bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symptomatic atherosclerotic plaque progression in a first-generation carotid stent: management and 5-year clinical and imaging outcome—a case report
Authors: Tekieli Lukasz , Mazurek Adam , Pieniazek Piotr , Musialek Piotr 
Published: December 2021

Abstract

Background
Restenosis in first-generation (single-layer) carotid stents (FGS) is believed to represent an exaggerated healing response of (neo)intimal hyperplasia (NIH) formation. Rather than NIH, we describe symptomatic in-FGS unstable plaque (neo)atherosclerosis mandating re-revascularization. To halt continued plaque evolution, we propose a novel treatment strategy involving a microNet-covered stent (MCS, second-generation carotid stent) to sequestrate the plaque from the vessel lumen. A durable long-term result is documented using multi-modal imaging.

Case summary
With a seemingly optimal result of FGS (Precise) symptomatic carotid lesion revascularization followed by optimal medical therapy, a late (≥3 years) progressive in-stent restenosis (ISR) arose. At Year 11, crescendo ipsilateral transient ischaemic attacks occurred. Angiography showed an ulcerated tight lesion throughout stent length. Intravascular ultrasound (IVUS) virtual histology imaging revealed thin-cap fibroatheroma. Reintervention was performed under distal protection. Undersized balloon predilatation to insert a stent caused symptomatic no-flow, and aspiration catheter was used to reduce the filter load. A MCS (CGuard) was implanted and post-dilated to ensure full lumen gain; IVUS confirmed complete plaque sequestration. The optimal anatomic result remained unchanged throughout 5 years (ultrasound and computed tomography verification); this was accompanied by clinical cure.

Discussion
This is the first demonstration of in-FGS (neo)atherosclerosis resolution using an MCS to sequestrate and insulate the atherosclerotic plaque. We show that ISR may be underlined by atherosclerotic plaque progression via the FGS single-layer stent struts that may show vulnerable plaque phenotype and may be associated with cerebral ischaemia. The anatomically and clinically effective exclusion of the atherosclerotic plaque by an MCS enabled lasting, optimal endovascular reconstruction and clinical cure.
Optical coherence tomographic insights of very late stent thrombosis of a second-generation drug-eluting stent: a case report
Authors: Otaal Parminder Singh , Gawalkar Atit A , Shunmugarajan Ajay 
Published: December 2021

Abstract

Background
Very-very late stent thrombosis (VVLST) occurring more than 5 years after implantation of drug-eluting stent (DES) is extremely rare, being restricted to few case reports. Mainly described with first-generation stents, this life-threatening complication has not been described with later-generation stents. We describe the first case of VVLST occurring 3309 days (&gt;9 years) after implantation of second-generation DES.

Case summary
A 62-year-old man presented with the acute coronary syndrome. He has a history of percutaneous coronary intervention (PCI) to the right coronary artery using the three second-generation DES more than 9 years ago. Coronary angiogram revealed in-stent restenosis (ISR) with doubtful angiographic thrombus. Optical coherence tomography (OCT) confirmed the diagnosis of stent thrombosis (STh) localized to the stent overlap zone with underlying ISR. Patient underwent OCT-guided PCI with DES implantation and was discharged on dual antiplatelet therapy including ticagrelor. He is doing well on follow-up at 6 months.

Discussion
Stent thrombosis can occur in second-generation stents nearly a decade after implant. Stent overlap segment is more prone to neo-atheroma formation and vulnerable plaque leading to STh. In addition to confirming the diagnosis, OCT provides exciting insights into the underlying mechanism. This has implications for long-term antiplatelet therapy in patients implanted with multiple stents.
Development of a machine learning model using electrocardiogram signals to improve acute pulmonary embolism screening
Authors: Somani Sulaiman S , Honarvar Hossein , Narula Sukrit , Landi Isotta , Lee Shawn , Khachatoorian Yeraz , Rehmani Arsalan , Kim Andrew , De Freitas Jessica K , Teng Shelly , Jaladanki Suraj , Kumar Arvind , Russak Adam , Zhao Shan P , Freeman Robert , Levin Matthew A , Nadkarni Girish N , Kagen Alexander C , Argulian Edgar , Glicksberg Benjamin S 
Published: December 2021

Abstract

Aims
Clinical scoring systems for pulmonary embolism (PE) screening have low specificity and contribute to computed tomography pulmonary angiogram (CTPA) overuse. We assessed whether deep learning models using an existing and routinely collected data modality, electrocardiogram (ECG) waveforms, can increase specificity for PE detection.

Methods and results
We create a retrospective cohort of 21 183 patients at moderate- to high suspicion of PE and associate 23 793 CTPAs (10.0% PE-positive) with 320 746 ECGs and encounter-level clinical data (demographics, comorbidities, vital signs, and labs). We develop three machine learning models to predict PE likelihood: an ECG model using only ECG waveform data, an EHR model using tabular clinical data, and a Fusion model integrating clinical data and an embedded representation of the ECG waveform. We find that a Fusion model [area under the receiver-operating characteristic curve (AUROC) 0.81 ± 0.01] outperforms both the ECG model (AUROC 0.59 ± 0.01) and EHR model (AUROC 0.65 ± 0.01). On a sample of 100 patients from the test set, the Fusion model also achieves greater specificity (0.18) and performance (AUROC 0.84 ± 0.01) than four commonly evaluated clinical scores: Wells’ Criteria, Revised Geneva Score, Pulmonary Embolism Rule-Out Criteria, and 4-Level Pulmonary Embolism Clinical Probability Score (AUROC 0.50–0.58, specificity 0.00–0.05). The model is superior to these scores on feature sensitivity analyses (AUROC 0.66–0.84) and achieves comparable performance across sex (AUROC 0.81) and racial/ethnic (AUROC 0.77–0.84) subgroups.

Conclusion
Synergistic deep learning of ECG waveforms with traditional clinical variables can increase the specificity of PE detection in patients at least at moderate suspicion for PE.
Cognitive Performance in Remote Work: Evidence from Professional Chess
Authors: Künn Steffen , Seel Christian , Zegners Dainis 
Published: December 2021

Abstract
During the COVID-19 pandemic, traditional (offline) chess tournaments were prohibited and instead held online. We exploit this unique setting to assess the impact of remote work policies on the cognitive performance of individuals. Using the artificial intelligence embodied in a powerful chess engine to assess the quality of chess moves and associated errors, we find a statistically and economically significant decrease in performance when an individual competes remotely versus offline in a face-to-face setting. The effect size decreases over time, suggesting an adaptation to the new remote setting.
Contemporary surgical outcome and symptomatic relief following vascular ring surgery in children: effect of prenatal diagnosis
Authors: Swarnkar Parinita , Speggiorin Simone , Austin B Conal , Nyman Andrew , Salih Caner , Zidere Vita , Simpson John M , Vigneswaran Trisha V 
Published: December 2021

AbstractOBJECTIVESOur goal was to describe postoperative complications and outcomes in a large contemporary cohort of children with an isolated double aortic arch (DAA) or a right aortic arch (RAA) with left arterial ligament and to assess the impact of foetal diagnosis on outcomes.METHODSWe performed a retrospective analysis of all patients who underwent surgery for DAA or RAA with left arterial ligament between 2005 and 2019.RESULTSA total of 132 children were operated on for a DAA (n = 77) or a RAA (n = 55). Prenatal diagnosis was made in 100/132 (75.8%). Median age at surgery for DAA was 5.0 (1.7–13.3) months and for RAA was 13.9 (6.4–20.1) months. There was no difference in the age at surgery between the prenatal and postnatal cases (8.6 [4.0–15.6] vs 5.4 months [1.8–17.7]; P = 0.37). No surgical deaths occurred. Vocal cord palsy was the most common complication, occurring in 12/132 (9%): of these, 11 resolved spontaneously and 1 required a temporary tracheostomy. Logistic regression demonstrated that older age at operation was the only predictor for a postoperative complication (P = 0.02). Overall, 21/67 (31%) of prenatally detected, symptomatic cases reported residual symptoms/signs 1 year after surgery compared to 18/28 (64%) of postnatally detected cases. Postnatal diagnosis was associated with persistent postoperative symptoms/signs [P = 0.006, odds ratio = 3.9 (95% confidence interval 1.5–9.4)].CONCLUSIONSSurgery to relieve a vascular ring resolves trache-oesophageal compressive symptoms in most cases, but parents/patients should be aware that symptoms/signs may persist in the first postoperative year despite effective release of the vascular ring. Earlier surgery and prenatal diagnosis may improve outcomes.
Construction of a gut microbiota-gene-pathway network to reveal the molecular mechanisms underlying right- and left-sided colorectal cancer
Authors: Du Kunli , Wang Xinyou , Li Shisen , Ren Jiahui , Li Ruikai , Wang Mian , Feng Fan , Du Hansong , Zheng Jianyong 
Published: December 2021

Abstract
Aiming to reveal the molecular mechanisms involved in right- and left-sided colorectal cancer (CRC) development, CRC gene expression data and a microorganism atlas were downloaded from The Cancer Genome Atlas and The Cancer Microbiome Atlas, respectively. The R package was used to screen differentially expressed genes (DEGs) between right- and left-sided CRC samples and identify those related to prognosis, a correlation analysis was performed between DEGs and prognosis-related microbiota, and an interaction network was created using Cytoscape. Finally, a taxon set enrichment analysis of the microbiota was performed and a gene-genus-pathway network was constructed after GO and KEGG analyses. In total, 9 out of 1557 identified DEGs had a significant correlation with prognosis, whereas 3 out of 211 bacterial genera (Fusobacterium, Bacteroides, and Parabacteroides) showed a significant correlation with prognosis. DEGs were mainly enriched in the PPAR pathway and vitamin metabolic and transport processes. According to a taxon set enrichment analysis, the microbes in the integrated network were significantly abundant in 28 host-intrinsic, 2 host-extrinsic, and 1 environment taxon sets. This study provides new insights for understanding the molecular mechanisms of left- and right- CRC.
Changes in fruit pigment accumulation, chloroplast development, and transcriptome analysis in the CRISPR/Cas9-mediated knockout of Stay-green 1 (slsgr1) mutant
Authors: Ma Liqun , Zeng Ni , Cheng Ke , Li Jinyan , Wang Keru , Zhang Chunjiao , Zhu Hongliang 
Published: December 2021

Abstract
The green-flesh (gf) mutant of the tomato fruit ripen to a muddy brown color and has been demonstrated previously to be a loss-of-function mutant. Here, we provide more evidence to support this view that SlSGR1 is involved in color change in ripening tomato fruits. Knocking out SlSGR1 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy showed obviously a muddy brown color with significantly higher chlorophyll and carotenoid content compared with wild-type (WT) fruits. To further verify the role of SlSGR1 in fruit color change, we performed transcriptome deep sequencing (RNA-seq) analysis, where a total of 354 differentially expressed genes (124/230 downregulated/upregulated) were identified between WT and slsgr1. Additionally, the expression of numerous genes associated with photosynthesis and chloroplast function changed significantly when SlSGR1 was knocked out. Taken together, these results indicate that SlSGR1 is involved in color change in ripening fruit via chlorophyll degradation and carotenoid biosynthesis.
Genome Sequence ofElaeagnus mollis, the First Chromosome-Level Genome of the Family Elaeagnaceae
Authors: Ren Baoqing , Ru Dafu , Chen Luqin , Duan Na , Li Yong , Shi Jianwei , Cao Jianting , Liu Bingbing 
Published: November 2021

AbstractElaeagnus mollis Diels (Elaeagnaceae) is a species of shrubs and/or dwarf trees that produces highly nutritious nuts with abundant oil and pharmaceutical properties. It is endemic to China but endangered. Therefore, to facilitate the protection of its genetic resources and the development of its commercially attractive traits we generated a high-quality genome of E. mollis. The contig version of the genome (630.96 Mb long) was assembled into 14 chromosomes using Hi-C data, with contig and scaffold N50 values of 18.40 and 38.86 Mb, respectively. Further analyses identified 397.49 Mb (63.0%) of repetitive sequences and 27,130 protein-coding genes, of which 26,725 (98.5%) were functionally annotated. Benchmarking Universal Single-Copy Ortholog assessment indicated that 98.0% of highly conserved plant genes are completely present in the genome. This is the first reference genome for any species of Elaeagnaceae and should greatly facilitate future efforts to conserve, utilize, and elucidate the evolution of this endangered endemic species.
100 years post-insulin: immunotherapy as the next frontier in type 1 diabetes
Authors: Pearson James A , McKinney Eoin F , Walker Lucy S K 
Published: December 2021

SummaryType 1 diabetes (T1D) is an autoimmune disease characterised by T cell-mediated destruction of the insulin-producing β cells in the pancreas. Similar to other autoimmune diseases, the incidence of T1D is increasing globally. The discovery of insulin 100 years ago dramatically changed the outlook for people with T1D, preventing this from being a fatal condition. As we celebrate the centenary of this milestone, therapeutic options for T1D are once more at a turning point. Years of effort directed at developing immunotherapies are finally starting to pay off, with signs of progress in new onset and even preventative settings. Here, we review a selection of immunotherapies that have shown promise in preserving β cell function and highlight future considerations for immunotherapy in the T1D setting.
The case for wearable proximity devices to inform physical distancing among healthcare workers
Authors: Keller Sara C , Salinas Alejandra B , Oladapo-Shittu Opeyemi , Cosgrove Sara E , Lewis-Cherry Robin , Osei Patience , Gurses Ayse P , Jacak Ron , Zudock Kristina K , Blount Kianna M , Bowden Kenneth V , Rock Clare , Sick-Samuels Anna C , Vecchio-Pagan Briana 
Published: December 2021

Abstract

Objective
Despite the importance of physical distancing in reducing SARS-CoV-2 transmission, this practice is challenging in healthcare. We piloted use of wearable proximity beacons among healthcare workers (HCWs) in an inpatient unit to highlight considerations for future use of trackable technologies in healthcare settings.

Materials and Methods
We performed a feasibility pilot study in a non-COVID adult medical unit from September 28 to October 28, 2020. HCWs wore wearable proximity beacons, and interactions defined as &lt;6 feet for ≥5 s were recorded. Validation was performed using direct observations.

Results
A total of 6172 close proximity interactions were recorded, and with the removal of 2033 false-positive interactions, 4139 remained. The highest proportion of interactions occurred between 7:00 Am–9:00 Am. Direct observations of HCWs substantiated these findings.

Discussion
This pilot study showed that wearable beacons can be used to monitor and quantify HCW interactions in inpatient settings.

Conclusion
Technology can be used to track HCW physical distancing.
The role and clinical relevance of the ligamentum teres: long-term outcomes after hip arthroscopic surgery of cam-type femoroacetabular impingement
Authors: Lee Jeong-Kil , Hwang Deuk-Soo , Kim Sang-Bum , Kang Chan , Hwang Jung-Mo , Lee Gi-Soo , Park Eugene Jae-Jin 
Published: December 2021

ABSTRACT
We aimed to compare clinical and radiologic outcomes in patients with cam-type femoroacetabular impingement (FAI), with and without a partial ligamentum teres (LT) tear, who underwent hip arthroscopy (HA) with ≥10 years of follow-up. Among the patients who underwent HA for a cam-type FAI diagnosis with a labral tear, 28 patients (28 hips) with a partial LT tear and 87 patients (99 hips) with an intact LT were assigned to Groups A and B, respectively. All patients underwent partial labral debridement and femoroplasty. Debridement and thermal shrinkage were performed for LT tears. The grade of chondral damage was measured intraoperatively. Clinical items were assessed preoperatively and at the last follow-up. Patients’ satisfaction with the surgery and changes in postoperative sports ability in those who had previously been active in sports were assessed at the last follow-up. The Tönnis grade was assessed preoperatively and at the last follow-up for radiologic evaluation. Chondral damage to the acetabular and femoral head detected intraoperatively was significantly different between the groups (P = 0.005 and P &lt; 0.001). At the last follow-up, Group A patients experienced more difficulty performing sports activities than Group B patients (P = 0.056), and significantly, more Group A patients had stopped exercising despite their active participation in sports preoperatively (P = 0.002). Regarding the Tönnis grade, significant differences were found only at the final follow-up (P = 0.020). Patients with partial LT tear showed a higher grade of chondral damage, experienced decreased exercise capacity and had significantly worsened Tönnis grades, suggesting hip osteoarthritis progression compared to those with an intact LT.
Primary meningococcal septic arthritis associated with joint calcium oxalate crystals: A case report and review of the literature
Authors: Cimé-Aké Erik , Carranza-Enríquez Fabián , Hurtado-Arias José Joel , Muñoz-Castañeda Wallace Rafael A , Medina-Fonseca Benjamín , Barrera-Vargas Ana , Lizardo-Thiebaud María J , Saeb-Lima Marcela , Merayo-Chalico Javier 
Published: December 2021

ABSTRACT
Primary meningococcal septic arthritis (PMSA) is an extremely rare local infection by Neisseria meningitidis in the absence of meningitis or meningococcaemia syndrome. A 30-year-old healthy, immunocompetent man presented with arthralgia, fever, chest rash, and significant swelling of the right knee. On admission, a disseminated maculopapular and purpuric rash, oligoarthritis, neutrophilia, and elevated acute phase reactants were documented. Following arthrocentesis of the right knee, isolation of N. meningitidis and the presence of calcium oxalate crystals in the synovial fluid were reported. The diagnosis of PMSA was made. Histological analysis of the skin lesion showed leucocytoclastic vasculitis. He was treated with intravenous ceftriaxone plus open surgical drainage and ambulatory cefixime with adequate response. After 1 month, he presented resolution of the pathological process. We performed an extensive review of the literature, finding that the key elements supporting the diagnosis of PMSA are prodromal upper respiratory tract symptoms and skin involvement prior to or synchronous with the arthritis. Also, the most frequently involved joint is the knee. This report is the first case of a patient presenting with PMSA associated with calcium oxalate crystals in the synovial fluid. Herein, we discuss the most frequent clinical manifestations, the unusual histological features, the recommended treatment, and the reported prognosis of this rare entity.
Misregulation of the expression and activity of DNA methyltransferases in cancer
Authors: Mensah Isaiah K , Norvil Allison B , AlAbdi Lama , McGovern Sarah , Petell Christopher J , He Ming , Gowher Humaira 
Published: December 2021

Abstract
In mammals, DNA methyltransferases DNMT1 and DNMT3’s (A, B and L) deposit and maintain DNA methylation in dividing and nondividing cells. Although these enzymes have an unremarkable DNA sequence specificity (CpG), their regional specificity is regulated by interactions with various protein factors, chromatin modifiers, and post-translational modifications of histones. Changes in the DNMT expression or interacting partners affect DNA methylation patterns. Consequently, the acquired gene expression may increase the proliferative potential of cells, often concomitant with loss of cell identity as found in cancer. Aberrant DNA methylation, including hypermethylation and hypomethylation at various genomic regions, therefore, is a hallmark of most cancers. Additionally, somatic mutations in DNMTs that affect catalytic activity were mapped in Acute Myeloid Leukemia cancer cells. Despite being very effective in some cancers, the clinically approved DNMT inhibitors lack specificity, which could result in a wide range of deleterious effects. Elucidating distinct molecular mechanisms of DNMTs will facilitate the discovery of alternative cancer therapeutic targets. This review is focused on: (i) the structure and characteristics of DNMTs, (ii) the prevalence of mutations and abnormal expression of DNMTs in cancer, (iii) factors that mediate their abnormal expression and (iv) the effect of anomalous DNMT-complexes in cancer.
RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes
Authors: Stephenson Maria , Nip Ka Ming , HafezQorani Saber , Gagalova Kristina K , Yang Chen , Warren René L , Birol Inanc 
Published: December 2021

Abstract
Recent advances in single-cell RNA sequencing technologies have made detection of transcripts in single cells possible. The level of resolution provided by these technologies can be used to study changes in transcript usage across cell populations and help investigate new biology. Here, we introduce RNA-Scoop, an interactive cell cluster and transcriptome visualization tool to analyze transcript usage across cell categories and clusters. The tool allows users to examine differential transcript expression across clusters and investigate how usage of specific transcript expression mechanisms varies across cell groups.
Structure-based deep learning for binding site detection in nucleic acid macromolecules
Authors: Kozlovskii Igor , Popov Petr 
Published: December 2021

Abstract
Structure-based drug design (SBDD) targeting nucleic acid macromolecules, particularly RNA, is a gaining momentum research direction that already resulted in several FDA-approved compounds. Similar to proteins, one of the critical components in SBDD for RNA is the correct identification of the binding sites for putative drug candidates. RNAs share a common structural organization that, together with the dynamic nature of these molecules, makes it challenging to recognize binding sites for small molecules. Moreover, there is a need for structure-based approaches, as sequence information only does not consider conformation plasticity of nucleic acid macromolecules. Deep learning holds a great promise to resolve binding site detection problem, but requires a large amount of structural data, which is very limited for nucleic acids, compared to proteins. In this study we composed a set of ∼2000 nucleic acid-small molecule structures comprising ∼2500 binding sites, which is ∼40-times larger than previously used one, and demonstrated the first structure-based deep learning approach, BiteNetN, to detect binding sites in nucleic acid structures. BiteNetN operates with arbitrary nucleic acid complexes, shows the state-of-the-art performance, and can be helpful in the analysis of different conformations and mutant variants, as we demonstrated for HIV-1 TAR RNA and ATP-aptamer case studies.