bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of the Increased SF-1 Expression Induced by DNA Hypomethylation through DNMTs in Endometrial Decidualization
Authors: Mou Chun-Feng , Luo Li , Li Fang-Fang , Wang Ying-Xiong , Ge Lu-Xing , He Fan , Ding Yu-Bin 
Published: March 2023

Abstract
Abnormal endometrial decidualization is closely related to embryo implantation failure and other pregnancy complications. Steroidogenic factor-1 (SF-1), which is also known as nuclear receptor subfamily 5 group A member 1, is a transcriptional activator that is involved in sexual differentiation and formation of the primary steroidogenic tissues. Its regulatory role in mouse and human endometrial decidualization remains unclear. In normal pregnant mice models, the expression of SF-1 was detected by immunohistochemistry and Western blot analysis. In normal pregnant mice, the expression of SF-1 at the implantation site is higher than that in the inter-implantation site. In the artificial decidualization in vivo and in vitro models, the expression of SF-1 increased with the deepening of decidualization. The high expression of SF-1 could promote the decidualization of endometrial stromal cells (ESCs). Based on the detection results of bisulfite sequencing PCR (BSP), the methylation of the CpG island in the SF-1 promoter region decreased after the decidualization of mouse endometrium. The interference of DNA methyltransferase (DNMT) expression promoted the expression of SF-1. The methylation inhibitor 5-aza resulted in the decrease in DNMTs, increase in SF-1 expression, and decidualization of ESCs. With the decidualization of the endometrium, the expression of SF-1 increased, whereas the DNA methylation of the SF-1 promoter decreased. The decrease in DNMTs resulted in increased SF-1 expression and promoted the decidualization of the endometrium. This study provides clues for the diagnosis and treatment of embryo implantation failure associated with abnormal decidualization.
Polarisation of Decayless Kink Oscillations of Solar Coronal Loops
Authors: Zhong Sihui , Nakariakov Valery , Kolotkov Dmitrii , Chitta Lakshmi Pradeep , Antolin Patrick , Verbeeck Cis , Berghmans David 
Published: March 2023

Abstract
Decayless kink oscillations of plasma loops in the solar corona may contain an answer to the enigmatic problem of solar and stellar coronal heating. The polarisation of the oscillations gives us a unique information about their excitation mechanisms and energy supply. However, unambiguous determination of the polarisation has remained elusive. Simultaneous detection of a 4-min decayless kink oscillation from two non-parallel lines-of-sights, separated by about 104 degrees, provided by unique combination of the High Resolution Imager on Solar Orbiter and the Atmospheric Imaging Assembly on Solar Dynamics Observatory, reveals, for the first time, a horizontal or weakly oblique linear polarisation of the oscillation. This conclusion is based on the comparison of observational results with forward modelling of the observational manifestation of various kinds of polarisation of kink oscillations. The revealed polarisation favours the sustainability of these oscillations by quasi-steady flows which may hence supply the energy for coronal heating.
Divergent selection for IMF in rabbits: A story told by plasma metabolites
Authors: Zubiri-Gaitán Agostina , BLASCO AGUSTIN , Hernández Pilar 
Published: March 2023

Abstract
This study provides a thorough comparison of the plasma metabolome of two rabbit lines divergently selected for intramuscular fat content (IMF). The divergent selection led to a correlated response in the overall adiposity, turning these lines into a valuable animal material to study also the genetics of obesity. Over 900 metabolites were detected, and the adjustment of multivariate models, both discriminant and linear, allowed to identify 322 with differential abundances between lines, which also adjusted linearly to the IMF content. The most affected pathways were those of lipids and amino acids, with differences between lines ranging from 0.23 to 6.04 standard deviations, revealing a limited capacity of the low-IMF line to obtain energy from lipids, and a greater branched-chain amino acids catabolism in the high-IMF line related to its increased IMF content. Additionally, changes in metabolites derived from microbial activity confirmed its relevant role in the lipid deposition.
Field root ecology and contribution of dominant vegetations in rhizoliths formation in Badain Jaren Desert, China
Authors: Sun Qingfeng , Yan Junli , Mustoe George , Zamanian Kazem , Tariq Akash , Wiesenberg Guido , Zhang Xuechen , Zeng Fanjiang 
Published: March 2023

Abstract
The authors have requested that this preprint be removed from Research Square.
Perceptions of state measures and media coverage during the COVID-19 pandemic by people with long COVID - A qualitative interview study in Germany
Authors: Schmachtenberg Tim , Wegener Greta , Königs Gloria , Müller Frank , Müllenmeister Christina , Schröder Dominik 
Published: March 2023

Abstract
Background

Since its outbreak, the COVID-19 pandemic has been discussed in various media channels. In Germany, state measures such as contact restrictions have been implemented to contain the incidence of infection. Nevertheless, there are many people who have been infected with the coronavirus and are affected by persistent symptoms such as fatigue, shortness of breath, or pain. How these people perceive pandemic-related coverage and state measures has not yet been adequately researched.

Methods

To address this gap, we conducted guided qualitative interviews with 25 adults with long COVID. The interviews were transcribed in terms of content-semantics and analyzed using qualitative content analysis. Results were then compared with other scientific findings.

Results

The interviews indicated a high approval of restrictive interventions to protect the public from the consequences of the COVID-19 pandemic in this sample. About three-quarters of the participants rated the pandemic containment measures as appropriate. However, twelve of the 25 respondents were dissatisfied with the media coverage of the pandemic and protective measures. Besides inconsistent coverage, the discourse on coronavirus vaccination was specifically criticized. Several participants felt that the coverage of this issue was one-sided or noted a lack of government resolve. Furthermore, respondents criticized the repeal of state measures such as the mask obligation in Germany.

Conclusions

Overall, a need for more consideration of the concerns of people with long COVID in the public discourse on the pandemic becomes apparent. Part of an adapted communication strategy should be: (1) a transparent and target group-related information transfer on the newest findings and regulations during the COVID-19 pandemic, (2) an increased presence of the topic, long COVID, in society through various media. Additionally, the relevant public bodies should expand their engagement in this field. Moreover, the findings ot this study could be used as a starting point for a debate on the long-term implementation of measures to protect vulnerable populations.
Trial registration: The study is registered in the German register for clinical trials (DRKS00026007).
Daemullim: Empirical Evidence for Negative Pay-It-Forward Reciprocity in Hierarchical Situations
Authors: Kang Hyeran , Kim Juyoung , Kim Daeeun , Kim Hackjin 
Published: March 2023

Abstract
Fairness is one of fundamental norms in human society, where people expect others to be reciprocally fair. When people are treated unfairly, they tend to reciprocate unfairness directly. Moreover, unfairness may spread beyond the person directly involved, and affect innocent individuals, which is known as pay-it-forward (PIF) reciprocity. In this study, we examined the impact of unfair treatment on subsequent interactions with new partners whose rankings were superior, equivalent, or inferior compared to the participant. Participants (N = 47) were randomly assigned to receive either fair or unfair treatment in the first round of dictator game. They were then given the opportunity to distribute money to partners occupying different hierarchies. We investigated whether the degree of unfairness passed on to the new partners depended on their ranking. The results demonstrated that the participants’ decision was strongly influenced by the distribution made by the prior partner and the posterior partner’s hierarchy. The findings revealed that participants were more generous toward partners with higher social status, even if they had been treated unfairly, while they were more ruthless toward partners with lower social status in the same situation. These findings provide evidence for negative PIF reciprocity in hierarchical situations.
GPU-accelerated Dynamic Time Warping for Selective Nanopore Sequencing
Authors: Sadasivan Harisankar , Stiffler Daniel , Tirumala Ajay , Israeli Johnny , Narayanasamy Satish 
Published: March 2023

Abstract
The design and supply of RT-PCR primers for accurate virus testing is a complex process. The MinION is a revolutionary portable nanopore DNA sequencer that may be used to sequence the whole genome of a target virus in a biological sample. Human samples have more than 99% of non-target host DNA and Read Until is a protocol that enables the MinION to selectively eject reads in real-time. However, the MinION does not have any in-built compute power to select non-target reads. SquiggleFilter is a prior work that identified the accuracy and throughput challenges in performing Read Until using the state-of-the-art solution and proposed a hardware-accelerated subsequence Dynamic Time Warping (sDTW) based programmable filter on an ASIC. However, SquiggleFilter does not work for genomes larger than 100Kb. We optimize SquiggleFilter’s sDTW algorithm onto the more commonly available GPUs. DTWax better uses tensor core pipes, 2X-SIMD FP16 computations and efficient data handling strategies using offline pre-processing, coalesced global memory loads, warp shuffles and shared memory buffering among other optimizations. DTWax enables Read Until and yields ∼1.92X sequencing speedup and ∼3.64X compute speedup: costup over a sequencing workflow that does not use Read Until.
Efferocytosis-Related LncRNA Signatures for Predicting Prognosis and Immune Landscape of Gastric Cancer
Authors: Zhang Shengxiong , Zhao Xiuzhen , Liu Linxi , Fang Jiansong , Liu Wei , Zhang Haibo 
Published: March 2023

Abstract
Background
Gastric cancer (GC) is a highly malignant form of cancer with a high level of morbidity and mortality. The detection of biomarkers is useful, but still need more evaluation criteria to guide the diagnosis and treatment in clinical practice. This study focuses on identifying long non-coding RNAs(lncRNAs) and find the relation with efferocytosis to predict prognosis and target drug.
Methods
We got the transcriptomic data and clinical data from TCGA platform. Risk model were identified by the least absolute shrinkage and selection operator (LASSO). Then samples were randomly divided into two groups, including training groups and test group. We analyzed the different groups with complete data on lncRNA expression and clinical information, building a risk model and verifying its feasibility. Then we conducted prognostic, pathway, and immune analyses of the risk model. We also looked at drug sensitivity to the risk model, and explored the potential function of the model.
Results
We constructed a risk model containing five efferocytosis-related lncRNAs (ERLs) signatures (LINC01614, AC016717.2, AC068790.7, SCAT1, and PVT1). Then the feasibility of the risk model is verified. We conducted a Cox regression analysis and constructed ROC curves to evaluate the predictive performance of risk features for overall survival (OS) in GC patients, as well as other clinical and pathological characteristics. The risk model had the highest AUC value among these characteristics. We developed a nomogram based on risk scores and clinical characteristics including age, grade, gender, and stage. We used a calibration plot to demonstrate good consistency between the nomogram and the predicted 1-year, 3-year, and 5-year survival rates. These results suggested that the risk model feature is valuable for GC patients. We then evaluated the immune response between different groups, demonstrated that individuals with a high risk score tended to have a higher state of immune infiltration. We also conducted sensitivity screening for guideline drugs, and eight drugs showed significant differences.
Conclusion
The 5-ERLs signatures is useful for predicting prognosis of OS, forecasting the immune response and improving treatment modalities for further clinical application in GC.
Public Attitudes Toward Organ Donation. Development and Validation of a New Instrument (PAOD)
Authors: Othman Elham , Al-salhi Adham , AlOsta Mohammad 
Published: March 2023

Abstract
The number of patients in need of life-saving organ transplants continues to exceed the number of available. One of the most important factors influencing peoples’ practices and rates of organ donation is their attitude and beliefs toward it. However, there is no validated comprehensive instrument that evaluates peoples’ attitudes toward organ donation. Thus, this study aimed to develop and validate such tool. A questionnaire was prepared after reviewing literature. The initial items (n = 45) were evaluated by 15 nonexperts pilot to verify face validity, then content validity was established by three experts, and construct validity was established by Exploratory Factorial Analysis. Afterward, internal consistency was checked using Cronbach’s alpha analysis. Eventually, a total of 31 items were included in the questionnaire, distributed on four subscales. According to the results, we found that the Public Attitude toward Organ Donation questionnaire has adequate validity and reliability to assess the peoples’ attitudes toward organ donation.
Smith-specific regulatory T cells halt the progression of lupus nephritis
Authors: Ooi Joshua , Cheong Rachel , Eggenhuizen Peter , Chang Janet , Broury Ashraf , Ng Boaz , Loh Khai , Tay Elean , Shen Chanjuan , Monk Julie , Zhong Yong , Lim Steven , Chung Jia Xi , Kandane-Rathnayake Rangi , Koelmeyer Rachel , Hoi Alberta , Chaudhry Ashutosh , Snelgrove Sarah , Ting Yi Tian , Morand Eric 
Published: March 2023

Abstract
Antigen-specific regulatory T cells (Tregs) suppress pathogenic autoreactivity and are potential therapeutic candidates for autoimmune diseases such as systemic lupus erythematosus (SLE). Lupus nephritis is associated with autoreactivity to the Smith (Sm) autoantigen and the human leucocyte antigen (HLA)-DR15 haplotype; hence, we investigated the potential of Sm-specific Tregs (Sm-Tregs) to suppress disease. We identified a novel HLA-DR15 restricted immunodominant Sm T cell epitope using biophysical affinity binding assays, then identified high-affinity Sm-specific T cell receptors (TCRs) using high-throughput single-cell sequencing. Using lentiviral vectors, we transduced an lead Sm-specific TCR onto Tregs derived from patients with SLE who were anti-Sm and HLA-DR15 positive. Compared with polyclonal Tregs, Sm-Tregs potently suppressed Sm-specific pro-inflammatory responses in vitro and suppressed disease progression in a humanized mouse model of lupus nephritis. These results show that Sm-Tregs are a promising therapy for SLE.
Structure of a Rpd3/HDAC holoenzyme complex bound to the nucleosome
Authors: Wang Xuejuan , Zhang Yueyue , Cai Gang 
Published: March 2023

Abstract
The Sin3/HDAC complexes are highly conserved from yeast to humans and function by deacetylating histones, condensing chromatin, and modulating gene expression. Despite the continued analysis of HDAC inhibitors in clinical trials, our mechanistic understanding of the HDAC activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae Rpd3S/Sin3B bound to a nucleosome, at atomic resolution. In the structure, two copies of Rco1 and two copies of Eaf3 are integrated through the scaffold subunit Sin3, which wraps the catalytic Rpd3/HDAC. Rco1 and Eaf3 recognize the H3 tails with a specific methylation pattern. N-terminal disordered region of Rco1 contacts the histones at the acidic patch. Furthermore, Rco1, Eaf3 and the Sin3 subunits also bind to extranucleosomal and nucleosomal DNA. These multivalent interactions not only facilitate detaching histone tails from nucleosomes but also optimally orient the complex to H3 tail, catalyzing deacetylation of H3K18 in our structure. The complex architecture and dimeric Rco1-Eaf3 heterodimer offer the ergonomics allowing one Rpd3S simultaneously engages two neighboring nucleosomes. Our study elucidates the central roles played by the non-catalytic subunits in a class I HDAC complex provides a structural framework for the understanding of HDAC regulation by histone modifications.
Compare the effect of Orthokeratology and Highly Aspherical Lenslets on slowing the progression of myopia
Authors: Li Chao , Gong WeiFen , Lou ZhiYin , Zhang MingZhi 
Published: March 2023

Abstract
Purpose: To evaluate the efficacy of Highly Aspherical Lenslets (HAL) in slowing myopia progression among school children and compare it to Orthokeratology.
Methods: This retrospective cohort study included 186 cases of myopic individuals aged between 7 to 15 years, with myopia ranging from -0.75 to -8.00D and astigmatism of ≤ 4.0D. Each group consisted of 62 subjects, and only the right eye was included in the analysis. The study involved six-monthly measurements of both cycloplegic refraction and axial length to track changes over time.
Results: The baseline average age, gender, Spherical equivalent refraction (SER), and axial length (AL) in the SV group, HAL group, and Ortho-K group were no statistically significant differences (P>0.05). At six months, average (SER) myopia progression was -0.44±0.34 D in the single vision (SV) lenses group and -0.16±0.32 D in the HAL group. Average axial elongation was 0.22±0.13mm in the SV group, 0.08±0.14mm in the HAL group and 0.04±0.11mm in the orthokeratology group. As compared to the SV group, the HAL group reduced myopia progression (SER) to 65.9% (mean difference 0.29±0.46D, P＜0.001). Compared with the SV group, the HAL group axial elongation more slowly(63.6%, mean difference 0.14±0.19mm, P＜0.001). Likewise, axial elongation more slowly at 81.8% for orthokeratology group subjects than the SV group (mean difference 0.18±0.20mm， P＜0.001). In terms of individual issues, 35 of 62 children wearing HAL had no myopia progression after 6 months, higher than the SV group (15 of 62, 24.2%, P＜0 .001). In addition, 30.6% of children with HAL revealed no axial elongation, compared with 3.2% of those with SV lenses (2 of 62, P＜0 .001). The axial elongation of HAL and Ortho-K lenses (28 of 62, 45.2%) was similar (P> 0.05).
Conclusions: Wearing the HAL daily slows myopia progression in myopic children and significantly reduces axial elongation. Additionally, both the daily employment of HAL and overnight Orthokeratology demonstrate comparable efficacy in slowing axial elongation in myopic children.
Bosonic spectrum of a correlated multiband system, BaFe1.80Co0.20As2, obtained via infrared spectroscopy
Authors: Hwang Jungseek , Panda Candan , Lee Hang Gu , Park Hwiwoo , Jung Soon-Gil , Choi Ki-Young 
Published: March 2023

Abstract
We investigated a single crystal BaFe2-xCoxAs2 (Co-doped BaFe2As2: Co-Ba122) to obtain a bosonic spectrum using infrared spectroscopy. We used the generalized Allen formula, an extended Drude-Lorentz model for the normal state, and a two-parallel-channel approach for the superconducting (SC) state to obtain the bosonic spectrum from the optical conductivity. This analysis required a couple of Lorentz modes at very low-energy, but these modes were not necessary to analyze the K-doped BaFe2As2 (K-Ba122) and LiFeAs. Various physical quantities, such as the coupling constant, maximum SC transition temperature, SC coherence length, and upper critical field, were extracted from the bosonic spectrum. The superfluid plasma frequency and the London penetration depth were also obtained from the optical conductivity. The physical properties of Co-Ba122 and K-Ba122 were also compared and discussed in this study. We believe that our results will be helpful in figuring out the microscopic pairing mechanism for superconductivity in doped Ba122 systems and will provide useful information on their applications.
Association between Air Pollutants and Initiation of Biological Therapy in Patients with Ankylosing Spondylitis: A Nationwide, Population-Based Case-Control Study
Authors: Kao Chung-Mao , Chen Yi-Ming , Huang Wen-Nan , Chen Yi-Hsing , Chen Hsin-Hua 
Published: March 2023

Abstract
Background: Outdoor air pollution has been found to trigger systemic inflammatory responses and aggravate the activity of certain rheumatic diseases. However, few studies have explored the influence of air pollution on the activity of ankylosing spondylitis (AS). As patients with active AS in Taiwan can be reimbursed through the National Health Insurance program for biological therapy, we investigated the association between air pollutants and the initiation of biologics for active disease in patients with AS.
Methods: Since 2011, hourly concentrations of ambient air pollutants, including PM2.5, PM10, NO2, CO, SO2 and O3 have been estimated in Taiwan. Using Taiwanese National Health Insurance Research Database, we identified patients with newly diagnosed AS from 2003 to 2013. We selected 584 patients initiating biologics from 2012 to 2013 and 2,336 gender-, age at biologic initiation-, year of AS diagnosis- and disease duration-matched controls. We examined the associations of biologics initiation with air pollutants exposure within one year prior to biologic use while adjusting for potential confounders, including disease duration, urbanisation level, monthly income, Charlson comorbidity index (CCI), uveitis, psoriasis, inflammatory bowel disease and the use of medications for AS. Results are shown as adjusted odds ratio (aOR) with 95% confidence intervals (CIs).
Results: The initiation of biologics was associated with exposure to CO (per 1 ppm) (aOR, 8.58; 95% CI, 2.02–36.35), and NO2 (per 10 ppb) (aOR, 0.23; 95% CI, 0.11–0.50). Other independent predictors included disease duration (incremental year, aOR, 8.97), CCI (aOR, 1.31), psoriasis (aOR, 25.06), use of non-steroidal anti-inflammatory drugs (aOR, 23.66), methotrexate use (aOR, 4.53; 95% CI, 2.93–7.00), sulfasalazine use (aOR, 12.15; 95% CI, 8.98–15.45) and prednisolone equivalent dosages (mg/day, aOR, 1.11).
Conclusions: This nationwide, population-based study revealed that the initiation of biologics was positively associated with CO levels, but negatively associated with NO2 levels.