bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of methylation estimates obtained via MinION nanopore sequencing and sanger bisulfite sequencing in the TRPA1 promoter region
Authors: Gombert Sara , Jahn Kirsten , Pathak Hansi , Burkert Alexandra , Schmidt Gunnar , Wiehlmann Lutz , Davenport Colin , Brändl Björn , Müller Franz-Josef , Leffler Andreas , Deest Maximilian , Frieling Helge 
Published: October 2023

Abstract
Background
Bisulfite sequencing has long been considered the gold standard for measuring DNA methylation at single CpG resolution. However, in recent years several new approaches like nanopore sequencing have been developed due to hints for a partial error-proneness of bisulfite sequencing. Since these errors were shown to be sequence-specific, we aimed to verify the methylation data of a particular region of the TRPA1 promoter from our previous studies obtained by bisulfite sequencing.

Methods
We compared methylation rates determined by direct bisulfite sequencing and nanopore sequencing following Cas9-mediated PCR-free enrichment.

Results
We could show that CpG methylation levels above 20% corroborate well with our previous data. Within the range between 0 and 20% methylation, however, Sanger sequencing data have to be interpreted cautiously, at least in the investigated region of interest (TRPA1 promotor region).

Conclusion
Based on the investigation of the TRPA1- region as an example, the present work can help in choosing the right method out of the two current main approaches for methylation analysis for different individual settings regarding many factors like cohort size, costs and prerequisites that should be fulfilled for each method. All in all, both methods have their raison d’être. Furthermore, the present paper contains and illustrates some important basic information and explanation of how guide RNAs should be located for an optimal outcome in Cas9 mediated PCR free target enrichment.
Performance of ultra-sensitive malaria rapid diagnostic test to detect Plasmodium falciparum infection in pregnant women in Kinshasa, the Democratic Republic of the Congo
Authors: Kabalu Tshiongo Japhet , Luzolo Flory , Kabena Melissa , Kuseke Lise , Djimde Moussa , Mitashi Patrick , Lumbala Crispin , Kayentao Kassoum , Menting Sandra , Mens Petra F. , Schallig Henk D. F. H. , Lutumba Pascal , Tinto Halidou , Muhindo Mavoko Hypolite , Maketa Vivi 
Published: October 2023

Abstract
Background
Low peripheral parasitaemia caused by sequestration of Plasmodium falciparum in the placenta hampers the diagnosis of malaria in pregnant women, leading to microscopy or conventional rapid diagnostic tests (RDTs) false-negative results. Although mainly asymptomatic, maternal malaria remains harmful to pregnant women and their offspring in endemic settings and must be adequately diagnosed. Ultra-sensitive RDTs (uRDTs) are thought to be more sensitive than RDTs, and their diagnostic performance was assessed in the current study in pregnant women living in Kinshasa, a stable malaria transmission area in the Democratic Republic of the Congo.

Methods
To assess and compare the diagnostic performances of both RDTs and uRDTs, 497 peripheral blood samples were tested using microscopy and quantitative polymerase chain reaction (qPCR) as the index and the reference tests, respectively. The agreement between the different diagnostic tests assessed was estimated by Cohen's Kappa test.

Results
The median parasite density by qPCR was 292 p/μL of blood [IQR (49.7–1137)]. Using qPCR as the reference diagnostic test, the sensitivities of microscopy, RDT and uRDT were respectively [55.7% (95% CI 47.6–63.6)], [81.7% (95%CI 74.7–87.3)] and [88% (95% CI 81.9–92.6)]. The specificities of the tests were calculated at 98.5% (95% CI 96.6–99.5), 95.2% (95% CI 92.5–97.2) and 94.4% (95% CI 91.4–96.6) for microscopy, RDT and uRDT, respectively. The agreement between qPCR and uRDT was almost perfect (Kappa = 0.82). For parasite density (qPCR) below 100 p/µL, the sensitivity of RDT was 62% (95% CI 47.1–75.3) compared to 68% (95% CI 53.3–80.4) for uRDT. Between 100 and 200 p/µL, the sensitivity of RDT was higher, but still lower compared to uRDT: 89.4% (95% CI 66.8–98.7) for RDT versus 100% (95% CI 82.3–100) for uRDT. In both cases, microscopy was lower, with 20% (95% CI 10–33.7) and 47.3% (95% CI 24.4–71.1) respectively.

Conclusions
uRDT has the potential to improve malaria management in pregnant women as it has been found to be slightly more sensitive than RDT in the detection of malaria in pregnant women but the difference was not significant. Microscopy has a more limited value for the diagnosis of malaria during the pregnancy, because of its lower sensitivity.
Cumulative live birth rates with autologous oocytes plateau with fewer number of cycles for each year of age > 42
Authors: Seifer David B. , Wang Sarah F. , Frankfurter David 
Published: October 2023

Abstract
Objective
To disaggregate the Society for Assisted Reproductive Technology Clinic Outcome Reporting System (SART CORS) age category of “ > 42” and compare age-stratified cumulative live birth rates (CLBR) > 42 years old.

Design
Retrospective cohort study of autologous linked ART cycles.

Setting
United States (US) National ART Database.

Patient(s)
Women > 42 years old without a history of prior ART cycles who underwent ART between 2014–2020 as reported to the SART CORS database.

Intervention(s)
Disaggregate the SART CORS age category of “ > 42” into age-stratified cumulative live birth rates (CLBR).

Main Outcome Measure(s)
Age-stratified cumulative live birth rates (CLBR) for women ≥ 43 years old.

Results
Between 2014–2020, 24,650 women > 42 years old without history of prior ART underwent 58,132 cycles, resulting in 1,982 live births. Women ages 43, 44, 45, 46, 47, 48, 49, ≥ 50 achieved maximal CLBR of 9.7%, 8.6%, 5.0%, 3.6%, 2.5%, 1.5%, 2.7%, 1.3%, respectively. CLBR for women between 43–45 were significantly higher compared to those 46 and older (p < 0.05). Among women 46 and older, CLBR were not significantly different. Women ages 43 and 44 did not exhibit a significant increase in CLBR beyond the 5th cycle. Age 45 and 46 reached CLBR plateau by the 3rd cycle. Age ≥ 47 CLBR plateaued after the first cycle. After adjusting for age, race/ethnicity, BMI, nulliparity, etiology of infertility, number of oocytes retrieved, embryos transferred, blastocyst transfer, use of ICSI, PGT, and ART treatment cycle number, there was no association between markers of ovarian reserve (day 3 FSH and random AMH levels) and live birth for women > 42.

Conclusions
While CLBR of autologous cycles from women 42 or younger generally plateau by cycle number 5, age-stratified cycles from women > 42 plateau after fewer cycles to maximize CLBR. Patient and physician expectations for maximum CLBR beyond 42 may be practically based on fewer planned cycles before reaching an age-specific CLBR plateau than may have been previously expected.
Preeclampsia-associated lncRNA FEZF1-AS1 regulates cell proliferation and apoptosis in placental trophoblast cells through the ELAVL1/NOC2L axis
Authors: Zhao Xudong , Su Fengyun , Guo Qing , Tao Xiuhong , Wang Huifeng , Wang Hongling , Li Qinwen , Zhang Wangmeng 
Published: October 2023

Abstract
Background
LncRNAs have been shown to be involved in and control the biological processes of multiple diseases, including preeclampsia (PE). The impairment of trophoblast cell proliferation is recognized as a significant anomaly contributing to the development of PE. LncRNA FEZF1-AS1 was found downregulated in placental tissues of PE patients. However, the precise regulatory mechanism of FEZF1-AS1 in placental trophoblast proliferation and apoptosis remains unclear.

Results
In this study, we conducted an investigation into the expression levels of FEZF1-AS1 and NOC2L in placental tissues obtained from patients diagnosed with PE. Subsequently, we employed CCK-8 and EdU assays to quantify cell proliferation, while TUNEL staining and western blot for apoptosis-related protein detection to assess apoptosis. Furthermore, the interactions between FEZF1-AS1 and ELAVL1, as well as NOC2L and ELAVL1, were confirmed through the implementation of RIP and RNA pull-down assays. We found a downregulation of lncRNA FEZF1-AS1 and NOC2L in placental tissues of PE patients. Overexpression of FEZF1-AS1 or NOC2L resulted in increased cell proliferation and inhibition of apoptosis, whereas knockdown of FEZF1-AS1 or NOC2L had the opposite effect. In addition, lncRNA FEZF1-AS1 stabilized NOC2L mRNA expression by interacting with ELAVL1. Moreover, partial reversal of the effects of FEZF1-AS1 overexpression on cell proliferation and apoptosis was observed upon suppression of ELAVL1 or NOC2L.

Conclusions
PE related lncRNA FEZF1-AS1 could regulate apoptosis and proliferation of placental trophoblast cells through the ELAVL1/NOC2L axis.
Prospective study of pain and patient outcomes in the emergency department: a tale of two pain assessment methods
Authors: Ku Nai-Wen , Cheng Ming-Tai , Liew Chiat Qiao , Chen Yun Chang , Sung Chih-Wei , Ko Chia-Hsin , Lu Tsung-Chien , Huang Chien-Hua , Tsai Chu-Lin 
Published: October 2023

Abstract
Background
Accurate pain assessment is essential in the emergency department (ED) triage process. Overestimation of pain intensity, however, can lead to unnecessary overtriage. The study aimed to investigate the influence of pain on patient outcomes and how pain intensity modulates the triage’s predictive capabilities on these outcomes.

Methods
A prospective observational cohort study was conducted at a tertiary care hospital, enrolling adult patients in the triage station. The entire triage process was captured on video. Two pain assessment methods were employed: (1) Self-reported pain score in the Taiwan Triage and Acuity Scale, referred to as the system-based method; (2) Five physicians independently assigned triage levels and assessed pain scores from video footage, termed the physician-based method. The primary outcome was hospitalization, and secondary outcomes included ED length of stay (EDLOS) and ED charges.

Results
Of the 656 patients evaluated, the median self-reported pain score was 4 (interquartile range, 0–7), while the median physician-rated pain score was 1.5 (interquartile range, 0–3). Increased self-reported pain severity was not associated with prolonged EDLOS and increased ED charges, but a positive association was identified with physician-rated pain scores. Using the system-based method, the predictive efficacy of triage scales was lower in the pain groups than in the pain-free group (area under the receiver operating curve, [AUROC]: 0.615 vs. 0.637). However, with the physician-based method, triage scales were more effective in predicting hospitalization among patients with pain than those without (AUROC: 0.650 vs. 0.636).

Conclusions
Self-reported pain seemed to diminish the predictive accuracy of triage for hospitalization. In contrast, physician-rated pain scores were positively associated with longer EDLOS, increased ED charges, and enhanced triage predictive capability for hospitalization. Pain, therefore, appears to modulate the relationship between triage and patient outcomes, highlighting the need for careful pain evaluation in the ED.
Work accident effect on the use of psychotropic drugs: the case of benzodiazepines
Authors: Barnay Thomas , Baudot François-Olivier 
Published: October 2023

Abstract
Background
A work accident constitutes a shock to health, likely to alter mental states and affect the use of psychotropic drugs. We focus on the use of benzodiazepines, which are a class of drugs commonly used to treat anxiety and insomnia. Prolonged use can lead to dependence. Our objective is to determine the extent to which work accidents lead to benzodiazepine use and overuse (i.e. exceedance of medical guidelines).

Method
We use a two-step selection model (the Heckman method) based on data from the French National Health Data System (Système National des Données de Santé, SNDS). Our study sample includes all general plan members who experienced a single work accident in 2016 (and not since 2007). This sample includes 350,000 individuals in the work accident group and more than 1.1 million people randomly drawn from the population without work accidents from 2007 to 2017 (the non-work accident group).

Results
The occurrence of a work accident leads to an increase in benzodiazepine use and overuse the following year. The selection model shows a clear influence of the accident on the use probability (+ 39%), but a very slight impact on the risk of overuse among users (+ 1.7%), once considered the selection effect. The effect on overuse risk is higher for more severe accidents and among women.

Conclusion
The increase in the risk of benzodiazepine overuse is due to an increase in the likelihood of using benzodiazepines after a work accident that leads to overuse, rather than an increase in likelihood of overuse among people who use benzodiazepines. Results call for targeting the first-time prescription to limit the risk of overuse after a work accident.
Efficient design of a wideband tunable microstrip filtenna for spectrum sensing in cognitive radio systems
Authors: Elabd Rania H. , Hussein Amr H. 
Published: October 2023

AbstractThis paper presents a novel design of a compact, wideband tunable microstrip filtenna system for effective spectrum sensing in cognitive radio (CR) applications. The proposed filtenna structure has a total bandwidth of $$1.63\,\text{GHz}$$

1.63

GHz

and flexible frequency scanning design throughout the frequency range from $$1.93\,\text{ to }\,3.56\,\text{ GHz}$$

1.93

to

3.56

GHz

with high selectivity and narrow bandwidths ranging from $$39.9\,\text{to}53\,\text{MHz}$$

39.9

to
53

MHz

. Frequency tuning is accomplished electrically via integrating a varactor diode into the filtenna construction. The filtenna is realized on a Rogers TMM4 substrate with $$h=1.52\,\text{mm}$$

h
=
1.52

mm

thickness and relative dielectric constant of $${\varepsilon }_{r}=4.5$$

ε
r

=
4.5

with dimensions of $$(25\times 35)\, {\text{mm}}^{2}$$

(
25
×
35
)

mm

2

. The obtained gain and efficiency of the filtenna ranged from $$0.7$$

0.7

to $$2.26\,\text{dBi}$$

2.26

dBi

and 49% to 60%, respectively, within the tuning range. Simple biasing circuitry, wideband operation, and compact planar structure are distinctive and appealing aspects of the design. For the manufactured prototypes, a significant level of agreement is found between the simulated and measured results in terms of scattering parameter $${\text{S}}_{11}$$

S
11

and radiation patterns at different operating frequencies.
Influence of adolescents’ and parental dietary knowledge on adolescents’ body mass index (BMI), overweight/obesity in 2004–2015: a longitudinal study
Authors: Cai Zhengjie , Jiang Ke , Wang Tiankun , Li Shengping , Xian Jinli , Zhao Yong , Shi Zumin 
Published: October 2023

Abstract
Objective
The global epidemic of overweight/obesity in children and adolescents poses a significant public health threat. This longitudinal study aims to investigate the relationship between adolescents’ and their parents’ dietary knowledge and overweight/obesity among adolescents in China.

Methods
Data were collected from the China Health and Nutrition Survey (CHNS) in 2004, 2006, 2009, 2011 and 2015. Overweight/obesity was defined according to the International Obesity Task Force (IOTF) cut-off for body mass index (BMI). A set of questions were used to assess the dietary knowledge scores of both adolescents and their parents during face-to-face interviews. Mixed effect models were used to analyze the data.

Results
A total of 2035 adolescents aged 12–17 years were included in the data analysis. The mean BMI increased from 19.2 in 2004 to 20.5 in 2015, with a significant increase in the prevalence of overweight and obesity from 6.8% and 0.5% in 2004 to 15.1% and 7.8% in 2015, respectively. Adolescents with medium-score dietary knowledge were less likely to be overweight/obese compared to those with low-score dietary knowledge (OR (95% CI): 0.20 (0.05–0.80), P < 0.05). However, there was no association between parental dietary knowledge and adolescents’ BMI or overweight/obesity (P > 0.05). Additionally, a significant interaction between adolescents’ dietary knowledge score and education in relation to adolescents’ BMI (P for interaction < 0.05).

Conclusion
Adolescents with medium dietary knowledge were less likely to be overweight/obese than those with low knowledge, but no association was found with parental knowledge. Promoting nutritional education and healthy eating habits is vital to prevent overweight/obesity.
Significant perioperative parameters affecting postoperative complications within 30 days following craniotomy for primary malignant brain tumors
Authors: Yang Yao-Chung , Chen Yao-Shen , Liao Wei-Chuan , Yin Chun-Hao , Lin Yung-Shang , Chen Meng-Wei , Chen Jin-Shuen 
Published: October 2023

AbstractBackgroundThe occurrence of postoperative complications within 30 days (PC1M) of a craniotomy for the removal of a primary malignant brain tumor has been associated with a poor prognosis. However, it is still unclear to early predict the occurrence of PC1M. This study aimed to identify the potential perioperative predictors of PC1M from its preoperative, intraoperative, and 24-h postoperative parameters.MethodsPatients who had undergone craniotomy for primary malignant brain tumor (World Health Organization grades III and IV) from January 2011 to December 2020 were enrolled from a databank of Kaohsiung Veterans General Hospital, Taiwan. The patients were classified into PC1M and nonPC1M groups. PC1M was defined according to the classification by Landriel et al. as any deviation from an uneventful 30-day postoperative course. In both groups, data regarding the baseline characteristics and perioperative parameters of the patients, including a new marker-kinetic estimated glomerular filtration rate, were collected. Logistic regression was used to analyze the predictability of the perioperative parameters.ResultsThe PC1M group included 41 of 95 patients. An American Society of Anesthesiologists score of > 2 (aOR, 3.17; 95% confidence interval [CI], 1.19–8.45;p = 0.021), longer anesthesia duration (aOR, 1.16; 95%CI, 0.69–0.88;p < 0.001), 24-h postoperative change in hematocrit by >  − 4.8% (aOR, 3.45; 95%CI, 1.22–9.73;p = 0.0019), and 24-h postoperative change in kinetic estimated glomerular filtration rate of < 0 mL/min (aOR, 3.99; 95%CI, 1.52–10.53;p = 0.005) were identified as independent risk factors for PC1M via stepwise logistic regression analysis. When stratified according to the age of ≥ 65 years (OR, 11.55; 95%CI, 1.30–102.79;p = 0.028), the reduction of kinetic estimated glomerular filtration rate was more robustly associated with a higher risk of PC1M.ConclusionsFour parameters were demonstrated to significantly influence the risk of PC1M in patients undergoing primary malignant brain tumor removal. Measuring and verifying these markers, especially kinetic estimated glomerular filtration rate, would help early recognition of PC1M risk in clinical care.
Transcriptome driven discovery of novel candidate genes for human neurological disorders in the telomer-to-telomer genome assembly era
Authors: Falker-Gieske Clemens 
Published: October 2023

Abstract
Background
With the first complete draft of a human genome, the Telomere-to-Telomere Consortium unlocked previously concealed genomic regions for genetic analyses. These regions harbour nearly 2000 potential novel genes with unknown function. In order to uncover candidate genes associated with human neurological pathologies, a comparative transcriptome study using the T2T-CHM13 and the GRCh38 genome assemblies was conducted on previously published datasets for eight distinct human neurological disorders.

Results
The analysis of differential expression in RNA sequencing data led to the identification of 336 novel candidate genes linked to human neurological disorders. Additionally, it was revealed that, on average, 3.6% of the differentially expressed genes detected with the GRCh38 assembly may represent potential false positives. Among the noteworthy findings, two novel genes were discovered, one encoding a pore-structured protein and the other a highly ordered β-strand-rich protein. These genes exhibited upregulation in multiple epilepsy datasets and hold promise as candidate genes potentially modulating the progression of the disease. Furthermore, an analysis of RNA derived from white matter lesions in multiple sclerosis patients indicated significant upregulation of 26 rRNA encoding genes. Additionally, putative pathology related genes were identified for Alzheimer’s disease, amyotrophic lateral sclerosis, glioblastoma, glioma, and conditions resulting from the m.3242 A > G mtDNA mutation.

Conclusion
The results presented here underline the potential of the T2T-CHM13 assembly in facilitating the discovery of candidate genes from transcriptome data in the context of human disorders. Moreover, the results demonstrate the value of remapping sequencing data to a superior genome assembly. Numerous potential pathology related genes, either as causative factors or related elements, have been unveiled, warranting further experimental validation.
Opioid-related polysubstance use and its effect on mortality and health resource utilization among trauma patients
Authors: Khadka Safalta , Bardes James M. , Al-Mamun Mohammad A. 
Published: October 2023

Abstract
Background
Pre-injury opioid use is common, but the effects of opioid-related polysubstance use on mortality and health resources utilization (HRU) have not been investigated yet. The objective of this study was to investigate the effects of opioid-related polysubstance use on mortality and HRU among patients in trauma centres in the US.

Methods
We conducted a retrospective cross-sectional study using the US National Trauma Databank from the year 2017 to 2019. Patients (≥ 18 years of age) who tested positive for opioids were included. Patients were analysed based on the number of substances used (i.e., opioids only, two substances (opioids + 1 substance), and three or more than three substances (opioids +  ≥ 2 substances)), and polysubstance by type (i.e., opioids only, opioids and alcohol, opioids and stimulants, opioids and benzodiazepine, and other combinations). Multivariate logistic regression was used to determine the association between polysubstance use, mortality and HRU (i.e., need for hospital admission, ICU, and mechanical ventilation).

Results
Both polysubstance by number and type analyses showed that opioid-related polysubstance use was not significantly associated with mortality compared to opioids only. The odds of hospital admission were higher among the opioids and benzodiazepines group (OR 1.15, 95% CI 1.06–1.24, p < 0.01). The need for ICU was magnified using benzodiazepines and stimulants with opioids (OR 1.44, 95% CI 1.27–1.63, p < 0.01) when compared to the opioids only group.

Conclusion
Opioid-related pre-injury polysubstance use was associated with higher HRU in trauma patients. The evidence can be used by policymakers and practitioners to improve patient outcomes in trauma centers.