bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Identification of Significant Genes Related to Systemic Lupus Erythematosus through the Integration of the Results of a Transcriptome-Wide Association Study and an mRNA Expression Profile Analysis
Authors: Li Shuai , Xu Jiawen , Tian Ye , Zeng Yi , Si Haibo , Wu Yuangang , Zhang Shaoyun , Shen Bin 
Published: November 2022

Abstract
Background
Systemic lupus erythematosus (SLE) is a polygenic autoimmune connective tissue disease in which heritable components play an essential role in the pathogenesis. However, the correlation between genetic variants and pathological changes in SLE is still unclear, and it is difficult to provide insights for the early diagnosis and treatment of SLE.
Methods
We conducted a transcriptome-wide association study (TWAS) of SLE by integrating a genome−wide association study (GWAS) summary dataset of SLE (538 diagnosed patients and 213,145 controls derived from the FinnGen consortium). To verify the results of the TWAS analysis, the significant genes were further compared with the mRNA expression profiles of SLE to screen for common genes. Finally, significant genes were analyzed using functional enrichment and annotation analysis in Metascape to examine SLE-related gene sets.
Results
The TWAS identified 30 genes with PTWAS−adjusted values < 1.33×10− 6 (0.05/37665 = 1.33×10− 6), including HCP5 (PTWAS =8.74×10− 15) and APOM (PTWAS = 4.57×10− 12). Four common genes were identified through the comparison of the TWAS results with the differentially expressed genes (DEGs) of SLE, including APOM (PTWAS = 4.57×10− 12, PDEG = 3.31×10− 02) and C2 (PTWAS = 8.04×10− 11, PDEG = 1.54×10− 02). Moreover, 36 terms were detected for the enrichment results of the TWAS, including antigen processing and presentation (logP value = -4.1938). By integrating the pathway and process enrichment analysis results of DEGs, 17 terms were identified, including allograft rejection (logP value = -7.5738).
Conclusion
The study identified a group of SLE-related genes and pathways, and the findings provide novel insights for the early diagnosis and intervention of SLE.
Asynchronous Counter in QCA Technology Using Novel D Flip-Flop
Authors: Amirzadeh Zaman , Gholami Mohammad 
Published: November 2022

Abstract

A strong need for high-speed and low-power consumption devices seems inevitable due to the high speed of technological advancement in the field of microelectronics. Designers are highly interested in designing and making nanoscale devices. The Quantum Cellular Automaton (QCA) is known as one of these technologies, which makes it feasible to implement digital circuits with a high operating speed. In this paper a 4-bits counter, a 3-bits bidirectional counter, a 4-bits counter with a reset terminal, and a 4-bit counter with both set and reset terminals are designed using the proposed D-latch to demonstrate that these circuits function accurately in more complex circuits. According to the results, the area was respectively reduced by 8.33% and 15.38% with a 4.76% reduction in the delay rate in the proposed 4-bits counter and 3-bits bidirectional counter compared to the best previous designs. All the designs and simulation results is being done in the QCAPro and QCADesigner software.
Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degeneration
Authors: Stevanin Giovanni , Hamed Ahlam , Mohamed Inaam , Elseed Maha , Salih Mustafa , Elsadig Sarah , Siddig Hassab Elrasoul , Nasreldien Ali , Abdullah Mohamed Ahmed , Elzubair Maha , Omer Farouk , BAKHIET Aisha , Abubaker Rayan , Abozar Fatima , Adil Rawaa , Emad Sara , Musallam Mhammed Alhassan , Eltazi Isra , Omer Zulfa , Malik Hiba , Mohamed Mayada , Elhassan Ali , Mohamed Eman , Ahmed Ahmed , Ahmed Elhami , Eltaraifee Esraa , Hussein Bidour , Allah Amal Abd , Mohamed Lina , Nimir Mohamed , Elseed Omnia Tag , Elhassan Tasneem , Elbashier Abubakr , Alfadul Esraa , Fadul Moneeb , Ali Khalil , Taha Shaimaa , Bushara Elfatih , Amin Mutaz , koko Mahmoud , Ibrahim Muntaser , Ahmed Ammar , Elsayed Liena , Yahia Ashraf 
Published: November 2022

Abstract

Hereditary spinocerebellar degenerative disorders (SCDs) is an umbrella term that covers a group of monogenic conditions that share common pathogenic mechanisms and include spastic paraplegia, spastic ataxia, cerebellar ataxia, and spinocerebellar ataxia. They are often complicated with axonal neuropathy and/or intellectual impairment. More than 200 genes and loci inherited through all modes of Mendelian inheritance are known. Autosomal recessive inheritance predominates in consanguineous communities; however, autosomal dominant and X-linked inheritance can also occur. Sudan is inhabited by genetically diverse populations, yet it has high consanguinity rates. We used next-generation sequencing, genotyping, bioinformatics analysis, and candidate gene approaches to study 90 patients from 38 unrelated Sudanese families segregating multiple forms of SCDs focusing on known human disease-associated genes. We reached the genetic diagnosis in 63% and up to 73% of the studied families when considering variants of unknown significance. Taking into account a series of Sudanese families that we previously analyzed, the combined success rate in the two series reached 52–59% (31–35/59 families). We also highlighted the genetic and clinical heterogeneity of SCDs in Sudan, as we identified no single major gene in our cohort and the potential for discovering novel SCDs genes in this population.
A Survey on Computational Metaphor Processing Techniques: From Identification, Interpretation, Generation to Application
Authors: Ge Mengshi , Mao Rui , Cambria* Erik 
Published: November 2022

Abstract

Metaphor is a figurative language that has been frequently used in our daily lives. Due to its significance for downstream natural language processing tasks, such as machine translation and sentiment analysis, computational metaphor processing has set off an upsurge in the community. With the development of Artificial Intelligence, an increasing number of technological tools and frameworks have been proposed in this domain. In this article, we aim to comprehensively summarize and categorize previous computational metaphor processing approaches regarding metaphor identification, interpretation, generation, and application. Meanwhile, we compare the strengths and weaknesses of current works and conceive future directions in this field.
Renewable energy investments, support schemes and the dirty option
Authors: De Giovanni Domenico , Iakimova Elena 
Published: November 2022

Abstract
In a real options framework, we analyse the behaviour of a large energy producer who can invest in a portfolio of Renewable Energy Source (RES) and dirty energy source. Competitive fuel prices challenge the investments in RES. Given a budget constraint, the agent allocates the optimal capacities of both energy instalments and selects the optimal investment time. We use the model to compare the effectiveness of classical support schemes such as Feed-in Tariffs or Green Certificate with respect to forms of taxation of dirty technology such as Carbon Taxes or Carbon Permits. This paper proposes a conceptual framework and qualitative analysis to understand which support system enhances the attractiveness of renewable energy investments.
Association between serum copper and stroke in general population: A Nationally Representative Study
Authors: Chen Zhiqiang , Ling Qin , Liu Xiao , Wu Zuxiang , Shi Yumeng , Hu Huan , Yu Peng , Ma Jianyong , Zhang Jin , Li Ping 
Published: November 2022

Abstract

OBJECTIVES:We aim to explore the association between serum copper and prevalence of stroke in American adults.METHODS:Data were obtained from 3 consecutive National Health and Nutrition Examination Survey (NHANES) cycles (2011-2016). Weighted multivariate logistic regression analysis was conducted to evaluate the association between serum copper and self-reported stroke.RESULTS:A total of 5,151 adults met the inclusion criteria for this study. A total of 181 (3.51%) stroke cases were identified. Compared with the lowest tertile (<16.4 umol/l), odds ratio(OR) and 95% confidence interval (CI) for participants in middle tertile(16.4-19.8 umol/l) and highest tertile (>19.8 umol/l) of serum copper were 0.99(95%CI: 0.44-2.25) and 2.36(95%CI: 1.01-5.52), respectively. Per standard deviation (SD) increment of serum copper was positively associated with the prevalence of stroke (OR: 1.44, 95%CI: 1.11-1.86). Dose-response analysis showed a positive linear association between serum copper and stroke (Pnonlinearity=0.554).CONCLUSIONS:This cross-sectional study suggest a positive association between serum copper and the prevalence of stroke in American adults.
Validation of the Self-applied Binge Eating Disorder Scale in Mexican Children
Authors: Unikel Claudia , Rangel Irais Castillo , Arias Ana Berenice Casillas , García Francisco Juárez , Castañeda Leticia Adriana Rivera , Hernández Aremis Villalobos , Serrato María Isidra Hernández , Márquez Miriam Barajas 
Published: November 2022

Abstract

The purpose of the study was to evaluate the psychometric characteristics of the Self-applied Children’s Binge Eating Disorder Scale (SA-C-BEDS) as a screening tool for risk of binge eating disorder (BED) in a Mexican child population.
Method: the self-applied version of the C-BEDS was translated into Spanish and adapted, and its reliability, and exploratory and confirmatory validity obtained. It was administered to two samples of elementary school pupils from May-July 2022 through an Internet link.
Results: a total of 378 children (girls=193 and boys=185) with a mean age of 10.22 years, with no differences by sex, answered the questionnaire. “Eating without being hungry” was the main behavior reported (44.8% and 33.7% in girls and boys), followed by eating associated with a certain mood (25% and 21.8% in girls and boys). The scale was distributed within a single factor with a total explained variance of 55%, a significant Bartlett’s test of sphericity, 0.80 on the Kaiser-Meyer-Olkin test and an ordinal Alpha reliability of 0.90. Confirmatory validity demonstrated that the model fits the data and is valid.
Conclusion: the SA-C-BEDS is a valid instrument for assessing binge eating behaviors in Mexican children and provides information for identifying and preventing BED cases in a timely manner.
Level of evidence: IV
A 10-Year Summary of the Safety and Economy of a New Method for Dispensing Ranibizumab/Conbercept in Same-day Bilateral Intravitreal Injection Using a Single Vial Running title: Bilateral Anti-VEGF Injection Using a Single Vial
Authors: Shao Yi-Run , Mao Jian-Bo , Zhao Shi-xin , Shen Li-Jun 
Published: November 2022

Abstract
Purpose
Analyze the safety and economy of a new method for dispensing ranibizumab/conbercept in same-day bilateral intravitreal injection using a single vial.
Methods
This is a retrospective study involving a total of 2775 patients 7646 injections during 2012 to 2021. 541 patients receiving same-day bilateral intravitreal injection using a single vial were defined as bilateral injection group and 2234 patients receiving unilateral injection were defined as unilateral injection group. The dispensing method was drawing all ranibizumab/conbercept drugs by the prepackaged syringe, dividing drugs by a disposable aseptic insulin syringe drawing from the prepackaged syringe. The equipment used in bilateral injection was new for each eye. Data of gender, age, diagnosis, the kind of anti-VEGF drugs and the occurrence of infectious endophthalmitis were recorded. The cost of bilateral injection and unilateral injection for the patients requiring bilateral treatment were compared.
Results
The mean age of bilateral injection group and unilateral injection group was 61.73 ± 13.41 and 62.23 ± 15.48 years old respectively (t = 0.67, P > 0.05). The incidence of infectious endophthalmitis was 0.026% (2/7646) totally. The incidence of infectious endophthalmitis in bilateral injection group was (1/2464, 0.041%) and in unilateral injection group was (1/5182, 0.020%). There was no significant difference between two groups (χ2 = 0.29, P > 0.05). No bilateral infectious endophthalmitis occurred. Bilateral injection using a single vial saved about 46.5% cost when comparing with unilateral injection.
Conclusions
The same-day bilateral intravitreal anti-VEGF therapy using a single vial didn’t increase the incidence of infectious endophthalmitis when comparing with unilateral injection and reduced nearly a half treatment cost.
CSF 14-3-3ζ is associated with tau pathology and elevated across the Alzheimer’s disease continuum
Authors: Qiang Qiang , Skudder-Hill Loren , Toyota Tomoko , Huang Zhe , Wei Wenshi , Adachi Hiroaki 
Published: November 2022

Abstract
14-3-3 is a family of conserved proteins that consist of seven isoforms which are highly expressed in the brain, and 14-3-3ζ is one of the isoforms encoded by the YWHAZ gene. Previous studies demonstrated that 14-3-3ζ is deposited in the neurofibrillary tangles of Alzheimer’s disease (AD) brains, and that 14-3-3ζ interacts with tau from the purified neurofibrillary tangles of AD brain extract. The present study examined the cerebrospinal fluid (CSF) 14-3-3ζ levels of 719 participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI), including cognitively normal (CN) participants, patients with mild cognitive impairment (MCI) and patients with AD dementia. CSF 14-3-3ζ levels were increased in prodromal AD, and further elevated in AD dementia stage. CSF 14-3-3ζ levels were associated with CSF phosphorylated tau 181(p-tau) and plasma p-tau, which are fluid biomarkers of tau pathology, and could predict tau positive status with high accuracy (area under the receiver operating characteristic curve [AUC], 0.891). CSF 14-3-3ζ levels were also associated with cognitive measurements and neuroimaging findings both at baseline and during follow up, and high CSF 14-3-3ζ levels were associated with subsequent progression to AD dementia in patients with MCI. In conclusion, this study suggests that CSF 14-3-3ζ is a potential diagnostic and prognostic biomarker of AD that may be useful in clinical practice.
Telomeric retrotransposons show high propensity to form G-quadruplexes in various species
Authors: Jedlicka Pavel , Tokan Viktor , Kejnovska Iva , Hobza Roman , Kejnovsky Eduard 
Published: November 2022

Abstract

Background:
Drosophila melanogaster telomeres are composed of three retrotransposons - Het-A, TART and TAHRE (HTT), which jump at the chromosome ends in orientation specific manner. Canonical telomeres, extended by telomerase, contain G-rich tandem repeats readily forming G-quadruplexes (G4). The G4 are formed just on one strand due to the GC strand bias. The HTT elements preserve the GC strand bias which is often found in telomere-targeting retrotransposons in other species as well. The G4-forming potential in these telomeric retrotranposons is unknown.
Results:
We searched for potential quadruplex-forming sequences (PQS) in the telomeric retrotransposons of the D. melanogaster fruit fly. We found that PQS are abundant in HTT elements and exhibit a strand-asymmetric distribution, being present only in non-coding strands and following the GC strand bias of canonical telomeres with possible G4 formation at G-rich ssDNA overhang. Our CD measurement showed that 13 out of 17 PQS formed G4 in vitro. This asymmetric PQS distribution in telomeric retrotransposons was common also for other Drosophila species, where evolutionary younger species have a tendency to accumulate more PQS. The majority (almost 70%) of PQS resides in the coding region of the gag gene and the regional PQS abundance correlates with the phenomenon of higher identity at the DNA level compared to amino acids. Moreover, the analysis of telomere-targeting retrotransposons from various species showed an independent selection of PQS-rich elements from distinct families.
Conclusions:
Our results support the importance of G4 in telomere maintenance and possibly represent a fundamental connection between telomerase-synthesized and non-canonical Drosophila telomeres.
Immunohistochemical detection of global epigenetic DNA modifications using antibodies to 5-methylcytosine and 5-hydroxymethylcytosine.
Impact of antigen retrieval protocols.
Authors: Moshi Jobran M. , Ummelen Monique , Broers Jos L. V. , Ramaekers Frans C.S. , Hopman Anton H.N. 
Published: November 2022

Abstract

The aim of this study was to compare three different pretreatment protocols for the detection of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) in nuclear DNA. Several types of human biological samples were analyzed, including formalin fixed, paraffin embedded (FFPE) normal squamous epithelium, ethanol fixed cultured cells and metaphase chromosomes. The antigen retrieval methods included the low pH citrate and high pH Tris/EDTA protocols, as well as a method including a pepsin pretreatment step combined with an HCl DNA denaturation step. We saw a gradual increase in the detection levels of 5-mC and 5-hmC when going from citrate via Tris/EDTA to pepsin/HCl retrieval. While the citrate retrieval protocol was the least efficient for the immunochemical detection of 5-mC and 5-hmC, it did preserve nuclear morphology and enabled the visualization of intra- and internuclear differences in FFPE tissue and cell culture samples. By simultaneous fluorescent detection, we assessed the differences in distribution patterns for both 5-mC and 5-hmC. In addition, (hydroxy)methylation levels in FFPE material were quantified using confocal and non-confocal microscopic imaging. As a result, we observed a significant heterogeneity, as well as differences between the levels for 5-mC and 5-hmC, within and between nuclei in the different compartments of normal squamous epithelium.
Antitumor Immune Mechanisms of the Anti-Complement Factor H Antibody GT103
Authors: Bushey Ryan T. , Saxena Ruchi , Campa Michael J. , Gottlin Elizabeth B. , He You-Wen , Patz Edward F. 
Published: November 2022

Abstract

Development of novel therapeutic antibodies that not only kill tumor cells but modulate the adaptive immune response has the potential to produce long term anti-cancer immunity and a durable clinical response. We previously reported the discovery of an anti-complement factor H (CFH) autoantibody in lung cancer patients that were associated with early stage disease and exceptional outcomes. The human monoclonal antibody GT103, produced from a single CFH autoantibody-expressing B cell of a lung cancer patient, recognizes a conformationally distinct epitope on tumor cells, kills tumor cells, and inhibits tumor growth in animal studies. Recent experiments have shown that GT103 restructures the tumor microenvironment and initiates a robust antitumoral adaptive immune response. The current study further elucidates several mechanisms by which GT103 kills tumor cells and drives the immune program. Here we show GT103 has specificity for tumor cells without binding to native soluble CFH or normal tissues. GT103 causes complement C3 split product deposition on tumor cellsin vitroandin vivo,triggers antibody-dependent cellular phagocytosis, and increases translocation of the danger associated molecular pattern molecule calreticulin to the plasma membrane.We also demonstrate that GT103 causes B cell activation and that GT103 antitumor activityin vivois B cell dependent. The complex mechanism of GT103, a tumor specific antibody that kills tumor cells and stimulates an immune response, supports further development of this human-derived antibody as a novel therapeutic option for patients with lung cancer.
Structure and compressibility of Fe-bearing Al-phase D
Authors: Criniti Giacomo , Ishii Takayuki , Kurnosov Alexander , Glazyrin Konstantin , Husband Rachel J. , Ballaran Tiziana Boffa 
Published: November 2022

Abstract
Due to its large thermal stability, Al-phase D, the (Al,Fe3+)2SiO6H2 member of the dense hydrous magnesium silicate (DHMS) phase D, may survive along hot subduction geotherms or even at ambient mantle temperatures in the Earth’s transition zone and lower mantle, therefore potentially playing a major role as a water reservoir and carrier in the Earth’s interior. We have investigated the crystal structure and high-pressure behavior of Fe-bearing Al-phase D with a composition of Al1.53(2)Fe0.22(1) Si0.86(1)O6H3.33(9) by means of single-crystal X-ray diffraction. While the structure of pure Al-phase D (Al2SiO6H2) has space group P63/mcm and consists of equally populated and half-occupied (Al,Si)O6 octahedra, Fe-incorporation in Al-phase D seems to induce partial ordering of the cations over the octahedral sites, resulting in a change of the space group from P63/mcm to P6322 and in well-resolved diffuse scattering streaks observed in X-ray images. The evolution of the unit-cell volume of Fe-bearing Al-phase D between room pressure and 38 GPa, determined by means of synchrotron X-ray diffraction in a diamond anvil cell, is well described by a third-order Birch-Murnaghan equation of state having an isothermal bulk modulus KT0 = 166.3(15) GPa and first pressure derivative KT0′ = 4.46(12). Above 38 GPa, a change in the compression behavior is observed, likely related to the high-to-low spin crossover of octahedrally coordinated Fe3+. The evolution of the unit-cell volume across the spin crossover was modeled using a recently proposed formalism based on crystal-field theory, which shows that the spin crossover region extends from approximately 30 to 65 GPa. Given the absence of abrupt changes in the compression mechanism of Fe-bearing Al-phase D before the spin crossover, we show that the strength of H-bonds and likely their symmetrization do not greatly affect the elastic properties of phase D solid solutions, independently of their compositions.
Experimental study of spatial hydraulic jump stabilization using lateral jet flow
Authors: Haghdoost Mohammadreza , Sajjadi SeyedMohsen , Fathi Moghadam Manoochehr , Ahadiyan Javad 
Published: November 2022

Abstract
The present experimental study analyzes the effects of lateral jet flow (LJF) in a stilling basin with abruptly expanding channels on the stabilization and the significant characteristics of spatial hydraulic jump. The experiments were carried out with three different inflow Froude numbers (8.77, 9.56, and 10.87), three different distances of the LJF from the abruptly expanding channel (0 m, 0.25 m, and 0.5 m), and one and two LJF (i.e., the number of active orifices in the LJF system). According to the results, the distances of the LJF from the narrow channel and the number of LJF improve the hydraulic jump's stabilization and flow pattern enhancement in the tailwater channel. Additionally, the average sequent depth and the spatial jump length decreased by 14% and 20%, respectively, compared to no LJF. Also, using LJF increases relative energy dissipation by 12.45% on average.