bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interrater agreement of multi-professional case review as reference standard for specialist palliative care need: a mixed-methods study
Authors: Müller Evelyn , Müller Michael Josef , Seibel Katharina , Boehlke Christopher , Schäfer Henning , Klein Carsten , Heckel Maria , Simon Steffen T. , Becker Gerhild 
Published: November 2023

Abstract
Background
A wide variety of screening tools for the need for specialist palliative care (SPC) have been proposed for the use in oncology. However, as there is no established reference standard for SPC need to compare their results with, their sensitivity and specificity have not yet been determined. The aim of the study was to explore whether SPC need assessment by means of multi-professional case review has sufficient interrater agreement to be employed as a reference standard.

Methods
Comprehensive case descriptions were prepared for 20 inpatients with advanced oncologic disease at the University Hospital Freiburg (Germany). All cases were presented to the palliative care teams of three different hospitals in independent, multi-professional case review sessions. The teams assessed whether patients had support needs in nine categories and subsequently concluded SPC need (yes / no). Interrater agreement regarding SPC need was determined by calculating Fleiss’ Kappa.

Results
In 17 out of 20 cases the three teams agreed regarding their appraisal of SPC need (substantial interrater agreement: Fleiss’ Kappa κ = 0.80 (95% CI: 0.55–1.0; p < 0.001)). The number of support needs was significantly lower for patients who all teams agreed had no SPC need than for those with agreed SPC need.

Conclusions
The proposed expert case review process shows sufficient reliability to be used as a reference standard. Key elements of the case review process (e.g. clear definition of SPC need, standardized review of the patients’ support needs) and possible modifications to simplify the process are discussed.

Trial registration
German Clinical Trials Register, DRKS00021686, registered 17.12.2020.
The impact of SARS-COV-2 infection on menstruation
Authors: Zhong Xiaozhu , Lu Keji , Liang Weiying , Jihu Luozi , Zeng Anqi , Ding Miao , Chen Dongmei , Xie Meiqing 
Published: November 2023

Abstract
Background
Recent study has demonstrated that the GnRH system in patients with post-COVID syndrome may be influenced by SARS-CoV-2. However, the impact of COVID-19 infection on women’s menstruation is still unknown.

Objective
We aimed to investigate the the relationship between coronavirus disease 2019 (COVID-19) and menstruation in premenopausal women.

Methods
This was a retrospective cohort study. Pre-menopausal women were invited to participate in the online questionnaire on wechat. Participants were divided into four groups according to whether they were infected with severe acute respiratory syndrome coronavirus-2 (SARS-COV-2) and whether they had menstrual changes during the pandemic. Sociodemographic characteristics, history of COVID-19, menstruation and menstrual changes of the participants were collected. Statistical analyses were performed using SPSS, version 25.0 (SPSS Inc., Chicago, IL, USA).

Results
A total of 1946 women were included in the study. 1800 participants had been or were currently infected with SARS-COV-2, and 146 people had not been infected. Among 1800 patients with COVID-19, 666 (37.0%) had changes in menstruation, and 1134 (63.0%) did not, which was significantly higher than the uninfected participants (c2 = 12.161, P = 0.000). The proportion of participants with menstrual cycle changes (450/67.6%) is larger than that of uninfected participants (c2 = 6.904, P = 0.009). COVID-19 vaccination was associated with lower odds of menstrual cycle change (OR, 0.855; 95% CI, 0.750–0.976). Participants who reported chest pain (OR, 1.750, 95% CI, 1.209–2.533) and dyspnea (OR, 1.446; 95% CI, 1.052–1.988) during infection had greater odds of changes to their menstrual cycle compared with the participants who did not.

Conclusions
The association between the COVID-19 and increased prevalence of menstrual cycle irregularity. COVID-19 vaccination is a protective factor in the long term, and participants with chest pain and dyspnea are more likely to develop AUB.
Female infertility and dietary antioxidant index (DAI); a case-control study
Authors: Kabodmehri Roya , Javaheri Fatemeh Sadat Hashemi , Alami Farkhondeh , Mahmoudi Zahra , Amjadi Arezoo , Saeedirad Zahra , Omidi Saeed , Sadeghi Shiva , Hoseini Mohadeseh Sadat Mousavi , Mohamadiyan Zahra , Salimi Zahra , Shafaei Hanieh , Rasekhmagham Reyhaneh , Sharami Seyedeh Hajar , Karimian Maryam , Karimi Hoora , Doaei Saeid 
Published: November 2023

Abstract
Background
Adequate intake of natural antioxidants may improve female fertility. The aim of this study was to examine the link between female infertility and dietary antioxidant index (DAI).

Methods
This case-control study was conducted on 125 women with recently diagnosis of reduced ovarian reserves (AMH < 1.1) as the case group and 125 women with normal ovarian reserve as the control group in Rasht, Iran. The amount of food intake was assessed using the food frequency questionnaire (FFQ) and the DAI was calculated to estimate the antioxidant capacity of the diet.

Results
Regarding dietary intake, the infertile women had a lower intake of potassium (2789.25 ± 777 vs. 2593.68 ± 443 mg/d, P = 0.02), magnesium (204.12 ± 66 vs. 189.73 ± 34 mg/d, P = 0.03), copper (0.93 ± 0.40 vs. 0.82 ± 0.20 mg/d, P < 0.01), vitamin C (133.99 ± 46 vs. 122.62 ± 24 mg/d, P = 0.02), and fiber (14.53 ± 3 vs. 13.44 ± 2 g/d, P < 0.05), and a higher intake of cholesterol (205.61 ± 58 vs. 227.02 ± 46 mg/d, P < 0.01) than the control group (All P < 0.05). The DAI was negatively associated with infertility (OR: 0.94, CI 95%: 0.88–0.97, P = 0.03). The association remained significant after adjustments for age, BMI, the underlying diseases, fertility frequency, IVF failure, and calorie intake.

Conclusion
Following an antioxidant-rich diet may reduce the risk of infertility. More longitudinal studies are warranted to confirm these results and discover the underlying mechanisms.
Ethics education among obstetrics and gynecologists in Saudi Arabia: a cross-sectional study
Authors: Althagafi Noha Abed , Alahmad Ghiath 
Published: November 2023

AbstractThere are a lot of efforts to promote ethics education and training at an undergraduate and postgraduate level around the world, including in Saudi Arabia. However, there is still a lack of structured ethics education curricula in obstetrics and gynecology residency programs in Saudi Arabia. In the current scenario, where new ethical dilemmas are emerging, an ethics education that only focuses on teaching the ethical principles does not enhance the competence to deal with the ethical challenges in daily practice. This study evaluates the lack of ethics education and training in obstetrics and gynecology residency programs in Saudi Arabia. A cross-sectional survey of working obstetricians and gynecologists in Saudi Arabia was conducted among all working levels of doctors (the residents, registrars, consultants, and program directors) from various hospitals of Saudi Arabia. 391 practitioners responded to the survey, representing a response rate of 39.1%, including 257 (66.4%) females and 130 (33.6%) males. 74 (23.0%) received formal education (medical school = 35%; residency programs = 11.8%; sub-specialty programs = 4.3%; postgraduate programs = 7.4%), 85 (26.4%) received informal education (online training = 12.8%; conferences = 18.9%; courses and workshops = 13.3%; self-learning = 31.7% and daily practices = 20.7%), and 78 (19.95%) received no ethics education. Almost all the respondents had a positive attitude towards ethical principles, but a least percent were competent to deal with the ethical challenges. The bottom line of this survey is the imperativeness of reinforcement of formal ethics education in obstetrics and gynecology postgraduate programs in Saudi Arabia.
Grading reflective essays: the construct validity and reliability of a newly developed Tool- GRE-9
Authors: Makarem Nisrine N. , Rahme Diana V. , Brome Dayana , Saab Bassem R 
Published: November 2023

Abstract
Background
The main objective of this study is to assess the construct validity and reliability of the Grading Reflective Essays-9 (GRE-9).

Methods
This study took place in a major tertiary academic medical center in Beirut, Lebanon. 104 reflective essays written by years 1–3 residents in the department of Family Medicine at the American University of Beirut Medical Center (AUBMC) were graded by 2 trained raters who independently scored the essays using GRE-9. GRE-9 scores were then correlated with scores on communication skills OSCE stations and in-training examinations to investigate, respectively, convergent and divergent validity. One of the 2 raters scored the essays twice one month apart to assess the reliability of the GRE-9 using intra rater reliability and internal consistency.

Results
There was a weak, non-significant correlation between GRE-9 score and In training examination (ITE) score (r = − .213, p = .395). There was a moderate, non-significant correlation between GRE-9 scores and the Objective structured clinical examination (OSCE) communication station scores (r = − .412 p = .162). The correlation coefficient between trails 1 and 2 was significant (r = .832, p = .000). Intra class correlation coefficient (ICC) analysis demonstrated almost perfect intra-rater agreement (0.819; 95% CI: 0.741–0.875) of the test ratings over time.

Conclusions
GRE-9, is a short, concise, easy-to-use reliable grading tool for reflective essays that has demonstrated moderate to substantial intra-rater reliability and evidence of divergent validity. The study found non-significant correlations between reflective writing scores OSCE communication scores demonstrating a lack of relationship between reflective writing and this measure of performance.
ClotCatcher: a novel natural language model to accurately adjudicate venous thromboembolism from radiology reports
Authors: Wang Jeffrey , de Vale Joao Souza , Gupta Saransh , Upadhyaya Pulakesh , Lisboa Felipe A. , Schobel Seth A. , Elster Eric A. , Dente Christopher J. , Buchman Timothy G. , Kamaleswaran Rishikesan 
Published: November 2023

Abstract
Introduction
Accurate identification of venous thromboembolism (VTE) is critical to develop replicable epidemiological studies and rigorous predictions models. Traditionally, VTE studies have relied on international classification of diseases (ICD) codes which are inaccurate – leading to misclassification bias. Here, we developed ClotCatcher, a novel deep learning model that uses natural language processing to detect VTE from radiology reports.

Methods
Radiology reports to detect VTE were obtained from patients admitted to Emory University Hospital (EUH) and Grady Memorial Hospital (GMH). Data augmentation was performed using the Google PEGASUS paraphraser. This data was then used to fine-tune ClotCatcher, a novel deep learning model. ClotCatcher was validated on both the EUH dataset alone and GMH dataset alone.

Results
The dataset contained 1358 studies from EUH and 915 studies from GMH (n = 2273). The dataset contained 1506 ultrasound studies with 528 (35.1%) studies positive for VTE, and 767 CT studies with 91 (11.9%) positive for VTE. When validated on the EUH dataset, ClotCatcher performed best (AUC = 0.980) when trained on both EUH and GMH dataset without paraphrasing. When validated on the GMH dataset, ClotCatcher performed best (AUC = 0.995) when trained on both EUH and GMH dataset with paraphrasing.

Conclusion
ClotCatcher, a novel deep learning model with data augmentation rapidly and accurately adjudicated the presence of VTE from radiology reports. Applying ClotCatcher to large databases would allow for rapid and accurate adjudication of incident VTE. This would reduce misclassification bias and form the foundation for future studies to estimate individual risk for patient to develop incident VTE.
Identification of compound heterozygous deletion of the WWOX gene in WOREE syndrome
Authors: Dong Xing-sheng , Wen Xiao-jun , Zhang Sheng , Wang De-gang , Xiong Yi , Li Zhi-ming 
Published: November 2023

Abstract
Background
Biallelic loss-of-function variants in WWOX cause WWOX-related epileptic encephalopathy (WOREE syndrome), which has been reported in 60 affected individuals to date. In this study, we report on an affected individual with WOREE syndrome who presented with early-onset refractory seizures and global neurodevelopmental delay and died at the age of two and a half years.

Methods
We present clinical and molecular findings in the affected individual, including biallelic pathogenic variants in the WWOX gene. We employed different molecular approaches, such as whole exome sequencing, quantitative real-time polymerase chain reaction (qPCR), and whole-genome sequencing, to identify the genetic variants. The breakpoints were determined through gap PCR and Sanger sequencing.

Result
Whole exome sequencing revealed homozygous exon 6 deletion in the WWOX gene in the proband. Quantitative real-time PCR confirmed that the parents were heterozygous carriers of exon 6 deletion. However, using whole-genome sequencing, we identified three larger deletions (maternal allele with exon 6–8 deletion and paternal allele with two deletions in proximity one in intron 5 and the other in exon 6) involving the WWOX gene in the proband, with deletion sizes of 13,261 bp, 53,904 bp, and 177,200 bp. The exact breakpoints were confirmed through gap PCR and Sanger sequencing. We found that the proband inherited the discontinuous deletion of intron 5 and exon 6 from the father, and the exons 6–8 deletion from the mother using gap PCR.

Conclusion
Our findings extend the variant spectrum of WOREE syndrome and support the critical role of the WWOX gene in neural development.
Clinical nomogram assisting in discrimination of juvenile dermatomyositis-associated interstitial lung disease
Authors: Hu Minfei , Shen Chencong , Zheng Fei , Zhou Yun , Teng Liping , Zheng Rongjun , Hu Bin , Wang Chaoying , Lu Meiping , Xu Xuefeng 
Published: November 2023

Abstract
Objective
To establish a prediction model using non-invasive clinical features for early discrimination of DM-ILD in clinical practice.

Method
Clinical data of pediatric patients with JDM were retrospectively analyzed using machine learning techniques. The early discrimination model for JDM-ILD was established within a patient cohort diagnosed with JDM at a children’s hospital between June 2015 and October 2022.

Results
A total of 93 children were included in the study, with the cohort divided into a discovery cohort (n = 58) and a validation cohort (n = 35). Univariate and multivariate analyses identified factors associated with JDM-ILD, including higher ESR (OR, 3.58; 95% CI 1.21–11.19, P = 0.023), higher IL-10 levels (OR, 1.19; 95% CI, 1.02–1.41, P = 0.038), positivity for MDA-5 antibodies (OR, 5.47; 95% CI, 1.11–33.43, P = 0.045). A nomogram was developed for risk prediction, demonstrating favorable discrimination in both the discovery cohort (AUC, 0.736; 95% CI, 0.582–0.868) and the validation cohort (AUC, 0.792; 95% CI, 0.585–0.930). Higher nomogram scores were significantly associated with an elevated risk of disease progression in both the discovery cohort (P = 0.045) and the validation cohort (P = 0.017).

Conclusion
The nomogram based on the ESIM predictive model provides valuable guidance for the clinical evaluation and long-term prognosis prediction of JDM-ILD.
Primary cardiac myxofibrosarcoma of the left atrium and pericardium: a case report
Authors: Azuma Ryota , Sato Kazuyoshi , Sunadoi Hiroki , Ishii Yasushi , Tomaru Utano , Motohashi Masatoshi 
Published: November 2023

Abstract
Background
Primary cardiac myxofibrosarcoma is rare and commonly occurs in the left atrium. Myxofibrosarcoma is aggressive and has a high mortality rate due to its high rate of recurrence. Complete surgical resection is considered important; however, effective treatment options have not been established.

Case presentation
We report the case of a 75-year-old woman who developed a myxofibrosarcoma spreading to the left atrium and pericardium. We performed surgical resection of the tumor to prevent sudden death due to mitral valve obstruction or cerebral infarction due to embolism of the scattered mass. However, we were unable to complete the resection of the tumors. The patient developed brain metastasis 2 months after surgery and eventually died due to brain hemorrhage 3 months after surgery.

Conclusions
In this report, we described a rare case of primary cardiac myxofibrosarcoma located not only in the left atrium but also in the pericardium. Considering preoperative laboratory findings, surgical and adjuvant therapy, and the patient’s wishes are important for the best therapeutic course for an individual.
Biochemical and molecular characterization of a novel glycerol dehydratase from Klebsiella pneumoniae 2e with high tolerance against crude glycerol impurities
Authors: Lin Zifeng , Xiao Yuting , Zhang Lu , Li Le , Dong Congying , Ma Jiangshan , Liu Gao-Qiang 
Published: November 2023

Abstract
Background
The direct bioconversion of crude glycerol, a byproduct of biodiesel production, into 1,3-propanediol by microbial fermentation constitutes a remarkably promising value-added applications. However, the low activity of glycerol dehydratase, which is the key and rate-limiting enzyme in the 1,3-propanediol synthetic pathway, caused by crude glycerol impurities is one of the main factors affecting the 1,3-propanediol yield. Hence, the exploration of glycerol dehydratase resources suitable for crude glycerol bioconversion is required for the development of 1,3-propanediol-producing engineered strains.

Results
In this study, the novel glycerol dehydratase 2eGDHt, which has a tolerance against crude glycerol impurities from Klebsiella pneumoniae 2e, was characterized. The 2eGDHt exhibited the highest activity toward glycerol, with Km and Vm values of 3.42 mM and 58.15 nkat mg−1, respectively. The optimum pH and temperature for 2eGDHt were 7.0 and 37 °C, respectively. 2eGDHt displayed broader pH stability than other reported glycerol dehydratases. Its enzymatic activity was increased by Fe2+ and Tween-20, with 294% and 290% relative activities, respectively. The presence of various concentrations of the crude glycerol impurities, including NaCl, methanol, oleic acid, and linoleic acid, showed limited impact on the 2eGDHt activity. In addition, the enzyme activity was almost unaffected by the presence of an impurity mixture that mimicked the crude glycerol environment. Structural analyses revealed that 2eGDHt possesses more coil structures than reported glycerol dehydratases. Moreover, molecular dynamics simulations and site-directed mutagenesis analyses implied that the existence of unique Val744 from one of the increased coil regions played a key role in the tolerance characteristic by increasing the protein flexibility.

Conclusions
This study provides insight into the mechanism for enzymatic action and the tolerance against crude glycerol impurities, of a novel glycerol dehydratase 2eGDHt, which is a promising glycerol dehydratase candidate for biotechnological conversion of crude glycerol into 1,3-PDO.
Key genes of electron transfer, the nitrogen cycle and tetracycline removal in bioelectrochemical systems
Authors: Zhao Xiaodong , Qin Xiaorui , Jing Xiuqing , Wang Teng , Qiao Qingqing , Li Xiaojing , Yan Pingmei , Li Yongtao 
Published: November 2023

Abstract
Background
Soil microbial fuel cells (MFCs) can remove antibiotics and antibiotic resistance genes (ARGs) simultaneously, but their removal mechanism is unclear. In this study, metagenomic analysis was employed to reveal the functional genes involved in degradation, electron transfer and the nitrogen cycle in the soil MFC.

Results
The results showed that the soil MFC effectively removed tetracycline in the overlapping area of the cathode and anode, which was 64% higher than that of the control. The ARGs abundance increased by 14% after tetracycline was added (54% of the amplified ARGs belonged to efflux pump genes), while the abundance decreased by 17% in the soil MFC. Five potential degraders of tetracycline were identified, especially the species Phenylobacterium zucineum, which could secrete the 4-hydroxyacetophenone monooxygenase encoded by EC 1.14.13.84 to catalyse deacylation or decarboxylation. Bacillus, Geobacter, Anaerolinea, Gemmatirosa kalamazoonesis and Steroidobacter denitrificans since ubiquinone reductase (encoded by EC 1.6.5.3), succinate dehydrogenase (EC 1.3.5.1), Coenzyme Q-cytochrome c reductase (EC 1.10.2.2), cytochrome-c oxidase (EC 1.9.3.1) and electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) served as complexes I, II, III, IV and ubiquinone, respectively, to accelerate electron transfer. Additionally, nitrogen metabolism-related gene abundance increased by 16% to support the microbial efficacy in the soil MFC, and especially EC 1.7.5.1, and coding the mutual conversion between nitrite and nitrate was obviously improved.

Conclusions
The soil MFC promoted functional bacterial growth, increased functional gene abundance (including nitrogen cycling, electron transfer, and biodegradation), and facilitated antibiotic and ARG removal. Therefore, soil MFCs have expansive prospects in the remediation of antibiotic-contaminated soil. This study provides insight into the biodegradation mechanism at the gene level in soil bioelectrochemical remediation.
Dual-game based UAV swarm obstacle avoidance algorithm in multi-narrow type obstacle scenarios
Authors: Lin Ye , Na Zhenyu , Feng Zilong , Lin Bin , Lin Yun 
Published: November 2023

AbstractDue to the advantages of rapid deployment, flexible response and strong invulnerability, unmanned aerial vehicle (UAV) swarm has been widely applied in collaborative warfare and emergency communication. However, UAV swarm in complex environments is prone to chaotic collapse due to obstructions. A UAV swarm obstacle avoidance system model for multi-narrow type obstacles is established. Due to the fact that only one UAV is allowed to pass through each small hole at any given moment, addressing the issue of congestion caused by swarming effects becomes crucial in addition to managing the competitive allocation of multiple UAVs to multiple holes. Aiming at this problem, a dual-game real-time obstacle avoidance scheme is proposed for UAV swarm with multi-narrow type obstacle scenarios, which divides the flight process of the UAV swarm into two stages: maintaining the flight state of the UAV swarm unchanged when no obstacles are encountered, and implementing matching separation and motion state switching by means of dual-game strategy when facing multi-narrow type obstacles, ultimately achieving orderly passage after multiple rounds of games. For the proposed scheme, a dual-game based Flocking (DGF) obstacle avoidance algorithm is proposed. Specifically, the motion state of each UAV obtained from the game is parameterized and integrated with the Flocking algorithm to calculate the motion control input for each UAV. The solution is iteratively obtained until the UAV swarm completes the obstacle avoidance. Simulation results demonstrate that the proposed DGF algorithm not only enables smooth obstacle avoidance for the UAV swarm in multi-narrow type obstacle scenarios, but also effectively resolves the internal chaos problem in the UAV swarm, thereby preventing rigid collisions.