bluuebunny/crossref_metadata_2025_split huggingface dataset:
A case of metastatic lymphoepithelial carcinoma of parotid gland identified on 68gallium DOTA-[Tyr3] octreotate PET CT
Authors: Low Han Chung , Loke Kelvin Siu Hoong , Wang Fu Qiang , Han Shuting , Jain Amit , Yeong Joe , Nei Wen Long 
Published: January 2024

Abstract
The authors present the case of a 59-year-old lady diagnosed with lymphoepithelial carcinoma (LEC) of the left parotid gland. The primary tumour was identified using contrast-enhanced CT, and diagnosis was confirmed via fine needle aspiration cytology and immunohistochemistry. Staging using fluorine-18 fluorodeoxyglucose PET CT revealed regional nodal metastases, while no distant metastasis was evident. Following radical radiotherapy, a favourable locoregional response was observed on MRI, yet the patient's plasma Epstein-Barr virus load continued to rise. Given her primary tumour’s somatostatin receptor type 2 (SSTR2) positivity, gallium-68 DOTA-[Tyr3] octreotate PET CT (68Ga-DOTATATE PET CT) was performed, revealing multiple distant metastases with DOTATATE avidity. Despite attempts at palliative chemotherapy and immunotherapy, disease progression led to the decision for the best supportive care. The unique presentation of metastatic LEC on 68Ga-DOTATATE PET CT suggests a potential role for SSTR2-targeted imaging in diagnosis and management.
Radiotherapy dose escalation using pre-treatment diffusion-weighted imaging in locally advanced rectal cancer: a planning study
Authors: Hearn Nathan , Leppien Alexandria , O’Connor Patrick , Cahill Katelyn , Atwell Daisy , Vignarajah Dinesh , Min Myo 
Published: January 2024

Abstract

Objectives
Diffusion-weighted MRI (DWI) may provide biologically relevant target volumes for dose-escalated radiotherapy in locally advanced rectal cancer (LARC). This planning study assessed the dosimetric feasibility of delivering hypofractionated boost treatment to intra-tumoural regions of restricted diffusion prior to conventional long-course radiotherapy.

Methods
Ten patients previously treated with curative-intent standard long-course radiotherapy (50 Gy/25#) were re-planned. Boost target volumes (BTVs) were delineated semi-automatically using 40th centile intra-tumoural apparent diffusion coefficient value with expansions (anteroposterior 11 mm, transverse 7 mm, craniocaudal 13 mm). Biased-dosed combined plans consisted of a single-fraction volumetric modulated arc therapy flattening-filter-free (VMAT-FFF) boost (phase 1) of 5, 7, or 10 Gy before long-course VMAT (phase 2). Phase 1 plans were assessed with reference to stereotactic conformality and deliverability measures. Combined plans were evaluated with reference to standard long-course therapy dose constraints.

Results
Phase 1 BTV dose targets at 5/7/10 Gy were met in all instances. Conformality constraints were met with only 1 minor violation at 5 and 7 Gy. All phase 1 and combined phase 1 + 2 plans passed patient-specific quality assurance. Combined phase 1 + 2 plans generally met organ-at-risk dose constraints. Exceptions included high-dose spillage to bladder and large bowel, predominantly in cases where previously administered, clinically acceptable non-boosted plans also could not meet constraints.

Conclusions
Targeted upfront LARC radiotherapy dose escalation to DWI-defined is feasible with appropriate patient selection and preparation.

Advances in knowledge
This is the first study to evaluate the feasibility of DWI-targeted upfront radiotherapy boost in LARC. This work will inform an upcoming clinical feasibility study.
A real-world evaluation of the diagnostic accuracy of radiologists using positive predictive values verified from deep learning and natural language processing chest algorithms deployed retrospectively
Authors: Bhatia Bahadar S , Morlese John F , Yusuf Sarah , Xie Yiting , Schallhorn Bob , Gruen David 
Published: January 2024

Abstract

Objectives
This diagnostic study assessed the accuracy of radiologists retrospectively, using the deep learning and natural language processing chest algorithms implemented in Clinical Review version 3.2 for: pneumothorax, rib fractures in digital chest X-ray radiographs (CXR); aortic aneurysm, pulmonary nodules, emphysema, and pulmonary embolism in CT images.

Methods
The study design was double-blind (artificial intelligence [AI] algorithms and humans), retrospective, non-interventional, and at a single NHS Trust. Adult patients (≥18 years old) scheduled for CXR and CT were invited to enroll as participants through an opt-out process. Reports and images were de-identified, processed retrospectively, and AI-flagged discrepant findings were assigned to two lead radiologists, each blinded to patient identifiers and original radiologist. The radiologist’s findings for each clinical condition were tallied as a verified discrepancy (true positive) or not (false positive).

Results
The missed findings were: 0.02% rib fractures, 0.51% aortic aneurysm, 0.32% pulmonary nodules, 0.92% emphysema, and 0.28% pulmonary embolism. The positive predictive values (PPVs) were: pneumothorax (0%), rib fractures (5.6%), aortic dilatation (43.2%), pulmonary emphysema (46.0%), pulmonary embolus (11.5%), and pulmonary nodules (9.2%). The PPV for pneumothorax was nil owing to lack of available studies that were analysed for outpatient activity.

Conclusions
The number of missed findings was far less than generally predicted. The chest algorithms deployed retrospectively were a useful quality tool and AI augmented the radiologists’ workflow.

Advances in knowledge
The diagnostic accuracy of our radiologists generated missed findings of 0.02% for rib fractures CXR, 0.51% for aortic dilatation, 0.32% for pulmonary nodule, 0.92% for pulmonary emphysema, and 0.28% for pulmonary embolism for CT studies, all retrospectively evaluated with AI used as a quality tool to flag potential missed findings. It is important to account for prevalence of these chest conditions in clinical context and use appropriate clinical thresholds for decision-making, not relying solely on AI.
Right-sided iliac vein compression syndrome: when the vein is compressed between the internal and external iliac arteries—a case report
Authors: Yamanaka Tetsuo , Ishihara Tatsuhiko , Hara Toru , Ichinohe Yoshimaro , Fukatsu Toru 
Published: January 2024

Abstract

Background
In its normal anatomical relationship, the inferior vena cava is located on the right side of the abdominal aorta. Iliac vein compression syndrome (IVCS) is a pathological condition in which a blood clot is formed due to blood flow obstruction when the left common iliac vein is compressed between the right common iliac artery and the vertebral body. Therefore, right-sided IVCS (RIVCS) is rare. The effectiveness of treatment for RIVCS has not been sufficiently investigated.

Case summary
A 51-year-old man developed deep vein thrombosis in the right lower extremity and non-massive pulmonary embolism during steroid treatment for IgA nephropathy. Magnetic resonance angiography (MRA) suggested iliac compression syndrome. Symptoms improved with the use of direct oral anticoagulants and compression stockings. At the 8-month follow-up, the clinical course was uneventful.

Discussion
The causes of RIVCS in this case are believed to be the effects of steroids, prolonged sitting, and compression of the right external iliac vein. However, considering that deep vein thrombosis did not form in the left lower limb where there was no venous compression, it can be considered that the compression of the right external iliac vein had a significant impact. This case has been followed up for 8 months with anticoagulants and is progressing well. This is the first case to report the course of RIVCS treated conservatively with anticoagulant therapy for 8 months. This case suggested that conservative treatment is effective for RIVCS.
Clinical and genetic diagnosis of familial hypercholesterolaemia in patients undergoing coronary angiography: the Ludwigshafen Risk and Cardiovascular Health Study
Authors: Molnar Stefan , Scharnagl Hubert , Delgado Graciela E , Krämer Bernhard K , Laufs Ulrich , März Winfried , Kleber Marcus E , Katzmann Julius L 
Published: January 2024

Abstract

Aims
To investigate the prevalence of familial hypercholesterolaemia (FH) and compare the performance of clinical criteria and genetic testing in patients undergoing coronary angiography.

Methods and results
The prevalence of FH was determined with the Dutch Lipid Clinical Network (DLCN), US ‘Make Early Diagnosis to Prevent Early Death’ (US-MEDPED), Simon Broome (SB) criteria, the ‘familial hypercholesterolaemia case ascertainment tool’ (FAMCAT), and a clinical algorithm. Genetic screening was conducted with a custom array from Affymetrix (CARRENAL array) harbouring 944 FH mutations.
The study cohort consisted of 3267 patients [78.6% with coronary artery disease (CAD)]. FH was diagnosed in 2.8%, 2.2%, 3.9%, and 7.9% using the DLCN, US-MEDPED, SB criteria, and the FAMCAT. The clinical algorithm identified the same patients as the SB criteria. Pathogenic FH mutations were found in 1.2% (1.2% in patients with CAD, 1.0% in patients without CAD). FH was more frequently diagnosed in younger patients. With genetic testing as reference, the clinical criteria achieved areas under the ROC curve [area under the curves (AUCs)] in the range of 0.56–0.68. Using only low-density lipoprotein cholesterol (LDL-C) corrected for statin intake, an AUC of 0.68 was achieved.

Conclusion
FH is up to four-fold more prevalent in patients undergoing coronary angiography than in contemporary cohorts representing the general population. Different clinical criteria yield substantially different diagnosis rates, overestimating the prevalence of FH compared with genetic testing. LDL-C testing alone may be sufficient to raise the suspicion of FH, which then needs to be corroborated by genetic testing.

Lay summary
In this study, we investigated the frequency of familial hypercholesterolaemia—a common genetic condition leading to markedly elevated low-density lipoprotein (LDL) cholesterol and increased risk of atherosclerosis—in 3267 patients undergoing coronary angiography according to commonly used diagnostic scoring systems and genetic testing.
Innovations in measuring and mitigating phytohemagglutinins, a key food safety concern in beans
Authors: Lu Chenze , Fang Zhihui , Yang Su , Ning Kang , Xu Min , Buhot Arnaud , Hou Yanxia , Hu Peiya , Xu Pei 
Published: January 2024

Abstract
Phytohemagglutinin (PHA) is a seed storage protein and a type of lectin originally discovered in the common bean (Phaseolus vulgaris) for its blood-agglutinating effect. Due to its interactions with gut epithelia and digestive enzymes and its potential to trigger allergic reactions, PHA can lead to various symptoms in the human body. As a result, it has been regarded as a significant antinutritional factor in beans and other legumes. While several published works have summarized its structural, biochemical, and toxicological features, there is a scarcity of literature that reviews the detection, quantification, and reduction of PHA in beans, which is fundamental for the development of safer bean varieties. In this review, we present a comprehensive analysis of traditional and innovative bio-sensing methods for measuring PHA, including the recently available ultrapure liquid chromatography–tandem mass spectrometry and emerging aptamer sensor-based techniques, while discussing their respective advantages and disadvantages. We also revisit existing studies dedicated to creating PHA-depleted common bean varieties and explore the potential for reducing PHA content in beans without compromising their resistance to biotic stress. Additionally, we offer insights into the potential for controlling PHA content using the latest biotechnologies and breeding strategies. Overall, this review compiles rare and valuable information from studies that solely focuses on detection and depletion of PHA to shed light on and apply technological advancements in addressing potential food safety risks associated with the consumption of common beans.
New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system
Authors: Bittner Meriel J , Bannon Catherine C , Rowland Elden , Sundh John , Bertrand Erin M , Andersson Anders F , Paerl Ryan W , Riemann Lasse 
Published: January 2024

Abstract
Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74–117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.
HME, NFE, and HAE-1 efflux pumps in Gram-negative bacteria: a comprehensive phylogenetic and ecological approach
Authors: Bodilis Josselin , Simenel Olwen , Michalet Serge , Brothier Elisabeth , Meyer Thibault , Favre-Bonté Sabine , Nazaret Sylvie 
Published: January 2024

Abstract
The three primary resistance-nodulation-cell division (RND) efflux pump families (heavy metal efflux [HME], nodulation factor exporter [NFE], and hydrophobe/amphiphile efflux-1 [HAE-1]) are almost exclusively found in Gram-negative bacteria and play a major role in resistance against metals and bacterial biocides, including antibiotics. Despite their significant societal interest, their evolutionary history and environmental functions are poorly understood. Here, we conducted a comprehensive phylogenetic and ecological study of the RND permease, the subunit responsible for the substrate specificity of these efflux pumps. From 920 representative genomes of Gram-negative bacteria, we identified 6205 genes encoding RND permeases with an average of 6.7 genes per genome. The HME family, which is involved in metal resistance, corresponds to a single clade (21.8% of all RND pumps), but the HAE-1 and NFE families had overlapping distributions among clades. We propose to restrict the HAE-1 family to two phylogenetic sister clades, representing 41.8% of all RND pumps and grouping most of the RND pumps involved in multidrug resistance. Metadata associated with genomes, analyses of previously published metagenomes, and quantitative Polymerase Chain Reaction (qPCR) analyses confirmed a significant increase in genes encoding HME permeases in metal-contaminated environments. Interestingly, and possibly related to their role in root colonization, genes encoding HAE-1 permeases were particularly abundant in the rhizosphere. In addition, we found that the genes encoding these HAE-1 permeases are significantly less abundant in marine environments, whereas permeases of a new proposed HAE-4 family are predominant in the genomes of marine strains. These findings emphasize the critical role of the RND pumps in bacterial resistance and adaptation to diverse ecological niches.
Epidemiology and microbiology of recurrent UTI in women in the community in Oxfordshire, UK
Authors: Vazquez-Montes Maria D L A , Fanshawe Thomas R , Stoesser Nicole , Walker A Sarah , Butler Christopher , Hayward Gail 
Published: January 2024

Abstract

Background
Recurrent urinary tract infection (rUTI) contributes to significant morbidity and antibiotic usage.

Objectives
To characterize the age of women experiencing rUTI, the microbiology of rUTIs, and the risk of further rUTIs in Oxfordshire, UK.

Patients and methods
We retrospectively analysed de-identified linked microbiology and hospital admissions data (Infections in Oxfordshire Research Database), between 2008 and 2019, including positive urine cultures from women aged ≥16 years in community settings. We defined rUTI as ≥2 positive urine cultures within 6 months or ≥3 within 12 months.

Results
Of 201 927 women with urine culture performed, 84 809 (42%) had ≥1 positive culture, and 15 617 (18%) of these experienced ≥1 rUTI over a median (IQR) follow-up of 6 (3–9) years. Women with rUTI were 17.0 (95% CI: 16.3–17.7) years older on average. rUTI was commonest (6204; 40%) in those aged 70–89 years. Post-rUTI, the risk of further UTI within 6 months was 29.4% (95% CI: 28.7–30.2). Escherichia coli was detected in 65% of positive cultures. Among rUTIs where the index UTI was E. coli associated, the second UTI was also E. coli associated in 81% of cases.

Conclusions
rUTIs represent a substantial healthcare burden, particularly in women &gt;60 years. One-third of women experiencing rUTI have a further microbiologically confirmed UTI within 6 months.
Sex-specific effects of Fat-1 transgene on bone material properties, size, and shape in mice
Authors: Bermudez Beatriz , Brown Kenna C , Vahidi Ghazal , Ferreira Ruble Ana C , Heveran Chelsea M , Ackert-Bicknell Cheryl L , Sherk Vanessa D 
Published: January 2024

Abstract
Western diets are becoming increasingly common around the world. Western diets have high omega 6 (ω-6) and omega 3 (ω-3) fatty acids and are linked to bone loss in humans and animals. Dietary fats are not created equal; therefore, it is vital to understand the effects of specific dietary fats on bone. We aimed to determine how altering the endogenous ratios of ω-6:ω-3 fatty acids impacts bone accrual, strength, and fracture toughness. To accomplish this, we used the Fat-1 transgenic mice, which carry a gene responsible for encoding a ω-3 fatty acid desaturase that converts ω-6 to ω-3 fatty acids. Male and female Fat-1 positive mice (Fat-1) and Fat-1 negative littermates (WT) were given either a high-fat diet (HFD) or low-fat diet (LFD) at 4 wk of age for 16 wk. The Fat-1 transgene reduced fracture toughness in males. Additionally, male BMD, measured from DXA, decreased over the diet duration for HFD mice. In males, neither HFD feeding nor the presence of the Fat-1 transgene impacted cortical geometry, trabecular architecture, or whole-bone flexural properties, as detected by main group effects. In females, Fat-1-LFD mice experienced increases in BMD compared to WT-LFD mice; however, cortical area, distal femur trabecular thickness, and cortical stiffness were reduced in Fat-1 mice compared to pooled WT controls. However, reductions in stiffness were caused by a decrease in bone size and were not driven by changes in material properties. Together, these results demonstrate that the endogenous ω-6:ω-3 fatty acid ratio influences bone material properties in a sex-dependent manner. In addition, Fat-1 mediated fatty acid conversion was not able to mitigate the adverse effects of HFD on bone strength and accrual.
Adult neuro-oncology trials in the United States over 5 decades: Analysis of trials completion rate to guide the path forward
Authors: Smith Emily J , Naik Anant , Goel Mahima , Wen Patrick Y , Lim Michael , Chang Susan M , Germano Isabelle M 
Published: January 2024

Abstract

Background
Clinical trials are important to close the gap between therapeutic unmet needs and scientific advances in neuro-oncology. This study analyzes the landscape of neuro-oncology trials to identify completion rates and guide strategies for the path forward.

Methods
US-registered adult neuro-oncology clinical trials were extracted from www.clinicaltrials.gov (1966–2019), including funding source, trial type, scope, phase, and subjects’ demographics. Completed trials defined as those that had completed participants’ examinations or intervention administration for the purpose of the final collection of data for the primary outcome were dichotomized against those that failed to reach completion. Univariate and multivariate analyses were used to detect differences across factors comparing the last 2 decades (2000–2009, 2010–2019).

Results
Our search yielded 4522 trials, of which 1257 are eligible for this study. In 25 US states, neuro-oncology trial availability is &lt;0.85/100,000 population. Comparing the past 2 decades, trial completion rate decreased from 88% to 64% (P &lt; .001) and National Institutes of Health funding decreased from 47% to 24% (P &lt; .001). Inclusion of subjects &gt;65-year-old and women increased, while inclusion of Hispanic subjects decreased (P &lt; .001). The top 2 reasons for lack of completion included accrual and operational difficulties. A larger proportion of women, non-Hispanic subjects, and older adults were enrolled in completed trials than in those that failed completion.

Conclusions
Our study is the first report on the neuro-oncology clinical trial landscape in the United States and supports the development of strategies to further improve access to these trials. Additionally, attention is needed to identify and modify other factors contributing to lack of completion.
Exposure frequency and radiation dose from CT examinations in Huaian
Authors: Huo Binbin , Chen Xiaomin , Xu Zhiyong , He Dongdong , Wang Jin 
Published: January 2024

Abstract
This study quantified the exposure frequency and established the local diagnostic reference levels (DRLs) for the most common computed tomography (CT) examinations. A combined method census and sampling survey was used to quantify both frequency and radiation dose of CT examinations. Data were acquired through Picture Archiving and Communication System (PACS) or Radiology Information System (RIS). The annual frequency of CT examinations was 239.8 per 1000 inhabitants. The P75 of volume CT dose index (CTDIvol) to adult patients from CT scanning for head, chest, abdomen and lumbar spine examinations were 63.0, 12.4, 20.0 and 24.0 mGy, respectively. The P75 of dose-length product were 858.6, 416.0, 620.7 and 559.2 mGy·cm, respectively. This dose audit of CT practice can act as a starting point for establishing Huaian local DRLs and could be a reference for dose optimisation in China. This study compared DRLs in different countries and analysed some reasons for the rapid growth of CT examination frequency in Huaian.