bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovering patterns in outpatient neurology appointments using state sequence analysis
Authors: Biggin Fran , Ashcroft Quinta , Howcroft Timothy , Knight Jo , Emsley Hedley 
Published: November 2023

Abstract
Background
Outpatient services in the UK, and in particular outpatient neurology services, are under considerable pressure with an ever-increasing gap between capacity and demand. To improve services, we first need to understand the current situation. This study aims to explore the patterns of appointment type seen in outpatient neurology, in order to identify potential opportunities for change.

Methods
We use State Sequence Analysis (SSA) on routinely collected data from a single neurology outpatient clinic. SSA is an exploratory methodology which allows patterns within sequences of appointments to be discovered. We analyse sequences of appointments for the 18 months following a new appointment. Using SSA we create groups of similar appointment sequence patterns, and then analyse these clusters to determine if there are particular sequences common to different diagnostic categories.

Results
Of 1315 patients 887 patients had only one appointment. Among the 428 patients who had more than one appointment a 6 monthly cycle of appointments was apparent. SSA revealed that there were 11 distinct clusters of appointment sequence patterns. Further analysis showed that there are 3 diagnosis categories which have significant influence over which cluster a patient falls into: seizure/epilepsy, movement disorders, and headache.

Conclusions
Neurology outpatient appointment sequences show great diversity, but there are some patterns which are common to specific diagnostic categories. Information about these common patterns could be used to inform the structure of future outpatient appointments.
Axonal polyneuropathy and ataxia in children: consider Perrault Syndrome, a case report
Authors: Munson Hannah E. , De Simone Lenika , Schwaede Abigail , Bhatia Avanti , Mithal Divakar S. , Young Nancy , Kuntz Nancy , Rao Vamshi K. 
Published: November 2023

Abstract
Background
Perrault Syndrome (PRLTS) is a rare, autosomal recessive disorder that presents with bilateral sensorineural hearing loss in all patients and gonadal dysfunction in females. It has been linked to variants in CLPP, ERAL1, HARS2, HSD17B4, LARS2, and TWNK genes. All reported cases due to TWNK variants have included neurologic features, such as ataxia and axonal sensorimotor neuropathy.

Case presentation
A 4.5-year-old female presented to neuromuscular clinic due to ataxia. Neurological examination revealed truncal ataxia and steppage gait, reduced deep tendon reflexes, and axonal sensorimotor polyneuropathy. Auditory brainstem response testing revealed an uncommon type of sensorineural hearing loss known as auditory neuropathy/auditory synaptopathy (AN/AS) affecting both ears. Magnetic Resonance Imaging (MRI) revealed subtle cauda equina enhancement. Nerve conduction studies led to a provisional diagnosis of chronic inflammatory demyelinating polyneuropathy (CIDP), and intravenous immune globulin (IVIG) was initiated. The patient was unresponsive to treatment, thus whole exome testing (WES) was conducted in tandem with IVIG weaning. WES revealed a compound heterozygous state with two variants in the TWNK gene and a diagnosis of Perrault Syndrome was made.

Conclusions
Perrault Syndrome should be considered in the differential for children who present with bilateral sensorineural hearing loss, axonal polyneuropathy, and ataxia. Further examination includes testing for ovarian dysgenesis and known PRLTS genetic variants.
RB1 screening of retinoblastoma patients in Sri Lanka using targeted next generation sequencing (NGS) and gene ratio analysis copy enumeration PCR (GRACE-PCR)
Authors: Kugalingam Nirosha , De Silva Deepthi , Abeysekera Hiranya , Nanayakkara Sriyani , Tirimanne Shamala , Ranaweera Dinali , Suravajhala Prashanth , Chandrasekharan Vishvanath 
Published: November 2023

Abstract
Background
Retinoblastoma (RB) a tumour affecting those under 5 years, has a prevalence of 1 in 20,000, with around twenty new diagnoses per year in Sri Lanka. Unilateral and bilateral RB presents around 24 and 15 months respectively. Approximately 10% are familial. Systematic genetic testing for germline pathogenic variants of RB1, the only gene associated with an inherited risk of RB, is unavailable in Sri Lanka. Genetic testing optimizes management of affected children and at-risk siblings. This study aimed to develop accessible genetic testing to identify children with a germline pathogenic variant of RB1 in Sri Lanka.

Methods
Targeted next generation sequencing (NGS) for detecting pathogenic sequence variants and Gene Ratio Analysis Copy Enumeration PCR (GRACE-PCR) for detecting RB1 copy number variations (CNVs) were performed for 49 consecutive RB patients treated between 2016 and 2020 at the designated RB care unit, Lady Ridgway hospital, Colombo. Patients (bilateral RB (n = 18; 37%), unilateral n = 31) were recruited following ethical clearance and informed consent.

Results
There were 26 (53%) females. Mean age at diagnosis was 18 months. Thirty-five patients (71%) had undergone enucleation. Germline pathogenic variants of RB1 identified in 22/49 (45%) patients including 18 (37%; 12 bilateral and 6 unilateral) detected by targeted NGS (2 missense, 7 stop gained, 1 splice donor, 8 frameshift variants). Six were previously undescribed, likely pathogenic frameshift variants. Four bilateral RB patients had GRACE-PCR detected CNVs including one whole RB1, two intragenic deletions (exon 12/13; exon 11 and 23) and a partial duplication of exon 27. The only familial case (affected mother and child) shared the duplication. Only 2 of 4 CNVs and 10 of 18 pathogenic variants were confirmed by whole exome sequencing and Sanger sequencing respectively, due to funding limitations.

Conclusions
The study identified pathogenic or likely pathogenic germline RB1 sequence variants and copy number variants in 16/18 (89%) bilateral and 6/31(19%) unilateral cases, which is comparable to worldwide data (10–15% unilateral, 80–85% bilateral). Targeted NGS combined with GRACE-PCR significantly reduce the cost of RB1 testing in Sri Lanka, and may widen access for genetic diagnosis of RB patients in other low and middle income countries.
Targeting FLT3-TAZ signaling to suppress drug resistance in blast phase chronic myeloid leukemia
Authors: Shin Ji Eun , Kim Soo-Hyun , Kong Mingyu , Kim Hwa-Ryeon , Yoon Sungmin , Kee Kyung-Mi , Kim Jung Ah , Kim Dong Hyeon , Park So Yeon , Park Jae Hyung , Kim Hongtae , No Kyoung Tai , Lee Han-Woong , Gee Heon Yung , Hong Seunghee , Guan Kun-Liang , Roe Jae-Seok , Lee Hyunbeom , Kim Dong-Wook , Park Hyun Woo 
Published: November 2023

Abstract
Background
Although the development of BCR::ABL1 tyrosine kinase inhibitors (TKIs) rendered chronic myeloid leukemia (CML) a manageable condition, acquisition of drug resistance during blast phase (BP) progression remains a critical challenge. Here, we reposition FLT3, one of the most frequently mutated drivers of acute myeloid leukemia (AML), as a prognostic marker and therapeutic target of BP-CML.

Methods
We generated FLT3 expressing BCR::ABL1 TKI-resistant CML cells and enrolled phase-specific CML patient cohort to obtain unpaired and paired serial specimens and verify the role of FLT3 signaling in BP-CML patients. We performed multi-omics approaches in animal and patient studies to demonstrate the clinical feasibility of FLT3 as a viable target of BP-CML by establishing the (1) molecular mechanisms of FLT3-driven drug resistance, (2) diagnostic methods of FLT3 protein expression and localization, (3) association between FLT3 signaling and CML prognosis, and (4) therapeutic strategies to tackle FLT3+ CML patients.

Results
We reposition the significance of FLT3 in the acquisition of drug resistance in BP-CML, thereby, newly classify a FLT3+ BP-CML subgroup. Mechanistically, FLT3 expression in CML cells activated the FLT3-JAK-STAT3-TAZ-TEAD-CD36 signaling pathway, which conferred resistance to a wide range of BCR::ABL1 TKIs that was independent of recurrent BCR::ABL1 mutations. Notably, FLT3+ BP-CML patients had significantly less favorable prognosis than FLT3− patients. Remarkably, we demonstrate that repurposing FLT3 inhibitors combined with BCR::ABL1 targeted therapies or the single treatment with ponatinib alone can overcome drug resistance and promote BP-CML cell death in patient-derived FLT3+ BCR::ABL1 cells and mouse xenograft models.

Conclusion
Here, we reposition FLT3 as a critical determinant of CML progression via FLT3-JAK-STAT3-TAZ-TEAD-CD36 signaling pathway that promotes TKI resistance and predicts worse prognosis in BP-CML patients. Our findings open novel therapeutic opportunities that exploit the undescribed link between distinct types of malignancies.

Graphical Abstract
The association between triglyceride-glucose index and cognitive function in nondiabetic elderly: NHANES 2011–2014
Authors: Wei Baojian , Dong Qianni , Ma Jinlong , Zhang Aihua 
Published: November 2023

Abstract
Background
The relationship between Insulin resistance (IR) evaluated through homeostasis model assessment insulin resistance (HOMA-IR) and cognitive function is controversial among nondiabetic individuals. No study so far has reported the association between the IR evaluated through triglyceride glucose (TyG) index and cognitive function among nondiabetics. This study aims to assess this association among US nondiabetic older elderly.

Methods
Data were obtained from the 2011–2014 National Health and Nutrition Examination Survey (NHANES). Low cognitive function was evaluated using the Consortium to Establish a Registry for Alzheimer’s Disease Battery for immediate word list learning (CERAD-WL) and delayed recall (CERAD-DR) test, the Animal Fluency Test (AFT), and the Digit Symbol Substitution Test (DSST). Logistic regression analyses were conducted to compute the odds ratio (OR) and 95% confidential interval (CI) to examine the association between the TyG index (continuous and quartiles) and low cognitive function.

Results
A total of 661 nondiabetic older adults were included with a mean age of 68.62 ± 6.49 years. Compared to the 1st quartile of the TyG index, participants in the TyG index 4th quartile were associated with low cognitive function evaluated through the CERAD test (CERAD-WL and CERAD-DR) [OR: 2.62; 95% CI (1.31, 5.23); P < 0.05]. Subgroup analyses showed that females (ORQ4 VS Q1: 3.07; 95% CI (1.04, 9.05); P < 0.05) and smokers (OR Q4 VS Q1: 2.70; 95% CI (1.01, 7.26); P < 0.05) categories were related with a higher risk of low cognitive function.

Conclusions
A high TyG index was strongly correlated with low cognitive function evaluated through the CERAD test (CERAD-WL and CERAD-DR) among US nondiabetic older women. The management of IR in women might be beneficial to primarily prevent low cognitive function among nondiabetic older elderly.
Precision medicine in nasopharyngeal carcinoma: comprehensive review of past, present, and future prospect
Authors: Siak Pui Yan , Heng Win Sen , Teoh Sharon Siew Hoon , Lwin Yu Yu , Cheah Shiau-Chuen 
Published: November 2023

AbstractNasopharyngeal carcinoma (NPC) is an aggressive malignancy with high propensity for lymphatic spread and distant metastasis. It is prominent as an endemic malignancy in Southern China and Southeast Asia regions. Studies on NPC pathogenesis mechanism in the past decades such as through Epstein Barr Virus (EBV) infection and oncogenic molecular aberrations have explored several potential targets for therapy and diagnosis. The EBV infection introduces oncoviral proteins that consequently hyperactivate many promitotic pathways and block cell-death inducers. EBV infection is so prevalent in NPC patients such that EBV serological tests were used to diagnose and screen NPC patients. On the other hand, as the downstream effectors of oncogenic mechanisms, the promitotic pathways can potentially be exploited therapeutically. With the apparent heterogeneity and distinct molecular aberrations of NPC tumor, the focus has turned into a more personalized treatment in NPC. Herein in this comprehensive review, we depict the current status of screening, diagnosis, treatment, and prevention in NPC. Subsequently, based on the limitations on those aspects, we look at their potential improvements in moving towards the path of precision medicine. The importance of recent advances on the key molecular aberration involved in pathogenesis of NPC for precision medicine progression has also been reported in the present review. Besides, the challenge and future outlook of NPC management will also be highlighted.
Reporting of determinants of health inequities and participant characteristics in randomized controlled trials of juvenile idiopathic arthritis in Canada: a scoping review
Authors: Gheshlaghi Niloofar , Thomas Megan , Trehan Natasha , Harrison Mark , De Vera Mary A. 
Published: November 2023

Abstract
Background
Juvenile Idiopathic Arthritis (JIA) is the most common form of childhood inflammatory arthritis. The disease burden of JIA is substantial as patients require specialized medical practitioners for diagnosis and chronic treatments that are both costly and time intensive. Discrepancies in access to care due to health inequities such as socioeconomic status or geographic location may lead to vastly different health outcomes. As research informs advances in care, is important to consider inclusion and diversity in JIA research.

Methods
We reviewed and synthesized randomized controlled trials for juvenile idiopathic arthritis, the most common type of arthritis among children and adolescents, in Canada with the aim of characterizing participants and identifying how determinants of health inequities are reported. To do so, we searched Medline (1990 to July 2022), Embase (1990 to July 2022), and CENTRAL (inception to July 2022) for articles meeting all of the following criteria: Canadian randomized controlled trials evaluating pharmacological or non-pharmacological interventions on juvenile idiopathic arthritis populations. Data extraction was guided by the Campbell and Cochrane Equity Methods Group’s PROGRESS-Plus framework on determinants that lead to health inequities (e.g., Place of residence; Race; Occupation; Gender/Sex; Religion; Education; Socioeconomic status; and Social capital).

Results
Of 4,074 unique records, 5 were deemed eligible for inclusion. From these determinants of health inequities, Gender/Sex and Age were the only that were reported in all studies with most participants being female and 12.6 years old on average. In addition, Race, Socioeconomic status, Education and Features of relationships were each reported once in three different studies. Lastly, Place of residence, Occupation, Religion, Social Capital and Time-dependent relationships were not reported at all.

Conclusions
This scoping review suggests limited reporting on determinants of health inequities in randomized controlled trials for JIA in Canada and a need for a reporting framework that reflects typical characteristics of juvenile patient populations.
Heterogeneous deposition of regular and mentholated little cigar smoke in the lungs of Sprague-Dawley rats
Authors: Lin Kaisen , Wallis Christopher , Wong Emily M. , Edwards Patricia , Cole Austin , Van Winkle Laura , Wexler Anthony S. 
Published: November 2023

Abstract
Background
Quantifying the dose and distribution of tobacco smoke in the respiratory system is critical for understanding its toxicity, addiction potential, and health impacts. Epidemiologic studies indicate that the incidence of lung tumors varies across different lung regions, suggesting there may be a heterogeneous deposition of smoke particles leading to greater health risks in specific regions. Despite this, few studies have examined the lobar spatial distribution of inhaled particles from tobacco smoke. This gap in knowledge, coupled with the growing popularity of little cigars among youth, underscores the need for additional research with little cigars.

Results
In our study, we analyzed the lobar deposition in rat lungs of smoke particles from combusted regular and mentholated Swisher Sweets little cigars. Twelve-week-old male and female Sprague-Dawley rats were exposed to smoke particles at a concentration of 84 ± 5 mg/m3 for 2 h, after which individual lung lobes were examined. We utilized Inductively Coupled Plasma Mass Spectrometry to quantify lobar chromium concentrations, serving as a smoke particle tracer. Our findings demonstrated an overall higher particle deposition from regular little cigars than from the mentholated ones. Higher particle deposition fraction was observed in the left and caudal lobes than other lobes. We also observed sex-based differences in the normalized deposition fractions among lobes. Animal study results were compared with the multi-path particle dosimetry (MPPD) model predictions, which showed that the model overestimated particle deposition in certain lung regions.

Conclusions
Our findings revealed that the particle deposition varied between different little cigar products. The results demonstrated a heterogenous deposition pattern, with higher particle deposition observed in the left and caudal lobes, especially with the mentholated little cigars. Additionally, we identified disparities between our measurements and the MPPD model. This discrepancy highlights the need to enhance the accuracy of models before extrapolating animal study results to human lung deposition. Overall, our study provides valuable insights for estimating the dose of little cigars during smoking for toxicity research.
Prediction nomogram for coronary artery aneurysms at one month in Kawasaki disease
Authors: Tang Yunjia , Ding Chuxin , Xu Qiuqin , Zhou Wanping , Qin Yiming , Lu Meihua , Lv Haitao 
Published: November 2023

Abstract
Background
Coronary status at one month after Kawasaki disease (KD) onset had a great significance. The present study aimed to establish a prediction model for coronary artery aneurysms (CAA) at one month in children with KD.

Methods
Patients with a diagnosis of KD between May 2017 and Dec 2018 were enrolled as the development cohort to build a prediction model. The model was validated by internal and external validation. Patients between Jan 2019 and Dec 2019 were enrolled as the validation cohort. The adaptive least absolute shrinkage and selection operator (LASSO) was used to select the possible predictors. Receiving operating characteristic curve (ROC), calibration plots, and decision curve analysis (DCA) were used to evaluate the performance of the model. The performance of the Son score was also assessed.

Results
LASSO regression demonstrated that age, sex, and CALs in the acute stage were predictors for CAA at one month. The area under the ROC (AUC) was 0.946 (95% confidence interval: 0.911–0.980) with a sensitivity of 92.5% and a specificity of 90.5%. The calibration curve and the DCA showed a favorable diagnostic performance. The internal and external validation proved the reliability of the prediction model. The AUC of our model and the Son score were 0.941 and 0.860, respectively (P < 0.001).

Conclusion
Our prediction model for CAA at one month after disease onset in KD had an excellent predictive utility.
How is overall survival assessed in randomised clinical trials in cancer and are subsequent treatment lines considered? A systematic review
Authors: Royle Kara-Louise , Meads David , Visser-Rogers Jennifer K. , White Ian R. , Cairns David A. 
Published: November 2023

Abstract
Background
Overall survival is the “gold standard” endpoint in cancer clinical trials. It plays a key role in determining the clinical- and cost-effectiveness of a new intervention and whether it is recommended for use in standard of care. The assessment of overall survival usually requires trial participants to be followed up for a long period of time. In this time, they may stop receiving the trial intervention and receive subsequent anti-cancer treatments, which also aim to extend survival, during trial follow-up. This can potentially change the interpretation of overall survival in the context of the clinical trial. This review aimed to determine how overall survival has been assessed in cancer clinical trials and whether subsequent anti-cancer treatments are considered.

Methods
Two searches were conducted using MEDLINE within OVID© on the 9th of November 2021. The first sought to identify papers publishing overall survival results from randomised controlled trials in eight reputable journals and the second to identify papers mentioning or considering subsequent treatments. Papers published since 2010 were included if presenting or discussing overall survival in the context of treating cancer.

Results
One hundred and thirty-four papers were included. The majority of these were presenting clinical trial results (98, 73%). Of these, 45 (46%) reported overall survival as a (co-) primary endpoint. A lower proportion of papers including overall survival as a (co-) primary endpoint compared to a secondary endpoint were published in recent years. The primary analysis of overall survival varied across the papers. Fifty-nine (60%) mentioned subsequent treatments. Seven papers performed additional analysis, primarily when patients in the control arm received the experimental treatment during trial follow-up (treatment switching).

Discussion
Overall survival has steadily moved from being the primary to a secondary endpoint. However, it is still of interest with papers presenting overall survival results with the caveat of subsequent treatments, but little or no investigation into their effect. This review shows that there is a methodological gap for what researchers should do when trial participants receive anti-cancer treatment during trial follow-up. Future research will identify the stakeholder opinions, on how this methodological gap should be addressed.