bluuebunny/crossref_metadata_2025_split huggingface dataset:
FLAMS: Find Lysine Acylations and other Modification Sites
Authors: Longin Hannelore , Broeckaert Nand , Langen Maarten , Hari Roshan , Kramarska Anna , Oikarinen Kasper , Hendrix Hanne , Lavigne Rob , van Noort Vera 
Published: January 2024

Abstract

Summary
Today, hundreds of post-translational modification (PTM) sites are routinely identified at once, but the comparison of new experimental datasets to already existing ones is hampered by the current inability to search most PTM databases at the protein residue level. We present FLAMS (Find Lysine Acylations and other Modification Sites), a Python3-based command line and web-tool that enables researchers to compare their PTM sites to the contents of the CPLM, the largest dedicated protein lysine modification database, and dbPTM, the most comprehensive general PTM database, at the residue level. FLAMS can be integrated into PTM analysis pipelines, allowing researchers to quickly assess the novelty and conservation of PTM sites across species in newly generated datasets, aiding in the functional assessment of sites and the prioritization of sites for further experimental characterization.

Availability and implementation
FLAMS is implemented in Python3, and freely available under an MIT license. It can be found as a command line tool at https://github.com/hannelorelongin/FLAMS, pip and conda; and as a web service at https://www.biw.kuleuven.be/m2s/cmpg/research/CSB/tools/flams/.
ReMASTER: improved phylodynamic simulation for BEAST 2.7
Authors: Vaughan Timothy G 
Published: January 2024

Abstract

Summary
Phylodynamic models link phylogenetic trees to biologically-relevant parameters such as speciation and extinction rates (macroevolution), effective population sizes and migration rates (ecology and phylogeography), and transmission and removal/recovery rates (epidemiology) to name a few. Being able to simulate phylogenetic trees and population dynamics under these models is the basis for (i) developing and testing of phylodynamic inference algorithms, (ii) performing simulation studies which quantify the biases stemming from model-misspecification, and (iii) performing so-called model adequacy assessments by simulating samples from the posterior predictive distribution. Here I introduce ReMASTER, a package for the phylogenetic inference platform BEAST 2 that provides a simple and efficient approach to specifying and simulating the phylogenetic trees and population dynamics arising from phylodynamic models. Being a component of BEAST 2 allows ReMASTER to also form the basis of joint simulation and inference analyses. ReMASTER is a complete rewrite of an earlier package, MASTER, and boasts improved efficiency, ease of use, flexibility of model specification, and deeper integration with BEAST 2.

Availability and Implementation
ReMASTER can be installed directly from the BEAST 2 package manager, and its documentation is available online at https://tgvaughan.github.io/remaster. ReMASTER is free software, and is distributed under version 3 of the GNU General Public License. The Java source code for ReMASTER is available from https://github.com/tgvaughan/remaster.
Phylogeography of a commercially important reef fish, Lutjanus ehrenbergii, from the coastal waters of the Arabian Peninsula
Authors: Griffiths Marylka H , Wade Christopher M , D’Agostino Daniele , Berumen Michael L , Burt John A , DiBattista Joseph D , Feary David A 
Published: January 2024

Abstract
The coastal waters of the Arabian Peninsula include a heterogeneous marine region comprising the Persian/Arabian Gulf and Sea of Oman at its northeastern boundary and the Arabian Sea, Gulf of Aden, and Red Sea at its southern and western boundary. The environment within this region shifts from highly variable coral cover and extreme temperatures within the Persian/Arabian Gulf to sparse coral cover, lower summer temperatures, and nutrient-rich upwelling within the Sea of Oman. Within the Gulf of Aden and Red Sea there is high coral cover and warm, stable conditions. We tested for barriers to pelagic dispersal across this peninsula for the commercially important blackspot snapper Lutjanus ehrenbergii using mitochondrial DNA sequences. We found scant evidence for population genetic differences when comparing within northern and southern sections, but instead found strong evidence of genetic differentiation between northern and southern sections, with the Persian/Arabian Gulf and Sea of Oman populations being highly differentiated from the Gulf of Aden and Red Sea populations. Low levels of haplotype sharing between the Persian/Arabian Gulf – Sea of Oman and the Gulf of Aden – Red Sea probably reflect scenarios of historical colonization into these peripheral bodies of water, or the presence of a contemporary ecological barrier preventing further genetic exchange.
Gamma delta lymphoma: a pictorial review of F-18 fluorodeoxyglucose PET/CT findings and a brief review of the literature
Authors: Rayamajhi Sampanna J , Ponisio Maria R , Mehta-Shah Neha 
Published: January 2024

Abstract
Gamma Delta (γδ) T-cell lymphomas are uncommon and aggressive neoplasms originating from the γδ receptor-bearing lymphocytes. The most frequent entities include primary hepatosplenic γδ T-cell lymphomas, primary cutaneous γδ lymphoma, and monomorphic epitheliotropic T-cell lymphoma. F-18 fluorodeoxyglucose (FDG) PET/CT is an important modality in the staging of Hodgkin’s and various non-Hodgkin’s lymphoma. However, literature is scare on imaging findings of γδ lymphoma on F-18 FDG PET/CT. In this review, we discuss briefly the clinical and biological features and present the spectrum of F-18 FDG PET/CT findings of γδ lymphoma.
Novel implementation of cardiac magnetic resonance first-pass perfusion imaging for semi-quantitatively evaluating microvascular dysfunction in paediatric patients with Duchenne muscular dystrophy
Authors: Xie Linjun , Cai Xiaotang , Guo Yingkun , Yu Li , Li Xuesheng , Fu Chuan , Xu Ke , Song Yu , Xu Rong , Liu Hanmin , Xu Huayan 
Published: January 2024

Abstract

Objectives
The current study aimed to assess myocardial microcirculation dysfunction via cardiac magnetic resonance (CMR) first-pass perfusion imaging in children with Duchenne muscular dystrophy (DMD).

Methods
In total, 67 children with DMD and 15 controls who underwent contrast-enhanced CMR first-pass perfusion imaging were enrolled in this study. CMR first-pass perfusion and late gadolinium enhancement (LGE) sequences were acquired. Further, the global, regional, and coronary artery distribution area perfusion indexes (PI), upslope (%BL), maximum signal intensity (MaxSI), time to maximum signal intensity (TTM), and baseline SI were analysed. The perfusion parameters of the LGE positive (+), LGE negative (−), and control groups were compared. Pearson correlation analysis was performed to assess the association between myocardial microcirculation and conventional cardiac function and LGE parameters.

Results
The LGE+ group had a significantly lower global and apical-ventricular MaxSI than the control group (all P &lt; .05). The left anterior descending arterial (LAD), left circumflex coronary arterial (LCX), and right coronary arterial (RCA) segments of the LGE+ group had a lower upslope and MaxSI than those of the control group (all P &lt; .05). The LAD segments of the LGE− group had a lower MaxSI than those of the control group (41.10 ± 11.08 vs 46.36 ± 13.04; P &lt; .001). The LCX segments of the LGE− group had a lower PI and upslope than those of the control group (11.05 ± 2.84 vs 12.46 ± 2.82; P = .001; 59.31 ± 26.76 vs 68.57 ± 29.99; P = .002). Based on the correlation analysis, the upslope, MaxSI, and TTM were correlated with conventional cardiac function and LGE extent.

Conclusions
Paediatric patients with DMD may present with microvascular dysfunction. This condition may appear before LGE and may be correlated with coronary artery blood supply and LGE extent.

Advances in knowledge
First-pass perfusion parameters may reveal the status of myocardial microcirculation and reflect the degree of myocardial injury at an earlier time in DMD patients. Perfusion parameters should be analysed not only via global or base, middle, and apical segments but also according to coronary artery distribution area, which may detect myocardial microvascular dysfunction at an earlier stage, in DMD patients with LGE−.
Lesion-specific pericoronary adipose tissue CT attenuation improves risk prediction of major adverse cardiovascular events in coronary artery disease
Authors: Chen Meng , Hao Guangyu , Hu Su , Chen Can , Tao Qing , Xu Jialiang , Geng Yayuan , Wang Ximing , Hu Chunhong 
Published: January 2024

Abstract

Objectives
To determine whether lesion-specific pericoronary adipose tissue CT attenuation (PCATa) is superior to PCATa around the proximal right coronary artery (PCATa-RCA) and left anterior descending artery (PCATa-LAD) for major adverse cardiovascular events (MACE) prediction in coronary artery disease (CAD).

Methods
Six hundred and eight CAD patients who underwent coronary CTA from January 2014 to December 2018 were retrospectively included, with clinical risk factors, plaque features, lesion-specific PCATa, PCATa-RCA, and PCATa-LAD collected. MACE was defined as cardiovascular death, non-fatal myocardial infarction, unplanned revascularization, and hospitalization for unstable angina. Four models were established, encapsulating traditional factors (Model A), traditional factors and PCATa-RCA (Model B), traditional factors and PCATa-LAD (Model C), and traditional factors and lesion-specific PCATa (Model D). Prognostic performance was evaluated with C-statistic, area under receiver operator characteristic curve (AUC), and net reclassification index (NRI).

Results
Lesion-specific PCATa was an independent predictor for MACE (adjusted hazard ratio = 1.108, P &lt; .001). The C-statistic increased from 0.750 for model A to 0.762 for model B (P = .078), 0.773 for model C (P = .046), and 0.791 for model D (P = .005). The AUC increased from 0.770 for model A to 0.793 for model B (P = .027), 0.793 for model C (P = .387), and 0.820 for model D (P = .019). Compared with model A, the NRIs for models B, C, and D were 0.243 (−0.323 to 0.792, P = .392), 0.428 (−0.012 to 0.835, P = .048), and 0.708 (0.152-1.016, P = .001), respectively.

Conclusions
Lesion-specific PCATa improves risk prediction of MACE in CAD, which is better than PCATa-RCA and PCATa-LAD.

Advances in knowledge
Lesion-specific PCATa was superior to PCATa-RCA and PCATa-LAD for MACE prediction.
Differentiation of bone metastases from benign red marrow depositions: utilizing qualitative and quantitative analysis of conventional T1-weighted imaging and fat-suppressed T2-weighted imaging
Authors: Park Sekyoung , Huh Jin Do 
Published: January 2024

Abstract

Objectives
To distinguish bone metastases (BMs) from benign red marrow depositions (BRMs) by qualitative and quantitative analyses of T1-weighted imaging and fat-suppressed T2-weighted imaging (T2 FS).

Methods
For 75 lesions including 38 BMs and 37 BRMs, two radiologists independently evaluated magnetic resonance images by qualitative (signal intensity [SI] of lesions compared to that of normal muscle [NM] or normal bone marrow [NBM]) and quantitative (parameters of the region of interests in the lesions, including T1 ratio [T1 SI ratio of lesion and NM], T2FMu ratio [T2 FS SI ratio of lesion and NM], and T2FMa ratio [T2 FS SI ratio of lesion and NBM]) analyses.

Results
Hyperintensity relative to NM or NBM on T2 FS was more frequent in BMs than in BRMs (100% vs 59.5%-78.4%, respectively; P ≤ 0.001) but also was present in more than half of BRMs. All quantitative parameters showed a significant difference between BMs and BRMs (T1 ratio, 1.075 vs 1.227 [P = 0.002]; T2FMu ratio, 2.094 vs 1.282 [P &lt; 0.001]; T2FMa ratio, 3.232 vs 1.810 [P &lt; 0.001]). The receiver operating characteristics areas under the curves of T2FMu and T2FMa ratios were clinically useful (0.781 and 0.841, respectively) and did not demonstrate statistically significant differences.

Conclusions
The quantitative analysis of T2 FS facilitates distinguishing between BMs and BRMs, regardless of whether the reference was NM or NBM.

Advances in knowledge
Quantitative parameters derived from T2 FS facilitate differentiation of BMs BRMs without additional scans. The role of NBM as an internal standard for T2 FS to differentiate between BMs and BRMs is similar to that of NM.
Diagnostic value of PET imaging in clinically unresponsive patients
Authors: Farg Hashim , Elnakib Ahmed , Gebreil Ahmad , Alksas Ahmed , van Bogaert Eric , Mahmoud Ali , Khalil Ashraf , Ghazal Mohammed , Abou El-Ghar Mohamed , El-Baz Ayman , Contractor Sohail 
Published: January 2024

Abstract
Rapid advancements in the critical care management of acute brain injuries have facilitated the survival of numerous patients who may have otherwise succumbed to their injuries. The probability of conscious recovery hinges on the extent of structural brain damage and the level of metabolic and functional cerebral impairment, which remain challenging to assess via laboratory, clinical, or functional tests. Current research settings and guidelines highlight the potential value of fluorodeoxyglucose-PET (FDG-PET) for diagnostic and prognostic purposes, emphasizing its capacity to consistently illustrate a metabolic reduction in cerebral glucose uptake across various disorders of consciousness. Crucially, FDG-PET might be a pivotal tool for differentiating between patients in the minimally conscious state and those in the unresponsive wakefulness syndrome, a persistent clinical challenge. In patients with disorders of consciousness, PET offers utility in evaluating the degree and spread of functional disruption, as well as identifying irreversible neural damage. Further, studies that capture responses to external stimuli can shed light on residual or revived brain functioning. Nevertheless, the validity of these findings in predicting clinical outcomes calls for additional long-term studies with larger patient cohorts suffering from consciousness impairment. Misdiagnosis of conscious illnesses during bedside clinical assessments remains a significant concern. Based on the clinical research settings, current clinical guidelines recommend PET for diagnostic and/or prognostic purposes. This review article discusses the clinical categories of conscious disorders and the diagnostic and prognostic value of PET imaging in clinically unresponsive patients, considering the known limitations of PET imaging in such contexts.
Acellular dermal matrix imaging features in breast reconstructive surgery: a pictorial review
Authors: Durando Manuela , Ferrando Pietro Maria , Dianzani Chiara , Galioto Francesca , Mariscotti Giovanna , Regini Elisa , Bartoli Germana , Malan Fabrizio , Bogetti Paolo , Fonio Paolo 
Published: January 2024

Abstract
Acellular dermal matrices (ADMs) are biological engineered tissues, which may provide an immunologically inert scaffold in breast reconstruction. Since the literature on imaging features of ADMs is limited, radiologists must be aware of the common imaging appearances of ADM, to differentiate normal conformation from residual or recurrent disease. Our purpose is to review the current role of ADMs in implant-based breast reconstruction, describing the normal imaging findings at ultrasound, mammography, and MRI also considering the possible changes over time. In this pictorial essay, we reviewed imaging features of ADMs described in the literature and we reported our experience in patients who underwent reconstructive surgery with human or animal ADM for newly diagnosed breast cancer.
Retroperitoneal bronchogenic cyst mimicking an adrenal cyst: case report
Authors: Idrees Hajra , Zarrar Raza , Taslicay Ceylan A , Elsayes Khaled M 
Published: January 2024

Abstract
Bronchogenic cysts are rare lesions that form during early embryogenesis and are commonly located in the mediastinum. Retroperitoneal bronchogenic cysts (RBs) are exceptionally rare, with only a handful of cases reported in the modern literature. Here, we report an RB found incidentally on imaging in a patient with suspected nephrolithiasis. We also review the unique imaging and histopathological findings of this entity and discuss why prophylactic surgery is considered the treatment of choice.
Vertebral anomalies and VACTERL association in pontine tegmental cap dysplasia: a paediatric case report
Authors: Klapper Rachel Jane , Strobel Joshua , Hebert Chance , Venkataraj Maamannan , Xu Tailong , Arevalo Espejo Octavio 
Published: January 2024

Abstract
This case report highlights vertebral segmental anomalies and the fact that the child presented has a rare neurologic condition called pontine tegmental cap dysplasia. Additionally, this case aims to educate learners in developing a differential diagnosis for vertebral and cardiac anomalies such as VACTERL syndromes and common syndromes associated with butterfly vertebrae in children and adolescents.
Two cases of parathyroid carcinoma associated with multiple brown tumours
Authors: Sakai Akihiro , Inagi Toshihide , Iijima Hiroaki , Ebisumoto Koji , Okami Kenji 
Published: January 2024

Abstract
We present two rare cases of parathyroid carcinomas associated with multiple brown tumours. Plain radiographs, computed tomography, and neck ultrasonography revealed the presence of bone and parathyroid tumours. Despite the use of 99m Tc-methoxy isobutyl isonitrile (99mTc-MIBI) or 18F-fluorodeoxyglucose-positron emission tomography (18F-FDG PET)/CT, it was difficult to differentiate bone metastases from brown tumours. Parathyroid carcinoma was confirmed by histopathological examination following parathyroidectomy, resulting in spontaneous bone lesion improvement. In patients with parathyroid carcinoma presenting with bone lesions suggestive of metastasis, understanding the potential for brown tumour accumulation through 99mTc-MIBI or 18F-FDG PET/CT is pivotal. With this understanding, it is possible to diagnose brown tumours with parathyroidectomy and follow up for improvement of bone lesion and avoid invasive biopsy or surgery.
Radiological findings and endovascular management of internal carotid artery pseudoaneurysm in the setting of mucormycosis and COVID-19
Authors: Seshadri Harini , Saraf Rashmi , Barchha Satyam 
Published: January 2024

Abstract
The coronavirus pandemic is now a public health emergency and has spread to nearly 206 countries across the globe. This novel disease has shaken the psycho-social, economic, and medical infrastructure of India. This has become even more challenging, considering the country’s huge population. With the increase in the number of coronavirus disease (COVID) cases, our country has seen an unforeseen, unprecedented rise in a potential life and organ-threatening disease—mucormycosis. Mucormycosis is a deadly, extremely morbid, possibly life-threatening, and most feared complication of the coronavirus, caused by environmental molds belonging to the order Mucorales. Here, we report 2 cases of massive epistaxis due to internal carotid artery (ICA) pseudoaneurysm secondary to mucormycosis, post-COVID-19 pneumonia, which was managed by the endovascular route. To the best of our knowledge, there is very sparse literature available describing endovascular treatment of intracranial ICA pseudoaneurysm in a patient with COVID-induced mucormycosis.
Idiopathic myointimal hyperplasia of mesenteric veins: radiological evaluation using CT angiography
Authors: Morimura Fumio , Edo Hiromi , Niwa Takafumi , Sugiura Hiroaki , Suyama Yohsuke , Okazaki Soya , Narimatsu Kazuyuki , Ohno Hiroki , Okamoto Koichi , Ueno Hideki , Yoshimatsu Shinya , Miyai Kosuke , Hamamoto Kohei , Shinmoto Hiroshi 
Published: January 2024

Abstract
A 44-year-old man presented with a chief complaint of constipation. Initial contrast-enhanced CT showed extensive bowel wall thickening, mainly in the left colon, with a thin cord-like inferior mesenteric vein (IMV), in contrast to ectatic mesenteric venous branches, suggesting bowel ischaemia owing to venous stasis. One month later, at the time of symptom exacerbation, CT angiography showed a cord-like IMV and ectatic mesenteric venous branches with early enhancement, suggesting the presence of an arteriovenous fistula (AVF). Owing to the progression of bowel ischaemia and necrosis with peritonitis, emergency surgery was performed. Surgical specimens showed focal myointimal hyperplasia of the proximal mesenteric veins in both ischaemic and non-ischaemic lesions of the resected colon, thus leading to the diagnosis of idiopathic myointimal hyperplasia of mesenteric veins (IMHMV) when combined with the clinical and imaging findings. IMHMV is a bowel ischaemic disease caused by non-thrombotic venous obstruction that requires bowel resection and has been suggested to be associated with AVF. Cord-like IMV and AVF in the mesentery are important CT findings that characterize IMHMV. CT angiography is useful in diagnosing IMHMV.
Outcomes after distal pancreatectomy with or without splenectomy for intraductal papillary mucinous neoplasm: international multicentre cohort study
Authors: Gorris Myrte , van Bodegraven Eduard A , Abu Hilal Mohammad , Bolm Louisa , Busch Olivier R , del Chiaro Marco , Habib Joseph , Hasegawa Kiyoshi , He Jin , van Hooft Jeanin E , Jang Jin-Young , Javed Ammar A , Kazami Yusuke , Kwon Wooil , Lee Mirang , Liu Rong , Motoi Fuyuhiko , Perri Giampaolo , Saiura Akio , Salvia Roberto , Sasanuma Hideki , Takeda Yoshinori , Wolfgang Christopher , Zelga Piotr , Castillo Carlos Fernandez - del , Marchegiani Giovanni , Besselink Marc G 
Published: January 2024

Abstract

Background
International guidelines on intraductal papillary mucinous neoplasm (IPMN) recommend a formal oncological resection including splenectomy when distal pancreatectomy is indicated. This study aimed to compare oncological and surgical outcomes after distal pancreatectomy with or without splenectomy in patients with presumed IPMN.

Methods
An international, retrospective cohort study was undertaken in 14 high-volume centres from 7 countries including consecutive patients after distal pancreatectomy for IPMN (2005–2019). Patients were divided into spleen-preserving distal pancreatectomy (SPDP) and distal pancreatectomy with splenectomy (DPS). The primary outcome was lymph node metastasis (LNM). Secondary outcomes were overall survival, duration of operation, blood loss, and secondary splenectomy.

Results
Overall, 700 patients were included after distal pancreatectomy for IPMN; 123 underwent SPDP (17.6%) and 577 DPS (82.4%). The rate of malignancy was 29.6% (137 patients) and the overall rate of LNM 6.7% (47 patients). Patients with preoperative suspicion of malignancy had a LNM rate of 17.2% (23 of 134) versus 4.3% (23 of 539) among patients without suspected malignancy (P &lt; 0.001). Overall, SPDP was associated with a shorter operating time (median 180 versus 226 min; P = 0.001), less blood loss (100 versus 336 ml; P = 0.001), and shorter hospital stay (5 versus 8 days; P &lt; 0.001). No significant difference in overall survival was observed between SPDP and DPS for IPMN after correction for prognostic factors (HR 0.50, 95% c.i. 0.22 to 1.18; P = 0.504).

Conclusion
This international cohort study found LNM in 6.7% of patients undergoing distal pancreatectomy for IPMN. In patients without preoperative suspicion of malignancy, SPDP seemed oncologically safe and was associated with improved short-term outcomes compared with DPS.