bluuebunny/crossref_metadata_2025_split huggingface dataset:
The successes and challenges of harmonising juvenile idiopathic arthritis (JIA) datasets to create a large-scale JIA data resource
Authors: Lawson-Tovey Saskia , Smith Samantha Louise , Geifman Nophar , Shoop-Worrall Stephanie , Ng Sandra , Barnes Michael R. , Wedderburn Lucy R. , Hyrich Kimme L. ,   CLUSTER consortium, Kartawinata Melissa , Wanstall Zoe , Jebson Bethany R. , McNeece Alyssia , Ralph Elizabeth , Alexiou Vasiliki , Dekaj Fatjon , Kimonyo Aline , Merali Fatema , Sumner Emma , Robinson Emily , Feilding Freya L. , Dick Andrew , Beresford Michael W. , Carlsson Emil , Fairlie Joanna , Gritzfeld Jenna F. , Ramanan Athimalaipet , Duerr Teresa , Eyre Stephen , Raychaudhuri Soumya , Morris Andrew , Yarwood Annie , Smith Samantha , Bowes John , Martin Paul , Tordoff Melissa , Stadler Michael , Thomson Wendy , Tarasek Damian , Wallace Chris , Lin Wei-Yu , Clarke Sarah , Kent Toby , Sornasse Thierry , Dastros-Pitei Daniela , Mukherjee Sumanta , Roberts Jacqui , Kallala Rami , Neale Helen , Ioannou John , Al-Mossawi Hussein 
Published: July 2023

Abstract
Background
CLUSTER is a UK consortium focussed on precision medicine research in JIA/JIA-Uveitis. As part of this programme, a large-scale JIA data resource was created by harmonizing and pooling existing real-world studies. Here we present challenges and progress towards creation of this unique large JIA dataset.

Methods
Four real-world studies contributed data; two clinical datasets of JIA patients starting first-line methotrexate (MTX) or tumour necrosis factor inhibitors (TNFi) were created. Variables were selected based on a previously developed core dataset, and encrypted NHS numbers were used to identify children contributing similar data across multiple studies.

Results
Of 7013 records (from 5435 individuals), 2882 (1304 individuals) represented the same child across studies. The final datasets contain 2899 (MTX) and 2401 (TNFi) unique patients; 1018 are in both datasets. Missingness ranged from 10 to 60% and was not improved through harmonisation.

Conclusions
Combining data across studies has achieved dataset sizes rarely seen in JIA, invaluable to progressing research. Losing variable specificity and missingness, and their impact on future analyses requires further consideration.
HIV-1 molecular transmission network and drug resistance in Chongqing, China, among men who have sex with men (2018–2021)
Authors: Tan Tianyu , Bai Chongyang , Lu Rongrong , Chen Fangfang , Li Long , Zhou Chao , Xiang Xu , Zhang Wei , Ouyang Ling , Xu Jing , Tang Houlin , Wu Guohui 
Published: July 2023

Abstract
Background
Over the past few years, HIV transmission among men who have sex with men (MSM) in China has increased significantly. Chongqing, located in the southwest of China, has the highest prevalence of HIV among MSM in the country.

Methods
Blood samples were taken from 894 MSM in Chongqing who had recently been diagnosed with HIV-1 infection and had not yet started getting treatment. In order to determine the distribution of HIV-1 subtypes, transmitted drug resistance, and assessments of molecularly transmitted clusters, we sequenced the Pol genes and employed them in phylogenetic analysis. The genetic distance between molecular clusters was 1.5%. To find potential contributing factors, logistic regression analyses were performed.

Results
Of the 894 HIV-1 pol sequences acquired from study participants, we discovered that CRF07_BC (73.6%) and CRF01_AE (19.6%) were the two most prevalent HIV-1 genotypes in Chongqing among MSM, accounting for 93.2% of all infections. In addition, CRF08_BC (1.1%), B subtype (1.0%), CRF55_01B (3.4%), and URF/Other subtypes (1.3%) were less frequently observed. Among MSM in Chongqing, transmitted drug resistance (TDR) was reported to be present at a rate of 5.6%. 48 clusters with 600 (67.1%, 600/894) sequences were found by analysis of the molecular transmission network. The distributions of people by age, sexual orientation, syphilis, and genotype were significantly differentially related to being in clusters, according to the multivariable logistic regression model.

Conclusion
Despite the low overall prevalence of TDR, the significance of genotypic drug resistance monitoring needs to be emphasized. CRF07_BC and CRF01_AE were the two main genotypes that created intricate molecular transmission networks. In order to prevent the expansion of molecular networks and stop the virus’s spread among MSM in Chongqing, more effective HIV intervention plans should be introduced.
Gut microbes involvement in gastrointestinal cancers through redox regulation
Authors: Yangyanqiu Wang , Jian Chu , Yuqing Yang , Zhanbo Qu , Shuwen Han 
Published: July 2023

AbstractGastrointestinal (GI) cancers are among the most common and lethal cancers worldwide. GI microbes play an important role in the occurrence and development of GI cancers. The common mechanisms by which GI microbes may lead to the occurrence and development of cancer include the instability of the microbial internal environment, secretion of cancer-related metabolites, and destabilization of the GI mucosal barrier. In recent years, many studies have found that the relationship between GI microbes and the development of cancer is closely associated with the GI redox level. Redox instability associated with GI microbes may induce oxidative stress, DNA damage, cumulative gene mutation, protein dysfunction and abnormal lipid metabolism in GI cells. Redox-related metabolites of GI microbes, such as short-chain fatty acids, hydrogen sulfide and nitric oxide, which are involved in cancer, may also influence GI redox levels. This paper reviews the redox reactions of GI cells regulated by microorganisms and their metabolites, as well as redox reactions in the cancer-related GI microbes themselves. This study provides a new perspective for the prevention and treatment of GI cancers.
MRI for nodal restaging after neoadjuvant therapy in rectal cancer with histopathologic comparison
Authors: Zhang Zhiwen , Chen Yan , Wen Ziqiang , Wu Xuehan , Que Yutao , Ma Yuru , Wu Yunzhu , Liu Quanmeng , Fan Wenjie , Yu Shenping 
Published: July 2023

Abstract
Background
After neoadjuvant therapy, most of the lymph nodes (LNs) will shrink and disappear in patients with rectal cancer. However, LNs that are still detectable on MRI carry a risk of metastasis. This study aimed to evaluate the performance of the European Society of Gastrointestinal and Abdominal Radiology (ESGAR) criterion (short-axis diameter ≥ 5 mm) in diagnosing malignant LNs in patients with rectal cancer after neoadjuvant therapy, and whether nodal morphological characteristics (including shape, border, signal homogeneity, and enhancement homogeneity) could improve the diagnostic efficiency for LNs ≥ 5 mm.

Methods
This retrospective study included 90 patients with locally advanced rectal cancer who underwent surgery after neoadjuvant therapy and performed preoperative MRI. Two radiologists independently measured the short-axis diameter of LNs and evaluated the morphological characteristics of LNs ≥ 5 mm in consensus. With a per node comparison with histopathology as the reference standard, a ROC curve was performed to evaluate the diagnostic performance of the size criterion. For categorical variables, either a χ2 test or Fisher’s exact test was used.

Results
A total of 298 LNs were evaluated. The AUC for nodal size in determining nodal status was 0.81. With a size cutoff value of 5 mm, the sensitivity, specificity, positive predictive value, negative predictive value and accuracy were 65.9%, 87.0%, 46.8%, 93.6% and 83.9%, respectively. No significant differences were observed in any of the morphological characteristics between benign and malignant LNs ≥ 5 mm (all P > 0.05).

Conclusions
The ESGAR criterion demonstrated moderate diagnostic performance in identifying malignant LNs in patients with rectal cancer after neoadjuvant therapy. It was effective in determining the status of LNs < 5 mm but not for LNs ≥ 5 mm, and the diagnostic efficiency could not be improved by considering nodal morphological characteristics.
Combatting rumors around the French election: the memorability and effectiveness of fact-checking articles
Authors: Fazio Lisa K. , Hong Min Kyung , Pillai Raunak M. 
Published: July 2023

AbstractAcross four studies, we examined the how design decisions influenced the effectiveness of fact-checking articles created by CrossCheck France during the 2017 French election. We measured both memory for the article and belief in the false rumor. We saw no difference in fact check efficacy based on the type of headline (question vs negation) or the number of newsroom logos present around the article (one, four, or seven). In addition, informative design features such as an icon identifying the type of misinformation were ignored by readers. Participants failed to remember many of the details from the article, but retrieval practice was beneficial in reducing forgetting over a 1-week delay. In both US and French samples, reading the fact check decreased belief in the false information, even 1 week later. However, the articles were much more effective in the US sample, who lacked relevant prior knowledge and political beliefs. Overall, fact-checking articles can be effective at reducing belief in false information, but readers tend to forget the details and ignore peripheral information.
Reproductive outcome and gynecologic comorbidities in women with endometriosis in a non-IVF setting: a retrospective study
Authors: Al Shukri Maryam Nasser , Al Riyami Al Shimaa Abdullah , Al Ghafri Wadha Mohammed , Gowri Vaidyanathan 
Published: July 2023

Abstract
Background
Endometriosis-related infertility is a disease associated with significant morbidity and distress to the couple and requires timely, multidisciplinary, and often high-cost care involving assisted reproductive technologies (ART). Many health care systems in the Middle East do not provide coverage for ART. This study aims to describe the reproductive outcome in a form of a clinical pregnancy rate in women with endometriosis-related infertility in a health care system that does not provide coverage for ART.

Results
This is a retrospective observational cohort study on women who attended the gynecology clinic in a tertiary center in Oman with the diagnosis of endometriosis from January 2011 to December 2019. Women of reproductive age seeking pregnancy were included in the analysis. Out of total women with endometriosis, (144/262) 55.0% were included in the analysis with a mean age of 31.10 ± 5.73 years. The mean duration of follow-up was 30.18 months and 43/144 (29.9%) of our patients had a follow-up > 60 months. Based on surgical staging, 11.8% had mild disease, 70.1% had moderate to severe disease and 18.1% were not operated. After a thorough assessment, (30.2%) were advised to seek in vitro fertilization (IVF) as a primary treatment for infertility but 23.08% declined the advice. Of the 144, 24.3% achieved a clinical pregnancy. (16/144), 11% conceived spontaneously. 11/144) 7.6% conceived with ovulation induction ± intrauterine insemination (OI ± IUI) and the rest conceived with a self-sponsored IVF. The overall clinical pregnancy rate was not statistically different between those who had surgery and those did not have surgery (P value 0.474). The pregnancy rate based on the management plan were; surgery + IVF (7/25, 28.0%), surgery + OI/IUI (10/47, 21.3%), surgery alone (9/33, 27.3%). The pregnancy rate was not statistically different between the groups (P value 0.782).
In addition to endometriosis, a significant proportion (63/144, 43.8%) of these women have a coexisting gynecologic morbidity including 2.1% non-endometrioma ovarian cyst, 13.9% myomas, 4.2% adenomyosis, 8.3% Mullerian anomalies, 2.1% polycystic ovary syndrome, 6.3% pelvic inflammatory disease or tubo-ovarian abscess and 1.4% biopsy-proven endometritis.

Conclusion
The reproductive outcome of patients with endometriosis in this study population was generally poorer than what is reported in the literature with an overall pregnancy rate of 24.3% and a spontaneous pregnancy rate of 11%. Several causes can be noted for such an outcome, including advanced disease stage, coexisting gynecologic morbidities, and poor access to advance fertility management.
Medical students' perspective of the motivations and limitations of studying medicine: a cross-sectional study from the United Arab Emirates
Authors: Amiri Leena , Al Mugaddam Fadwa , Javaid Syed Fahad 
Published: July 2023

Abstract
Background
Incentives and disincentives to study medicine are complex concepts and may involve a dynamic balancing act between financial, personal, and social reasons. These processes have not been adequately explored in the Middle East. This study explores students' thoughts and feelings about studying medicine at the United Arab Emirates University, Al-Ain. This descriptive cross-sectional study was conducted between April and August 2019. An online, self-administered questionnaire consisting of 22 questions was distributed to the students enrolled at the College of Medicine and Health Sciences, United Arab Emirates University. The survey questions focused on motivations to study medicine and limitations that prevent choosing medicine as a field of study.

Results
Two hundred and five (33%) of 621 students in the six-year program completed the questionnaire. Forty-three percent of the responders were from the first two years of medical school. The decision to study medicine was reported as their own by 92%. Eighty-eight percent of the students did not consider gender a limitation for studying medicine, and 62% had a defined medical specialty to pursue. One-third considered quitting medicine, mainly during the first two years. Reported difficulties included mental health problems (stress, anxiety, and depression), social isolation ('having no life,' 'being lonely'), curriculum content (overwhelming workload), college condition/rules (poor condition of the hostels, lack of support, scant passion, and strict rules), and rational thinking (inadequate high-school preparation).

Conclusions
These results justify implementing an effective counseling program, especially during the early academic years. The quality of high-school education requires careful thoughtfulness from the department of education with input from our medical schools. Other modifiable factors include the methods of assessment, available supportive resources, and extracurricular activities.
Status quo of operation procedures for soil sampling to analyze microplastics
Authors: Dorau Kristof , Hoppe Martin , Rückamp Daniel , Köser Jan , Scheeder Georg , Scholz Katrin , Fries Elke 
Published: July 2023

AbstractSince 2015, the determination of microplastics (MPs; < 5 mm) in soil has gained increasing attention. However, usual analytical protocols still render a comparison of results challenging. This structured review integrates an in-depth screening of scientific articles (n = 106; from 1980 to 2022) that focused on determining MPs in soils. The different studies were divided into groups regarding (i) MPs input pathways, (ii) study site information, (iii) sampling design, (iv) sample preparation, and (v) analytical methods for MPs detection. Most of the studies (63%) focused on a defined study site influenced by a known point source, whereas 37% measured MPs background contents related to delocalized MPs emission sources. Even though soil was the target compartment, only 26% classified the soil type, mostly using the World Reference Base (WRB) as a classification system. Additional information on soil properties was supplied within only 20% of the studies. However, this information is mandatory for evaluation of MPs recovery tests and analytical results. In nearly all studies, the mass of the single samples equaled the final mass of the composite sample, with a mean of 1.32 kg ± 1.07 kg. However, other procedures that involve a larger sample mass seem promising but are still seldom applied. Our structured review revealed that a standard operation procedure with harmonized methods is urgently needed with a coherent and comprehensive workflow, including field sampling and sample preparation. Such a procedure would ensure the reproducibility and representativeness of analytical results, which are mandatory for evaluating and restricting MPs pollution in soils in the future.
Graphical Abstract
The relationship between CMV reactivation, anti-cytokine treatment and mortality in critical COVID-19 patients
Authors: Gozukucuk Ramazan , KILIC Hasan Huseyin 
Published: July 2023

Objective: To examine the use of anti-cytokine treatment in critical COVID-19 patients and their association with the frequency of CMV cases, viral load level, and mortality in these patients.
Methods: This is a retrospective study. A total of 170 critical and/or intensive care patients with COVID-19 admitted to Hisar Hospital Intercontinental from March 15, 2020, to December 31, 2021 were divided into the use of anti-cytokine treatment group and the no anti-cytokine treatment group. Furthermore, the relationship between CMV reactivation, mortality and anti-cytokine treatment in patients was also examined.
Results: A total of 170 critical COVID-19 patients were included in the study, three of them were excluded. One hundred sixty seven were included in the study of which 38 (22.7%) were found to be CMV DNA positive. As an anti-cytokine treatment, it was observed that tocilizumab was used in 53 patients, anakinra was used in 27 patients, and no anti-cytokine treatment was used in 77 patients. CMV positivity in patients treated with anti-cytokines (31.11%) was found to be significantly higher than in patients who were not treated with it (16.88%) (p:0.033). Furthermore, it was determined that anti-cytokine treatment significantly decreased mortality (p: 0.003) and that there was no significant relationship between CMV reactivation and mortality (p: 0.399).
Conclusion: Even though CMV reactivation was high in critical COVID-19 patients who received anti-cytokine treatment, decrease in mortality were observed with early diagnosis and effective treatment. Therefore, CMV infection should be considered in patients receiving immunosuppressive treatment.
Clinical Trial Registration: HisarIH-101/NCT05419206
doi: https://doi.org/10.12669/pjms.39.5.7301
How to cite this: Gozukucuk R, Kilic HH. The relationship between CMV reactivation, anti-cytokine treatment and mortality in critical COVID-19 patients. Pak J Med Sci. 2023;39(5):---------. doi: https://doi.org/10.12669/pjms.39.5.7301
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Comparison of complete nasal packing with and without integrated airways
Authors: Jamil Afifa , Hameed Hira Abdul , Sidiqqui Atif Hafeez , Farrukh M. Shuja 
Published: July 2023

Objective: To compare the effects of nasal packing using a Nasopore nasal packing with and without an airway tube on postoperative pain, SpO2, nasal obstruction, and difficulty in breathing complaints.
Methods: This comparative study was conducted at Dow University of Health Sciences (DUHS), DMC Civil Hospital Karachi between September 18, 2021, to May 19, 2022. A total of 70 patients who underwent septoplasty for septal deviation and chronic hypertrophic rhinitis were equally divided into two groups. Group-A patients received nasal packing using a Nasopore nasal packing with an airway tube, and Group-B patients received nasal packing using a Nasopore nasal packing without an airway tube. Post-operation Nasal pain sensations were measured using the Wong-Baker Faces Pain Rating Scale at 2 and 12 hours. SpO2 was measured at 30 minutes pre-operatively with an O2 saturation monitor and 12 hours post-operatively during sleep.
Results: The postoperative pain at two hours and 12 hours was compared between the two groups, and a significant difference was observed. In Group-A, the average SpO2 decreased > 4% from baseline in 5.7% patients, and 37% in Group-B. A significant difference was observed in the severity of nasal obstruction and difficulty breathing, P-value < 0.05.
Conclusion: It is concluded that septoplasty followed by applying nasal packing with integrated airway reduces postoperative pain and improves oxygen saturation compared to nasal packing without integrated airways.
doi: https://doi.org/10.12669/pjms.39.5.7478
How to cite this: Jamil A, Hameed HA, Sidiqqui AH, Farrukh M.S. Comparison of complete nasal packing with and without integrated airways. Pak J Med Sci. 2023;39(5):---------. doi: https://doi.org/10.12669/pjms.39.5.7478
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Electrochemotherapy vs radiotherapy in the treatment of primary cutaneous malignancies or cutaneous metastases from primary solid organ malignancies: A systematic review and narrative synthesis
Authors: McMillan Angus Torry , McElroy Luke , O’Toole Lorcan , Matteucci Paolo , Totty Joshua Philip 
Published: July 2023

Background
Electrochemotherapy has gained international traction and commendation in national guidelines as an effective tool in the management of cutaneous malignancies not amenable to surgical resection. Despite this, no level 5 evidence exists comparing it to radiotherapy in the treatment of cutaneous malignancies. This systematic review aimed to examine the literature directly and indirectly comparing electrochemotherapy and radiotherapy in the treatment of primary cutaneous malignancies or cutaneous metastases from primary solid organ malignancies.

Materials & methods
The protocol for this review was registered on the PROSPERO International Prospective Register of Systematic Reviews with the protocol ID CRD42021285415. Searches of MEDLINE, Embase, CINAHL, CENTRAL and ClinicalTrials.gov databases were undertaken from database inception to 28 December 2021. Studies in humans comparing treatment with electrochemotherapy to radiotherapy and reporting tumour response with a minimum four week follow-up were eligible. Risk of bias was assessed using the ROBINS-I tool. Results are provided as a narrative synthesis.

Results
Two case series with a total of 92 patients were identified as relevant to this study. Both case series examined patients with cutaneous squamous cell carcinoma. One case series examined elderly patients with predominantly head/neck lesions. The other examined younger patients with predominantly limb lesions who had cutaneous squamous cell carcinoma directly attributable to a rare skin condition.

Conclusion
There is little literature presenting comparative data for electrochemotherapy and radiotherapy in the treatment of primary cutaneous malignancies or cutaneous metastases. Included studies were marred by serious risk of bias particularly due to confounding. The inherent bias and heterogeneity of the included studies precluded synthesis of a consolidated comparison of clinical outcomes between the two therapies. Further research is required in this domain in the form of clinical trials and observational studies to inform guidelines for electrochemotherapy treatment.