bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing
Authors: Xu Zhe , Cheng Si , Qiu Xin , Wang Xiaoqi , Hu Qiuwen , Shi Yanfeng , Liu Yang , Lin Jinxi , Tian Jichao , Peng Yongfei , Jiang Yong , Yang Yadong , Ye Jianwei , Wang Yilong , Meng Xia , Li Zixiao , Li Hao , Wang Yongjun 
Published: June 2023

Abstract
Background
In large-scale high-throughput sequencing projects and biobank construction, sample tagging is essential to prevent sample mix-ups. Despite the availability of fingerprint panels for DNA data, little research has been conducted on sample tagging of whole genome bisulfite sequencing (WGBS) data. This study aims to construct a pipeline and identify applicable fingerprint panels to address this problem.

Results
Using autosome-wide A/T polymorphic single nucleotide variants (SNVs) obtained from whole genome sequencing (WGS) and WGBS of individuals from the Third China National Stroke Registry, we designed a fingerprint panel and constructed an optimized pipeline for tagging WGBS data. This pipeline used Bis-SNP to call genotypes from the WGBS data, and optimized genotype comparison by eliminating wildtype homozygous and missing genotypes, and retaining variants with identical genomic coordinates and reference/alternative alleles. WGS-based and WGBS-based genotypes called from identical or different samples were extensively compared using hap.py. In the first batch of 94 samples, the genotype consistency rates were between 71.01%-84.23% and 51.43%-60.50% for the matched and mismatched WGS and WGBS data using the autosome-wide A/T polymorphic SNV panel. This capability to tag WGBS data was validated among the second batch of 240 samples, with genotype consistency rates ranging from 70.61%-84.65% to 49.58%-61.42% for the matched and mismatched data, respectively. We also determined that the number of genetic variants required to correctly tag WGBS data was on the order of thousands through testing six fingerprint panels with different orders for the number of variants. Additionally, we affirmed this result with two self-designed panels of 1351 and 1278 SNVs, respectively. Furthermore, this study confirmed that using the number of genetic variants with identical coordinates and ref/alt alleles, or identical genotypes could not correctly tag WGBS data.

Conclusion
This study proposed an optimized pipeline, applicable fingerprint panels, and a lower boundary for the number of fingerprint genetic variants needed for correct sample tagging of WGBS data, which are valuable for tagging WGBS data and integrating multi-omics data for biobanks.
Prevention of M2 polarization and temporal limitation of differentiation in monocytes by extracellular ATP
Authors: Scherr Benedikt F. , Reiner Martin F. , Baumann Flavia , Höhne Kerstin , Müller Tobias , Ayata Korcan , Müller-Quernheim Joachim , Idzko Marco , Zissel Gernot 
Published: June 2023

Abstract
Background
Elevated levels of extracellular adenosine triphosphate (ATP) modulate immunologic pathways and are considered to be a danger signal in inflammation, lung fibrosis and cancer. Macrophages can be classified into two main types: M1 macrophages are classically activated, pro-inflammatory macrophages, whereas M2 macrophages are alternatively activated, pro-fibrotic macrophages. In this study, we examined the effect of ATP on differentiation of native human monocytes into these macrophage subtypes. We characterized M1 and M2 like macrophages by their release of Interleukin-1beta (IL-1β) and Chemokine (C–C motif) ligand 18 (CCL18), respectively.

Results
Monocytes were stimulated with ATP or the P2X7 receptor agonist Benzoylbenzoyl-ATP (Bz-ATP), and the production of various cytokines was analyzed, with a particular focus on CCL18 and IL-1β, along with the expression of different purinergic receptors. Over a 72 h period of cell culture, monocytes spontaneously differentiated to M2 like macrophages, as indicated by an increased release of CCL18. Immediate stimulation of monocytes with ATP resulted in a dose-dependent reduction in CCL18 release, but had no effect on the concentration of IL-1β. In contrast, delayed stimulation with ATP had no effect on either CCL18 or IL-1β release. Similar results were observed in a model of inflammation using lipopolysaccharide-stimulated human monocytes. Stimulation with the P2X7 receptor agonist Bz-ATP mimicked the effect of ATP on M2-macrophage differentiation, indicating that P2X7 is involved in ATP-induced inhibition of CCL18 release. Indeed, P2X7 was downregulated during spontaneous M2 differentiation, which may partially explain the ineffectiveness of late ATP stimulation of monocytes. However, pre-incubation of monocytes with PPADS, Suramin (unselective P2X- and P2Y-receptor blockers) and KN62 (P2X7-antagonist) failed to reverse the reduction of CCL18 by ATP.

Conclusions
ATP prevents spontaneous differentiation of monocytes into M2-like macrophages in a dose- and time-dependent manner. These effects were not mediated by P2X and P2Y receptors.
Effects of intra-operative administration of subanesthetic s-ketamine on emergence from sevoflurane anesthesia: a randomized double-blind placebo-controlled study
Authors: Liu Tiantian , Zhang Xinxin , Li Ao , Liu Tingting , Yang Xue , Zhang Huanhuan , Lei Yanling , Yang Qianzi , Dong Hailong 
Published: June 2023

Abstract
Background
Ketamine is administered in the perioperative period for its benefits in analgesia, anti-agitation and anti-depression when administered at a small dose. However, it is not clear whether the intra-operative administration of ketamine would affect emergence under sevoflurane anesthesia. To investigate this effect, we designed this trial.

Methods
In this randomized, double-blind, placebo-controlled study, we enrolled 44 female patients aged 18–60 who were scheduled to elective laparoscopic gynecological surgeries. All patients were randomly assigned to saline or s-ketamine group. In s-ketamine group, patients received 0.125 mg/kg s-ketamine 30 min after the start of surgery. In saline group, patients were administered the same volume of saline. Sevoflurane and remifentanil were used to maintain general anesthesia. The primary outcome was emergence time. We also assessed postoperative agitation, cognitive function, and delirium. In addition, we collected and analyzed prefrontal electroencephalogram (EEG) during and after general anesthesia.

Results
There were no significant differences in emergence time between s-ketamine group and saline group (10.80 ± 3.77 min vs. 10.00 ± 2.78 min, P = 0.457). Neither postoperative agitation (4 [3, 4] vs. 4 [3, 4], P = 0.835) nor cognitive function (25.84 ± 2.69 vs. 25.55 ± 2.19, P = 0.412) differed between groups. No postoperative delirium was observed in either group. Subanesthetic s-ketamine resulted in active EEG with decreased power of slow (-0.35 ± 1.13 dB vs. -1.63 ± 1.03 dB, P = 0.003), delta (-0.22 ± 1.11 dB vs. -1.32 ± 1.09 dB, P = 0.011) and alpha (-0.31 ± 0.71 dB vs. -1.71 ± 1.34 dB, P = 0.0003) waves and increased power of beta-gamma bands (-0.30 ± 0.89 dB vs. 4.20 ± 2.08 dB, P < 0.0001) during sevoflurane anesthesia, as well as an increased alpha peak frequency (-0.16 ± 0.48 Hz vs. 0.31 ± 0.73 Hz, P = 0.026). EEG patterns did not differ during the recovery period after emergence between groups.

Conclusion
Ketamine administered during sevoflurane anesthesia had no apparent influence on emergence time in young and middle-aged female patients undergoing laparoscopic surgery. Subanesthetic s-ketamine induced an active prefrontal EEG pattern during sevoflurane anesthesia but did not raise neurological side effects after surgery.

Trial registration
Chinese Clinical Trial Registry, ChiCTR2100046479 (date: 16/05/2021).
Effects of intraoperative esketamine addition on gastrointestinal function after benign gynaecological laparoscopic surgery: a double-blind, randomized controlled study
Authors: Ma Yuhua , Zhang Ran , Cao Xue , Zhang Lin , Bao Suozhu , Ren Jie , Ma Weiwei 
Published: June 2023

Abstract
Background
Gastrointestinal hypokinesis can occur transiently after benign gynecologic surgery. Opioids cause the side effect of postoperative gastrointestinal hypokinesis, but an opioid-sparing anaesthetic protocol based on esketamine reduces intraoperative opioid consumption. Therefore, this study hypothesised that an opioid-sparing anaesthetic protocol based on esketamine would shorten the gastrointestinal function recovery time after benign gynaecological laparoscopic surgery.

Methods
This was a prospective randomized controlled double-blind study conducted in a single centre. All patients scheduled for elective benign laparoscopic gynaecological surgery at Xing’an Meng People’s Hospital, Inner Mongolia Autonomous Region, from November 2021 to April 2022 were consecutively enrolled and randomly divided into the opioid-sparing anaesthesia group (Group OS) and the conventional anaesthesia group (Group C). Postoperative first exhaust time, feeding time and postoperative nausea and/or vomiting (PONV) were analyzed in both groups.

Results
A total of 71 patients were enrolled in this study, including 35 in Group OS and 36 in Group C. The general condition, operative time, type of surgery, intraoperative bleeding, intraoperative fluid volume and intraoperative urine volume were not statistically different between the two groups. Compared with Group C, significantly shorter first postoperative flatus time (11 [8, 14] h vs. 14 [11, 18], p = 0.003) and anaesthesia resuscitation time (7 [6, 9] h vs. 9 [7, 11] h, p = 0.013)were observed in the OS group. The incidence of PONV in Group OS was significantly lower compared with Group C (11.4% vs. 41.7%, p = 0.007).

Conclusion
The esketamine-based opioid-sparing anaesthetic protocol can shorten the postoperative first flatus time after benign laparoscopic surgery in gynaecology, and reduce the incidence of PONV. In addition, the application of esketamine may reduce the postoperative opioid dose requirement of patients.

Trial registration
: This study was registered with the China Clinical Trials Registry (registration number: ChiCTR2100052528, 30/10/2021).
Associations between social support and poverty among older adults
Authors: Liao Hui , Li Sangsang , Han Dan , Zhang Mei , Zhao Jie , Wu Yunyi , Ma Ying , Yan Chaoyang , Wang Jing 
Published: June 2023

Abstract
Background
With population aging becoming a pressing global concern, social support is more meaningful for older adults. In particular, financial supports, such as health insurance and financial assistance derived from family, all play great role in assistance affairs. Research shows social support possibly has an impact on poverty, but the association between formal and informal supports is unclear. We are aimed at verifying the association between distinct social supports and exploring whether this association would affect poverty alleviation for older adults.

Methods
A total of 2,683 individuals aged 60 years or older who have medical expenses were included in a survey conducted by the China Health and Retirement Longitudinal Study in 2018. A chi-square analysis and an independent samples T test all were used to explore the differences of social supports among old people with different economic condition. A binary logistic regression was aimed at analyzing the association between social supports and poverty for older adults. The structural equation model was established to evaluate the association between formal support and informal support and the mechanism(s) of social supports affecting poverty.

Results
The overall average rate of reimbursement for outpatient care was 0.20 with standard deviation 0.22, and the average reimbursement rate of inpatient care for the poor older adults is nearly 5% lower than the average of the non-poor older adults. We found that having private health insurance and higher reimbursement rate of inpatient care were associated with lower likelihood of living in poverty for older adults. Formal support would directly affect poverty, but its impact on poverty through informal support is insignificant even if formal support is negatively associated with informal support.

Conclusion
A dilemma in reducing the economic burden of disease and receiving family assistance for older adults was revealed, and a more complete health security and higher level of medical expenses compensation would be beneficial to prevent poverty. Optimizing the primary healthcare and increasing the percentage of insurance compensation, policies that focus on the specific cultural values and strengthening the role of supplementary insurance are advantaged for alleviating poverty among older adults.
Analysis of m7G-Related signatures in the tumour immune microenvironment and identification of clinical prognostic regulators in breast cancer
Authors: Huang Qinghua , Mo Jianlan , Yang Huawei , Ji Yinan , Huang Rong , Liu Yan , Pan You 
Published: June 2023

Abstract
Background
Breast cancer is a malignant tumour that seriously threatens women’s life and health and exhibits high inter-individual heterogeneity, emphasising the need for more in-depth research on its pathogenesis. While internal 7-methylguanosine (m7G) modifications affect RNA processing and function and are believed to be involved in human diseases, little is currently known about the role of m7G modification in breast cancer.

Methods and Results
We elucidated the expression, copy number variation incidence and prognostic value of 24 m7G-related genes (m7GRGs) in breast cancer. Subsequently, based on the expression of these 24 m7GRGs, consensus clustering was used to divide tumour samples from the TCGA-BRCA dataset into four subtypes based on significant differences in their immune cell infiltration and stromal scores. Differentially expressed genes between subtypes were mainly enriched in immune-related pathways such as ‘Ribosome’, ‘TNF signalling pathway’ and ‘Salmonella infection’. Support vector machines and multivariate Cox regression analysis were applied based on these 24 m7GRGs, and four m7GRGs—AGO2, EIF4E3, DPCS and EIF4E—were identified for constructing the prediction model. An ROC curve indicated that a nomogram model based on the risk model and clinical factors had strong ability to predict the prognosis of breast cancer. The prognoses of patients in the high- and low-TMB groups were significantly different (p = 0.03). Moreover, the four-gene signature was able to predict the response to chemotherapy.

Conclusions
In conclusion, we identified four different subtypes of breast cancer with significant differences in the immune microenvironment and pathways. We elucidated prognostic biomarkers associated with breast cancer and constructed a prognostic model involving four m7GRGs. In addition, we predicted the candidate drugs related to breast cancer based on the prognosis model.
Factors associated with quality of life in patients receiving lung transplantation: a cross-sectional study
Authors: Takahashi Ryo , Takahashi Tamao , Okada Yoshinori , Kohzuki Masahiro , Ebihara Satoru 
Published: June 2023

Abstract
Background
With improved prognosis after lung transplantation (LTx), improving health-related quality of life (HRQL) in patients who have undergone LTx is a key goal. Although HRQL is improved significantly after transplantation, it is poorer than that in ordinary healthy people. However, the factors associated with poor HRQL remain unclear. This cross-sectional study aimed to identify the factors associated with poor HRQL in patients who have undergone LTx.

Methods
Between December 2018 and May 2022, 80 patients who had undergone LTx completed St. George’s Respiratory Questionnaire (SGRQ) as a disease-specific quality of life measure, the Short Form-12 (SF-12) as a generic quality of life measure, and modified Medical Research Council (mMRC) scale of dyspnea. The groups were assigned according to the median SGRQ-total score and the Japanese population standard for SF-12, and those with good HRQL were compared with those with poor HRQL. Independent factors were evaluated using multivariate analysis.

Results
With regard to the SGRQ, there were significant differences in the forced expiratory volume in 1 s (FEV1) (P = 0.041), use of bronchodilators (P = 0.026), 6-min walk distance (6MWD) (P < 0.001), and Mmrc (P < 0.001) between better and poorer HRQL. For the SF-12 physical component summary score (PCS), age (P = 0.017), sex (P = 0.011), FEV1 (P < 0.001), forced vital capacity (FVC) (P < 0.001), diagnosis (P = 0.011), handgrip force (P = 0.003), 6MWD (P < 0.001), and Mmrc (P < 0.001) varied. Multivariate analyses revealed that Mmrc was the only independent factor in the SGRQ (P < 0.001, odds ratio [OR] = 6.65, 95% confidence interval [CI]: 2.49–17.74) and SF-12 PCS (P = 0.001, OR = 0.185, 95% CI: 0.07–0.52). There were significant correlations between the SGRQ-Total score and SF-12 PCS (correlation coefficient = -0.612, P < 0.001).

Conclusions
Dyspnea may be an independent factor of poor disease-specific and generic HRQL in LTx patients. The management of dyspnea may improve the HRQL in patients who have undergone LTx.
Use of a comprehensive systemic ultrasound evaluation in the diagnosis and analysis of acute lateral region ankle sprain
Authors: Song Jae Hwang , Moon Jeong Jae , Shin Woo Jin , Ko Kwang Pyo 
Published: June 2023

Abstract
Background
For the diagnosis of acute lateral ankle sprain, many clinicians use ultrasound; they typically focus on the lateral ligament complex, which is the most common site of lesions in ankle sprain. However, this approach risks missing other foot and ankle lesions. The present study aimed to provide and analyze the results of a new ultrasound method of diagnosis for acute lateral ankle sprain which can thoroughly investigate overall lesions of the foot and ankle.

Methods
Retrospective cross-sectional cohort study of 123 patients who underwent diagnostic ultrasound within 1 week of acute lateral ankle injury was performed. Causes of ankle sprain, incidence and severity of each ligament injury, location of anterior talofibular ligament (ATFL) injury, accompanying ligament injury, and occult fracture were analyzed.

Results
Among the 102 cases of ATFL injuries, 60 (58.5%) had islolated ATFL injury, 28 (27.5%) had accompanying calcaneofibular ligament injury (CFL), and 14 (13.7%) had accompanying midtarsal or syndesmosis injury. ATFL injuries occurred on the fibula attachment in 48 (47.1%) cases, ligament mid-substance in 24 (23.5%) cases, and talus attachment in 30 (29.4%) cases. Among the 165 lesions from 123 cases, injuries of the fourth or fifth dorsal tarsometatarsal (12 cases, 7.3%), bifurcate (11 cases, 6.7%), and anterior tibiofibular (11 cases, 6.7%) ligaments were not rare.

Conclusion
These findings suggest that an ultrasound examination involving investigation of the midtarsal joint and syndesmotic ligament, as well as the ATFL and CFL, is useful for comprehensive, systemic diagnosis of acute lateral ankle sprain.
Extensive skin necrosis following total hip arthroplasty performed through the direct anterior approach
Authors: Idris Nimatullah , Zingg Matthieu , Gauthier Morgan , Oranges Carlo M. , Kalbermatten Daniel F. , Hannouche Didier 
Published: June 2023

Abstract
Background
Total hip arthroplasty is a widely performed surgical procedure, which enables patients to regain mobility, alleviates pain, and improves overall quality of life. Periarticular multimodal drug infiltration (PAI) is increasingly being used as an effective postoperative pain management, decreasing the systemic consumption of opioids. Extensive postoperative skin necrosis without a deep joint infection as a complication of total hip arthroplasty with PAI has not yet been described.

Case presentation
A 71-year-old patient who underwent total hip arthroplasty of the right hip for primary osteoarthritis through the Direct Anterior Approach presented postoperatively a large area of necrotic skin at the incision. Joint infection was excluded. An extensive debridement was performed and the tissue defect was reconstructed by a pedicled anterolateral thigh flap. The skin maintained a satisfactory appearance at 1 year postoperatively, and the hip was pain-free with restored ranges of motion. The patient was able to walk with no support and without limitation.

Conclusion
We address the possible risk factors, discuss the use of epinephrine in PAI and explore possible treatment options for such a complication.
Axillary skin crease incision versus conventional posterolateral incision in open repair of patent ductus arteriosus for extremely low birth weight infants: a retrospective study
Authors: Okamoto Mitsumasa , Tsuruno Yudai , Fukuzawa Hiroaki 
Published: June 2023

Abstract
Background
Thoracotomy with posterolateral incision (PLI) is commonly used for surgical repair of patent ductus arteriosus (PDA) in extremely low birth weight (ELBW) infants. Some reports have described thoracotomy for PDA using an axillary skin crease incision (ASCI) in consideration of cosmetic problems such as surgical wounds and thoracic deformities, but the details remain unclear.

Methods
In this study, we performed clipping ligation by thoracotomy with ASCI for ELBW infants with PDA from 2011 to 2015 for the purpose of improving cosmetic results, and retrospectively compared the results with those for conventional PLI cases performed from 2016 to 2020.

Results
ASCI was found to be associated with serious surgical complications and showed a significant difference in outcome parameters only for surgery time, suggesting a safety problem for ASCI. Considering these results, PLI allows clipping of the nearby PDA from the thoracotomy wound while looking straight ahead, whereas the PDA in ASCI is positioned deep and oblique to the thoracotomy wound, so the clipping angle is limited and accurate completion of the procedure is difficult.

Conclusions
Regarding PDA repair in ELBW infants, ASCI shows a high risk of serious surgical complications. Conventional PLI remains preferable for safe and accurate results.