bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fast and accurate method for SARS-CoV-2 genomic tracing
Authors: Ma Wentai , Shi Leisheng , Li Mingkun 
Published: October 2023

Abstract
To contain infectious diseases, it is crucial to determine the origin and transmission routes of the pathogen, as well as how the virus evolves. With the development of genome sequencing technology, genome epidemiology has emerged as a powerful approach for investigating the source and transmission of pathogens. In this study, we first presented the rationale for genomic tracing of SARS-CoV-2 and the challenges we currently face. Identifying the most genetically similar reference sequence to the query sequence is a critical step in genome tracing, typically achieved using either a phylogenetic tree or a sequence similarity search. However, these methods become inefficient or computationally prohibitive when dealing with tens of millions of sequences in the reference database, as we encountered during the COVID-19 pandemic. To address this challenge, we developed a novel genomic tracing algorithm capable of processing 6 million SARS-CoV-2 sequences in less than a minute. Instead of constructing a giant phylogenetic tree, we devised a weighted scoring system based on mutation characteristics to quantify sequences similarity. The developed method demonstrated superior performance compared to previous methods. Additionally, an online platform was developed to facilitate genomic tracing and visualization of the spatiotemporal distribution of sequences. The method will be a valuable addition to standard epidemiological investigations, enabling more efficient genomic tracing. Furthermore, the computational framework can be easily adapted to other pathogens, paving the way for routine genomic tracing of infectious diseases.
A Meta-analysis of Randomised Controlled Trials Comparing Combination Therapy as Second-line Treatment With Monotherapy in Advanced Non-small Cell Lung Cancer With Epidermal Growth Factor Receptor Mutation
Authors: Zhao Kai-xiang , Zhang Yan-fang , Zheng Lei , Pan Ya-fei , He Ze-huang 
Published: October 2023

Background:Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors are standard therapy for patients with non-small cell lung cancer (NSCLC) with EGFR mutation; however, resistance is common. Combinatorial strategies have been explored to improve survival. This meta-analysis assesses the efficacy and safety of combination therapy versus monotherapy in patients with advanced NSCLC who failed first-line EGFR-tyrosine kinase inhibitor treatment.Methods:We searched randomized controlled trials from PubMed, Web of Science, Google Scholar, Cochrane Library, and ClinicalTrial.gov. The efficacy and toxicity of combination treatment groups were assessed in terms of progression-free survival (PFS), overall response rate (ORR), disease control rate (DCR), and adverse events (AEs).Results:This meta-analysis included 6 randomized controlled trials covering 785 participants. The results showed that the combined regimen arm had no significant improvement of PFS (log hazard ratio = −0.228, 95% CI: −0.543 to 0.087,P= 0.157), ORR (odds ratio = 1.147 [95% CI: 0.577, 2.281],P= 0.695), DCR (odds ratio = 1.578 [95% CI: 0.428, 5.821],P= 0.493), and AEs, including fatigue and diarrhea (odds ratio = 0.833 [95% CI: 0.297, 2.333],P= 0.728 for fatigue and odds ratio = 2.268 [95% CI: 0.544, 9.448],P= 0.261 for diarrhea).Conclusions:Combination therapy may not provide a significant improvement in PFS, ORR, DCR, and incidence of AEs compared with monotherapy in patients with advanced NSCLC with EGFR mutations. Further research is needed to investigate the optimal sequencing of combination therapy in patients with NSCLC with different molecular targets to determine the most effective treatment strategy that can improve outcomes and quality of life for these patients.
Perioperative anaesthetic management and short-term outcome of neonatal repair of oesophageal atresia with or without tracheo-oesophageal fistula in Europe
Authors: van den Berg Johanneke , Johansen Mathias , Disma Nicola , Engelhardt Thomas , Hansen Tom Giedsing , Veyckemans Francis , Zielinska Marzena , de Graaff Jurgen C. 
Published: October 2023

BACKGROUND
Oesophageal atresia with or without a tracheo-oesophageal fistula is a congenital abnormality that usually requires surgical repair within the first days of life.

OBJECTIVE
Description of the perioperative anaesthetic management and outcomes of neonates undergoing surgery for oesophageal atresia with or without a tracheo-oesophageal fistula, included in the ‘neonate and children audit of anaesthesia practice in Europe’ (NECTARINE) database.

DESIGN
Sub-analyses of prospective observational NECTARINE study.

SETTING
European multicentre study.

PATIENTS
Neonates who underwent surgery for oesophageal atresia with or without a tracheo-oesophageal fistula in the NECTARINE cohort were selected.

MAIN OUTCOME MEASURES
Incidence rates with 95% confidence intervals were calculated for peri-operative clinical events which required a predetermined intervention, postoperative complications, and mortality.

RESULTS
One hundred and three neonates undergoing a first surgical intervention for oesophageal atresia with or without a tracheo-oesophageal fistula repair were identified. Their median gestational age was 38 weeks with a median birth weight of 2840 [interquartile range 2150 to 3150] grams. Invasive monitoring was used in 66% of the procedures. The incidence of perioperative clinical events was 69% (95% confidence interval 59 to 77%), of 30-day postoperative complications 47% (95% confidence interval 38 to 57%) and the 30- and 90 days mortality rates were 2.1% and 2.6%, respectively.

CONCLUSION
Oesophageal atresia with or without a tracheo-oesophageal fistula repair in neonates is associated with a high number of perioperative interventions in response to clinical events, a high incidence of postoperative complications, and a substantial mortality rate.
Pre-emptive TIPS in high-risk acute variceal bleeding. An updated and revised individual patient data meta-analysis
Authors: Nicoară-Farcău Oana , Han Guohong , Rudler Marika , Angrisani Debora , Monescillo Alberto , Torres Ferran , Casanovas Georgina , Bosch Jaime , Lv Yong , Dunne Philip D.J. , Hayes Peter C. , Thabut Dominique , Fan Daiming , Hernández-Gea Virginia , García-Pagán Juan C. ,   on behalf of the pre-emptive TIPS individual data metanalysis, International Variceal Bleeding Study and Baveno Cooperation Study groups
Published: October 2023

Background and Aims:
A previous individual patient data meta-analysis (IPD-MA) showed that compared with drugs+endoscopy, the placement of transjugular portosystemic shunt within 72 hours of admission (pre-emptive transjugular intrahepatic portosystemic shunt: p-TIPS) increases the survival of high-risk patients (Child-Pugh B+ active bleeding and Child-Pugh C<14 points) with cirrhosis and acute variceal bleeding. However, the previous IPD-MA was not a two-stage meta-analysis, did not consider the potential risk of selection bias of observational studies, and did not include the most recent randomized clinical trial. We performed an updated and revised IPD-MA to reassess the efficacy of p-TIPS, addressing all previous issues.

Approach and Results:
We included all studies from the previous IPD-MA and searched for other possible eligible publications until September 2022. We performed a two-stage IPD-MA of data from 8 studies (4 randomized clinical trials and 4 observational). In addition, we performed a sensitivity analysis excluding those patients dying up to the first 72 hours after admission in the Drugs+Endoscopy arms of the 4 observational studies. The primary end point was the effects of p-TIPS versus Drugs+Endoscopy on 1-year survival.
We identified 1389 patients (342 p-TIPS and 1047 Drugs+Endoscopy). The two-stage IPD-MA showed that p-TIPS significantly reduced the mortality in the overall population (HR=0·43, 95% CI: 0.32–0.60, p<0.001. This effect was observed in both subgroups of patients with Child-Pugh. The sensitivity analysis confirmed the survival benefit of p-TIPS.

Conclusions:
The updated two-stage IPD-MA confirms the significant survival advantage of p-TIPS in high-risk patients with cirrhosis and acute variceal bleeding. As a result, we recommend p-TIPS as the preferred first-choice treatment for these patients.
Quantitative lymphoscintigraphy of the lower limbs for the diagnosis of phlebolymphoedema
Authors: McMeekin Helena J. , Peters A. Michael , Burniston Maria T. , Vadrucci Manuela 
Published: October 2023

Introduction
Phlebolymphoedema is caused by the interaction of the venous and lymphatic systems in a state of chronic venous insufficiency in which increased microvascular filtration causes an increased rate of lymph production. Lymphatic drainage rate increases in response, but this is unsustainable and can cause lymphatic failure and oedema. We hypothesise that in phlebolymphoedema we could measure unusually high lymphatic drainage while the lymph system is still fully functional.

Method
Patients referred for lymphoscintigraphic investigation of swollen legs between April 2021 and December 2022 were reviewed. Quantitative lymphoscintigraphy was performed following the technique of Keramida et al. (2017) and ilio-inguinal nodal uptake (IIQ%) was calculated. The presence of scintigraphic features of increased lymph production was noted for each limb.

Results
A total of 39 patients were reviewed (78 limbs, 29F, 10M). Seven limbs were identified with supranormal lymphatic function (IIQ > 30%) plus three borderline. Of these 10 limbs, all had at least two scintigraphic features of increased lymph production.

Conclusion
Quantitative lymphoscintigraphy, although developed for diagnosing abnormally low lymphatic function, may also have utility at the upper end of the spectrum for identifying chronic venous insufficiency. An IIQ% upper normal limit of 30% could be used to diagnose venous insufficiency as the cause for limb swelling. This is of note for patients of large body habitus in whom venous ultrasound is difficult.
Epidemiology, causes, and morbidities of stroke in the young
Authors: Janas Anna M. , Barry Megan , Lee Sarah 
Published: October 2023

Purpose of review
The purpose is to describe the latest research on epidemiology, causes, and morbidities of stroke in neonates and children.

Recent findings
The global incidence of childhood stroke is approximately 2 per 100 000 person-years, which is significantly lower compared to neonates (20–40 per 100 000 live births) and adults (80–90 per 100 000 person-years). Placental abnormalities are a risk factor for perinatal stroke, although cause is usually multifactorial. In children, nonatherosclerotic arteriopathies and arteriovenous malformations are major causes of ischemic and hemorrhagic strokes, respectively. The perinatal period confers a high risk of stroke and can lead to long-term disability, including motor delay, cognitive or speech impairment, and epilepsy. Recent studies suggest that at least 50% of survivors of perinatal stroke have abnormal neurodevelopmental scores in long-term follow up. Childhood stroke is associated with significant morbidity, including epilepsy, motor impairments, and behavioral disability. Recent studies have also identified an association between pediatric stroke and behavioral disorders, such as attention deficit hyperactivity disorder and autism.

Summary
Perinatal and childhood strokes are important causes of neurological morbidity. Given the low incidence of childhood stroke, prospective research studies on epidemiology, causes, and outcomes remain limited, highlighting the need for continued multisite collaborations.
Current Situation and Problems in Diagnosis of Early Chronic Pancreatitis
Authors: Ito Koichi , Takasaki Yusuke , Fujisawa Toshio , Ishii Shigeto , Tomishima Ko , Takahashi Sho , Ikoma Ippei , Jimbo Yasuhisa , Ota Hiroto , Kabemura Daishi , Ikemura Muneo , Ushio Mako , Fukuma Taito , Suzuki Akinori , Isayama Hiroyuki 
Published: October 2023

Objectives
The Japan Pancreas Society introduced the concept of early chronic pancreatitis (ECP) in 2009, but its epidemiology remains unclear. This study investigated challenges in ECP diagnosis.

Methods
Early chronic pancreatitis was diagnosed in 4 cohorts between April 2019 and November 2021 using the Clinical Diagnostic Criteria for Chronic Pancreatitis 2019. These cohorts included patients with abdominal/back pain, abnormal pancreatic enzyme levels, ECP suspected due to other reasons, and those who underwent endoscopic ultrasonography for other diseases.

Results
A total of 2502 cases were analyzed and 150 (40 alcoholic and 110 nonalcoholic) cases with ECP findings on endoscopic ultrasonography were included. Early chronic pancreatitis was confirmed in 14 cases (9%), including 9 (22.5%) alcoholic and 5 (4.5%) nonalcoholic cases. Early chronic pancreatitis was confirmed in 15%, 0%, 2.2%, and 0.13% cases in the 4 cohorts, respectively. Early chronic pancreatitis was confirmed in 10 (48%) of the 21 (14%) cases with pancreatic pain.

Conclusions
Early chronic pancreatitis diagnostic rate was low, particularly in nonalcoholic cases, but was slightly higher in cases with pancreatic pain. The diagnostic rate was highest in the abdominal/back pain group. Further studies are required to establish appropriate diagnostic criteria for ECP.
Psychometric evaluation of the heart failure somatic perception scale in Iranian heart failure patients: a cross-sectional study
Authors: Ghorbani Vajargah Pooyan , Jafaraghaee Fateme , Maroufizadeh Saman , Karkhah Samad , Osuji Joseph , Karami Samaneh , Mirrazeghi Seyedeh Fatemeh , Javadi-Pashaki Nazila 
Published: October 2023

Background:
This study aimed to evaluate the psychometric evaluation of heart failure somatic perception scale (HFSPS) in Iranian heart failure patients.

Materials and methods:
A total of 220 heart failure (HF) patients were enroled in the study. Data gathering was conducted via consecutive sampling from August 2022 to April 2023. Face validity, content validity, construct validity, and internal consistency were used to evaluate the validity and reliability of the Persian version of the HFSPS. Construct validity was done through confirmatory factor analysis and convergent validity. Convergent validity between HFSPS and symptom status questionnaire-heart failure was measured using Pearson’s correlation coefficient. Cronbach’s alpha and Macdonald’s omega coefficient were used to evaluate the reliability of instruments.

Results:
A total of 220 HF patients participated in this study. Their mean age was 66.46 (SD=11.40). Among the participants, 70% were men. The results of the confirmatory factor analysis evaluation showed the goodness of fit indices of the final HFSPS model after modification was within an acceptable range (χ2=306.18 P<0.001, Minimum Discrepancy Function Divided by Degrees of Freedom=2.47, Comparative of Fit Index=0.91, Tucker-Lewis index=0.90, Adjusted goodness of fit index=0.81, Parsimonious norm fit index=0.70, root mean square error of approximation=0.082). Convergent validity between HFSPS and symptom status questionnaire-heart failure indicated a positive and significant correlation. Cronbach’s alpha coefficient in the HFSPS was 0.868, and McDonald’s omega coefficient in the HFSPS was 0.832.

Conclusion:
Overall, the Persian version of the HFSPS was determined to be a reliable and valid scale among Iranians with HF.
An enormous benign primary retroperitoneal mucinous cystadenoma: a case report and literature review of a seldom seen abdominal pathology
Authors: Al Laham Omar , Adi Amir , Alaitouni Aliaa , Sharaf Aldeen Rahaf , Alshiekh Ali , Hamed Hamoud 
Published: October 2023

Introduction and importance:
Retroperitoneal neoplasia comprise less than 2% of all tumours. benign primary retroperitoneal mucinous cystadenoma (PRMC) is an extremely rare tumour. Their clinical course is overall silent unless the patient presents with a vague abdominal or pelvic pain, abdominal distention, or a palpable mass. Their aetiology remains theorized and since 1989, only 46 cases (excluding ours) worldwide were documented in the literature. The majority of cases were discovered in females but the overall tumour incidence rate is still undetermined due to its rarity. Well-timed recognition of this pathology permits the necessary curative surgical intervention to take place.

Case presentation:
We hereby illustrate the rare case of a 23-year-old female who presented to the surgical clinic complaining solely of an unexplained gradual increase of the abdominal contour. Their presurgical radiological analysis yielded an intraabdominal large-sized well-demarcated retroperitoneal mass.

Clinical discussion:
Thorough resection of the mass was accomplished via open surgery. The subsequent microscopic analysis of excised tumour yielded the diagnosis of primary retroperitoneal mucinous cystadenoma of benign nature.

Conclusion:
Primary retroperitoneal mucinous cystadenoma is a seldom seen tumour. The scarcity of its occurrence is further highlighted by the published data. Based on their conclusive review of the available published English-based literature, ours is the 47th documented case of a benign PRMC and it is the first documented case from our country; Syria. The impact of these findings warrants raising awareness on the subject and considering PRMC as a differential diagnosis when presented with a similar case in the clinical practice.
Citrobacter freundii-associated osteomyelitis and thromboembolic events following Moderna COVID-19 vaccination: a rare case report from Nepal
Authors: Adhikari Subodh , KC Sony , Dev Santosh , Bhandari Sujata , Parajuli Prakriti , Poudel Man B. , Adhikari Yagya R. , Poudel Binod 
Published: October 2023

Introduction:Vaccination against coronavirus disease 2019 (COVID-19) is essential for controlling the ongoing cases of this disease. Citrobacter infections of the bones and joints are extremely uncommon. Thromboembolism and deep vein thrombosis (DVT) are very rare complications.Case presentation:The authors present a rare case of osteomyelitis, septic arthritis, deep venous thrombosis, and pulmonary embolism in a 15-year-old previously healthy boy occurring shortly after receiving the second dose of the Moderna COVID-19 vaccine. He experienced pain, swelling in the right leg, shortness of breath, and fever, followed by chest pain and leg edema. Treatment included anticoagulation, ketorolac for pain management, antipyretics, and intravenous antibiotics (Tazobactam/Piperacillin, Linezolid, Clindamycin) for osteomyelitis.Discussion:The risk of COVID-19 vaccine-related thrombotic events is minimal. Thrombotic events reported among mRNA is very rare.Citrobacter freundiibone and joint infections are very rare, accounting for a small percentage of cases. Some documented cases include cefotaxime-resistant strains causing necrotizing fascitis and osteomyelitis, including postarthroplasty infections. Due to the diverse range of susceptibility patterns and the widespread occurrence of drug resistance, personalized treatment based on culture and sensitivity testing is recommended. However, in rare cases, severe complications like DVT and joint infections associated with Citrobacter infection may occur and should be reported to the vaccine adverse events reporting system.Conclusion:Administering the COVID-19 vaccine to enhance natural antibodies is crucial, despite the low risk of infection, thromboembolism, and DVT. Healthcare providers should stay vigilant about adverse effects postvaccination and promptly report those cases.
Computed tomographic assessment of risk of anterior skull base injury of adult patients in tertiary care centre: a cross-sectional study
Authors: Katwal Shailendra , Kumar Ravi Ranjan , Ansari Mukhtar Alam , Suwal Sundar , Ghimire Prasoon 
Published: October 2023

Background and objectives:Functional endoscopic sinus surgery (FESS) carries the risk of anterior skull base injury. Understanding computed tomography of the paranasal sinuses (CT PNS) and anatomical variations is crucial before surgery. Several classifications, including Kero’s, Gera’s, and Thailand-Malaysia-Singapore (TMS), assess the risk of skull base injury. The objective was to determine the risk of anterior skull base injury using CT PNS in adult patients.Methods:A study of 188 patients with head and paranasal sinus pathologies used CT scans to measure olfactory fossa depth, the angle between lamina papyracea and horizontal plane, and the distance from the orbital rim to the cribriform plate. Variations were classified using Kero’s, Gera’s, and TMS classifications.Results:The study involved 188 individuals aged 18–85, with OF depths ranging from 0.1 to 0.52 cm. Kero’s Class I was observed in 82.44% and 81.38% of individuals, while distances from orbital floor to cribriform plate and ethmoidal roof ranged from 1.37 to 2.93 cm. TMS Type I was observed in all individuals, and the angle between lateral lamella of the cribriform plate and cribriform plate ranged from 34° to 85°. Gera’s Class II was observed in 77.12% and 84.57% of individuals.Conclusion:CT PNS provides important anatomical information for assessing the risk of skull base injury during FESS. Kero’s, Gera’s, and TMS classifications can be utilized to evaluate this risk. The study findings provide insights into the variations in olfactory fossa depth, distance measurements, and angle, which can aid in preoperative planning and reducing complications during FESS in Nepalese populations.
Perceptions of Military Experience Among Veterans Reporting Lifetime Warzone Moral Injury
Authors: Borges Lauren M. , Holliman Brooke Dorsey , Farnsworth Jacob K. , Barnes Sean M. 
Published: October 2023

Abstract
Exposures to potentially morally injurious events (PMIEs) and possible moral injury are risk factors for a range of difficulties impacting individual functioning. Although exposure to PMIEs is a somewhat common product of war, qualitative methods to understand Veterans' experiences of moral injury and Veterans Affairs treatment are limited. To better characterize Veterans' experiences, 14 male warzone Veterans who reported moral injury post–warzone deployment and completed posttraumatic stress disorder treatment in the past year were asked to describe their military service as part of a qualitative study. Through thematic analysis, we found two moral injury-consistent themes and four subthemes. The first theme was “military experiences were associated with morally questioning one's self” with subthemes of “moral shift” and “depersonalization.” The second theme was “military experiences were associated with morally questioning others” with subthemes of “disillusionment” and “resignation.” Based on these findings, we conclude with a discussion of treatment implications for moral injury.
A Literature Review Examining Virtual Reality Exposure Therapy for Individuals Diagnosed With Social Anxiety Disorder
Authors: Arif Rimsha , Ashraf Sahar , Bhatt Kesha , Shah Kaushal 
Published: October 2023

Abstract
Social anxiety disorder (SAD) is a specific subtype of anxiety disorder where individuals experience uncomfortable social situations that induce anxious feelings including nervousness and panic. Computer technology has been applied in interventions for many mental health disorders. We aim to understand and explore the use of virtual reality exposure therapy (VRET) to treat adults with SAD. We conducted a literature search using relevant mesh keywords in PubMed and PsycINFO. Six studies met inclusion criteria in our final qualitative synthesis review. Results showed a significant reduction in SAD symptom severity based on primary measures in all studies, suggesting that VRET is an effective option in treating SAD. Studies have shown the success of VRET in formats such as a single-user implementation, one-session treatment, and self-training intervention. In conclusion, VRET is effective in reducing SAD symptoms. The limitations of most studies included a small sample size and weak ecological validity. Future research can examine VRET with a more extensive clinical sample and broader social behaviors.