results showed that the specific surface area of Fe3O4@SiO2-NH2 (165.17 m2⋅g− 1) increased greatly compared to the pure Fe3O4 (49.07 m2⋅g− 1). The adsorption equilibrium was less than 2 h with an adsorption capacity of 29.76 mg⋅g− 1at pH = 6 of 15°C. The quasi second-order kinetic model described well the boron adsorption process and the Freundlich model was more suitable for characterizing the adsorption isotherms. Furthermore, the negative value of Gibbs free energy indicated that the adsorption was spontaneous and an exothermic process. The zeta potential and XPS analysis before and after adsorption revealed that the main adsorption mechanism was the hydrogen bonding formation between the terminal –NH2 groups of the adsorbent and the boric acid. In addition, the adsorbent still maintained a high adsorption performance after five adsorption-desorption cycles, which illustrated that the Fe3O4@SiO2-NH2 may be a potential adsorbent for the environmental boron removal treatment.
Dynamics of the gut microbiome in FAP patients undergoing intensive endoscopic removal of polyps
Authors: Yachida Shinichi , Mizutani Sayaka , Shiba Satoshi , Salim Felix , Yamada Masayoshi , Takamaru Hiroyuki , Nakajima Takeshi , Yoshida Naohisa , Ikuta Shoko , Yachida Tatsuo , Shibata Tatsuhiro , Soga Tomoyoshi , Saito Yutaka , Fukuda Shinji , Ishikawa Hideki , Yamada Takuji 
Published: October 2023

Abstract

To elucidate the intestinal environment in patients with familial adenomatous polyposis (FAP) and any association of the microbiome with high-risk factors for developing colorectal cancer, we performed shotgun metagenomic sequencing and metabolome analyses on a total of 287 fecal samples collected from 130 FAP patients without colectomy and 53 healthy subjects. Partial resemblance with the microbiome of other inflammatory bowel diseases was established. Notably, colorectal cancer-associated bacteria such as Fusobacterium nucleatum, Solobacterium moorei, and Gemella morbillorum were also increased along with tumor progression. Furthermore, FAP with high histological grade of polyps, large polyp size, and high polyp density was associated with the Prevotella-dominated gut microbiome. This first comprehensive analysis of the relationship between pre-cancerous lesions and intestinal microbiota in FAP provided novel insights into gut microbiome's roles in colorectal cancer.
Clinical characteristics of Chinese children with liver function test abnormalities: A single-center retrospective study
Authors: Wang Jiabing , Wang Shijian , Zhang Huating 
Published: October 2023

Abstract
Objectives: To study the clinical features of Chinese children with liver function test abnormalities to provide a reference for early clinical diagnosis and timely treatment.
Methods: This retrospective single-center cohort study included 133 children with unknown liver function abnormalities, who were hospitalized from January 2020 to December 2021 at Taizhou municipal hospital, and analyzed their clinical characteristics, etiology, and prognosis.
Results: Among the 133 children with abnormal liver function in this study, 68 were male (51.13%) and 65 were female (48.87%). The abnormal liver function was related to age, and it was most common in infants aged 0–12 months. Among the etiologies of the primary diseases, liver dysfunction caused by acute respiratory tract infection was the most common, followed by pathogenic infections, including virual, bacterial, mycoplasma, and chlamydia infections, with virual and bacterial infections being most common. Alanine aminotransferase was elevated in children with liver dysfunction, and the severity of liver dysfunction differed with different causes. Children with abnormal liver function only showed the manifestations of the primary disease. Sex and age did not affect abnormal liver function. Medical histories of implicated agents before hospital admission were reported in 72.39% of children; however, intrinsic etiologies were the main cause of abnormal liver function rather than the implicated agents.
Conclusion This retrospective single-center cohort study showed that routine liver function testing in children is important, especially for infants aged <12 months. Intrinsic etiologies were the main cause of liver dysfunction, and other factors should be detected and treated early. The etiological and liver protection treatments can ensure effective prevention and treatment of liver injury.
Abundant chaos in a mixer model with a hysteretic iron core inductance
Authors: Aminou Mahamat , Domguia Ulrich Simo , Abo Oumarou Sanda , Woafo Paul 
Published: October 2023

Abstract
Industrial mixers are equipment used in food, drug, chemical and semiconductor industries. Chaotic mixing has been proposed to improve the degree of homogeneity and reduce the energy consumption. This paper deals with dynamical studies of a mixer model with complex rotational movements. The complexity is generated by an inductance with hysteretic characteristics. Mathematical methods and numerical simulations are used to display the different dynamical states which are period-nT, pulse, bursting and chaotic signals. Good agreement is found between the mathematical and numerical results. In general, it is found that chaos is highly abundant in the model.
An unprecedented Cationic, [1,5]-aryl migrations through novel trihomologous-phenonium ion intermediates.
Authors: Baire Beeraiah , Sadhukhan Santu , Nair Sindoori R 
Published: October 2023

Abstract
Herein, we report the discovery and development of the first example of a cationic [1,5]-aryl migration reaction, through an unprecedented six-membered ring fused phenonium ions (which we termed as a trihomologous-phenonium ion). This reaction does not require any acid, base, transition metal-based catalyst or promoter, instead promoted by the water activated NXS reagents. It provides highly diastereoselective and rapid access to the medicinally and biologically important tetra-substituted olefins (allyl alcohols) as well as 2-oxaspiro[5.5]undecane-9-ones. The involvement of an ipso-carbon, as well as the trihomologous-phenonium ion during this novel, cationic [1,5]-aryl migration was strongly supported by the isolation of 2-oxaspiro[5.5]undecane-9-ones. This methodology is highly tolerable for a wide range of propargyl-benzyl ethers, resulting in a selective construction of structurally divergent library of mono-halo-tricarbon-substituted alkenes as well as 2-oxaspiro[5.5]undecane-9-ones. Synthetic application has also been demonstrated by converting two isomeric-iodo-olefins to respective E- and Z-isomers of tamoxifen in a stereospecific manner.
Enhanced production of α-galactosidase from novel strain Bacillus megaterium VHM1 in solid state fermentation by using citrus waste
Authors: Patil Aravind Goud G , Kote Nagangoud V , Mulimani Veerappa H , Kadakol Gurushantappa 
Published: October 2023

Abstract
A high yeild of α-galactosidase was achieved by citrus waste based solid state fermentation (SSF) using a novel strain Bacillus megaterium VHM1. The maximum production of α-galactosidase was obtained at 72 hours of fermentation. The optimal temperature and pH was 350C, 6.0 respectively. Higher enzyme production at 90% (58 U/g) was obtained with increase in inoculum volume upto 100% (w/v). With increase in moisture content 50-100%, the production of α-galactosidase was concomitantly enhanced from 28 to 56 U/g. Among the inorganic nitrogen source tested, yeast extract yielded higher enzyme production (52 U/g). The enzyme production was maximum when raffinose used as additional corbon source. Forcefully aereated packed bed bioreactor was constructed for enhanced production of α-galactosidase. This enzyme could potentially be used for processing of legumes in food processing industries to remove raffinose family oligosaccharides.
Characterization of Klebsiella pneumoniae carrying the bla NDM-1 gene in IncX3 plasmids and the rare In1765 in an IncFIB-IncHI1B plasmid
Authors: Ma Liman , Qu Ying , Wang Wenji , Wang Dongguo 
Published: October 2023

Abstract
Background
Today, the blaNDM gene is widely distributed on several plasmids from a variety of Gram-negative bacteria, primarily in transposons and gene cassettes within their multidrug-resistant (MDR) regions. This has led to the global spread of the blaNDM gene.
Methods
The determination of class A beta-lactamase, class B and D carbapenemases was performed according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI). Antimicrobial susceptibility testing was performed using both the BioMerieux VITEK2 system and antibiotic paper diffusion methods. Plasmid transfer was then evaluated by conjugation experiments and plasmid electroporation assays. To comprehensively analyze the complete genome of K. pneumoniae strain F11 and to investigate the presence of mobile genetic elements associated with antibiotic resistance and virulence genes, Nanopore and Illumina sequencing platforms were used, and bioinformatics methods were applied to analyze the obtained data.
Results
Our findings revealed that K. pneumoniae strain F11 carried class B carbapenemase and exhibited resistance to commonly used antibiotics, particularly tigecycline and ceftazidime/avibactam, due to the presence of relevant resistance genes. Plasmid transfer assays demonstrated successful recovery of plasmids pA_F11 and pB_F11, with average conjugation frequencies of 2.91×10− 4 and 1.56×10− 4, respectively. However, plasmids pC_F11 and pD_F11 failed in both conjugation and electroporation experiments. The MDR region of plasmid pA_F11 contained rare In1765, TnAs2, and TnAs3. The MDR2 region of plasmid pB_F11 functioned as a mobile genetic “island” and lacked the blaNDM−1 gene, serving as a “bridge”connecting the early composite structure of bleMBL and blaNDM−1 to the recent composite structure. Additionally, the MDR1 region of plasmid pB_F11 comprised In27, TnAs1, TnAs3, and Tn2; and plasmid pC_F11 harbored the recent composite structure of bleMBL and blaNDM−1 within Tn3000 which partiallycontained partial Tn125.
Conclusions
This study demonstrated that complex combinations of transposons and integron overlaps, along with the synergistic effects of different drug resistance andvirulence genes, led to a lack of effective therapeutic agents for strain F11, therefore its spread and prevalence should be strictly controlled.
Reduction of pulsed eddy current probe footprint using sequentially excited multiple coils
Authors: Xu Zhiyuan , Zhu Changchun , Jin Junqi , Song Kai 
Published: October 2023

Abstract
In the detection of corrosion under insulation (CUI) using pulsed eddy current testing (PECT) method, it is of great significance to reduce the footprint of the probe for improving the spatial resolution to local corrosion. This paper presents a novel method to reduce the probe footprint by modifying the excitation coil into multiple sub-coils and driving them with sequential pulses of different delay time. Finite element simulations are conducted to reveal the underlying mechanism. It is found that by using the sequential excitation scheme, the diffusion and decay of eddy currents in the test piece are regulated, and both the footprint reduction and signal enhancement can be achieved. Afterwards, the effects of the sequence and the delay amount of the applying pulses on the probe footprint are analyzed. Results show that the optimal excitation sequence is to apply pulses with increasing delay time to the sub-coils from outside to inside; the probe footprint decreases with the increase of the delay amount. Experimental work is finally performed to verify the simulation results. A graphical method for measuring the probe footprint is proposed by moving the probe on a step wedge plate and plotting the evaluated thickness against the probe position. Footprint measurement results of a conventional probe and the presented 4-subcoil probe are compared. The effectiveness of the proposed method are validated and the differences between experimental and simulation results are analyzed.