A case of hyalinizing trabecular tumor of the thyroid: diagnostic significance of PAX8-GLIS3 fusion

BACKGROUND

Hyalinizing trabecular tumor (HTT) is an uncommon follicular cell-derived thyroid tumor classified as a low-risk neoplasm by the World Health Organization Classification of Tumors of Endocrine Organs, 5th edition. The PAX8-GLIS3 gene fusion is reportedly a pathognomonic genetic alteration of HTT.

CASE PRESENTATION

A 43-year-old Japanese female was incidentally discovered to have an 8-mm, well-defined, hypoechoic mass in the left lobe of the thyroid gland by ultrasound examination. Contrast-enhanced computed tomography scan revealed a solid mass exhibiting slight homogeneous enhancement in the lower pole of the thyroid gland. The mass was diagnosed as atypia of undetermined significance by fine-needle aspiration cytology. The patient underwent left hemithyroidectomy with routine central compartment dissection. Histologic findings revealed tumor cells with elongated nuclei and intranuclear pseudoinclusions arranged with trabeculae architecture or small nests in hyalinized stroma. Weak membranous and cytoplasmic staining was found by MIB1 (Ki-67) immunostaining. The final diagnosis was HTT of the thyroid gland. Next-generation sequencing genetic analysis of a surgical specimen revealed no pathologic mutations, including BRAF, H/K/NRAS, or RET-PTC fusions. The PAX8-GLIS3 fusion was detected by RT-PCR.

CONCLUSIONS

A rare case of HTT was demonstrated through imaging, cytologic, histologic and molecular investigations. PAX8-GLIS3 fusion detected by RT-PCR and Sanger sequencing was confirmed to be a genetic hallmark of HTT.

Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis

BACKGROUND

Cell-cell interaction factors that facilitate the progression of adenoma to sporadic colorectal cancer (CRC) remain unclear, thereby hindering patient survival.

METHODS

We performed spatial transcriptomics on five early CRC cases, which included adenoma and carcinoma, and one advanced CRC. To elucidate cell-cell interactions within the tumour microenvironment (TME), we investigated the colocalisation network at single-cell resolution using a deep generative model for colocalisation analysis, combined with a single-cell transcriptome, and assessed the clinical significance in CRC patients.

FINDINGS

CRC cells colocalised with regulatory T cells (Tregs) at the adenoma-carcinoma interface. At early-stage carcinogenesis, cell-cell interaction inference between colocalised adenoma and cancer epithelial cells and Tregs based on the spatial distribution of single cells highlighted midkine (MDK) as a prominent signalling molecule sent from tumour epithelial cells to Tregs. Interaction between MDK-high CRC cells and SPP1+ macrophages and stromal cells proved to be the mechanism underlying immunosuppression in the TME. Additionally, we identified syndecan4 (SDC4) as a receptor for MDK associated with Treg colocalisation. Finally, clinical analysis using CRC datasets indicated that increased MDK/SDC4 levels correlated with poor overall survival in CRC patients.

INTERPRETATION

MDK is involved in the immune tolerance shown by Tregs to tumour growth. MDK-mediated formation of the TME could be a potential target for early diagnosis and treatment of CRC.

FUNDING

Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Science Research; OITA Cancer Research Foundation; AMED under Grant Number; Japan Science and Technology Agency (JST); Takeda Science Foundation; The Princess Takamatsu Cancer Research Fund.

Single-cell colocalization analysis using a deep generative model

Analyzing colocalization of single cells with heterogeneous molecular phenotypes is essential for understanding cell-cell interactions, and cellular responses to external stimuli and their biological functions in diseases and tissues. However, existing computational methodologies identified the colocalization patterns between predefined cell populations, which can obscure the molecular signatures arising from intercellular communication. Here, we introduce DeepCOLOR, a computational framework based on a deep generative model that recovers intercellular colocalization networks with single-cell resolution by the integration of single-cell and spatial transcriptomes. Along with colocalized population detection accuracy that is superior to existing methods in simulated dataset, DeepCOLOR identified plausible cell-cell interaction candidates between colocalized single cells and segregated cell populations defined by the colocalization relationships in mouse brain tissues, human squamous cell carcinoma samples, and human lung tissues infected with SARS-CoV-2. DeepCOLOR is applicable to studying cell-cell interactions behind various spatial niches. A record of this paper's transparent peer review process is included in the supplemental information.

Salivary Duct Carcinoma Arising in the Submandibular Gland in a Patient with Neurofibromatosis Type 1

A 71-year-old man with neurofibromatosis type 1 (NF1) presented to our department with a 1-week history of a painful mass in the left submandibular area. Computed tomography (CT) and magnetic resonance imaging revealed an irregular-shaped tumor with a diameter of 2.0 cm in the left submandibular gland and a metastatic lymph node with a diameter of 1.0 cm adjacent to the tumor. Fluorodeoxyglucose-positron emission tomography/CT revealed increased uptake in the tumor. Fine-needle aspiration cytology revealed atypical cells, suggesting salivary duct carcinoma (SDC). Left neck dissection with resection of the tumor and submandibular gland was performed under general anesthesia. Histologic examination revealed ductal formation with a solid, cystic, cribriform, and papillary structure with intraductal comedonecrosis, diagnosing as SDC originating in the submandibular gland (pT3N1M0 pStage III). Mutational analysis of 160 cancer-related genes by next-generation sequencing (NGS) revealed a germline and frameshift mutation in the NF1 gene (p.R2408Kfs*14) and a somatic and frameshift mutation in the TP53 gene (p.C176Wfs*22). The patient received postoperative radiotherapy to the left neck area at 66 Gy. No evidence of recurrence or metastasis has been observed as of 10 months postoperatively. This is the first reported case of SDC in the submandibular gland in a patient with NF1. The mutational data by NGS may contribute to a better understanding of the oncogenesis of SDC in patients with NF1.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

BRAF V600E mutation co-existing with oncogenic mutations is associated with aggressive clinicopathologic features and poor prognosis in papillary thyroid carcinoma

BACKGROUND

The aim of this study was to evaluate the correlation among mutations in cancer-related genes, clinicopathologic features, and clinical outcome in classical papillary thyroid carcinoma (PTC).

PATIENTS AND METHODS

A total of 130 patients with classical PTC who underwent curative surgery between April 2012 and June 2023 at Hokuto Hospital were included. Mutations in targeted regions of 160 cancer-related genes were detected by next-generation sequencing (NGS)-based cancer panel testing.

RESULTS

The BRAF V600E mutation was detected in 108 (83.1%) of 130 PTC patients. Among the 108 patients with the BRAF V600E mutation, other co-existing oncogenic mutations were found in 12 (9.2%) patients. When we divided into 3 groups of no mutations, BRAF V600E mutation alone, and BRAF V600E and other oncogenic mutations, significant differences were observed in terms of tracheal invasion (P = 0.0024), and bilateral neck lymph node metastasis (P = 0.0047). Kaplan-Meier analysis of overall survival (OS) revealed patients with BRAF V600E and other oncogenic mutations had significantly poorer survival than those with BRAF V600E mutation alone (P = 0.0026). Multivariate cox proportional hazard analysis revealed BRAF V600E and other oncogenic mutations was an independent prognostic factor for OS (HR: 10.559; 95%CI: 1.007-110.656, P = 0.0493).

CONCLUSIONS

The BRAF V600E mutation co-existing with other oncogenic mutations but not the BRAF V600E mutation alone was associated with aggressive clinicopathologic features, resulting in poor prognosis in patients with classical PTC. Detection of oncogenic mutations using NGS-based cancer panel testing could enhance understanding of the clinical features of classical PTC.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

Internal carotid artery dissection caused by elongated styloid process

A 69-year-old man with impaired consciousness, right hemiplegia, and aphasia was admitted to our emergency room for thorough examination. Magnetic resonance imaging (MRI) and 3-dimensional computed tomography (3D CT) scan of the head revealed a cerebral infarction due to dissection of the left internal carotid artery. Contrast-enhanced CT prior to internal carotid artery stenting showed that the left elongated styloid process ran in close proximity to the left internal carotid artery, with a minimum distance of 2 mm. The patient underwent stenting at the internal carotid artery 16 days after disease onset. The patient was referred to our department for left elongated styloid process resection to reduce the risk of further internal carotid artery injury. Resection of the left styloid process through a cervical incision was performed. Six months after surgery, there was no recurrence of the internal carotid artery dissection.

Subclonal accumulation of immune escape mechanisms in microsatellite instability-high colorectal cancers

BACKGROUND

Intratumor heterogeneity (ITH) in microsatellite instability-high (MSI-H) colorectal cancer (CRC) has been poorly studied. We aimed to clarify how the ITH of MSI-H CRCs is generated in cancer evolution and how immune selective pressure affects ITH.

METHODS

We reanalyzed public whole-exome sequencing data on 246 MSI-H CRCs. In addition, we performed a multi-region analysis from 6 MSI-H CRCs. To verify the process of subclonal immune escape accumulation, a novel computational model of cancer evolution under immune pressure was developed.

RESULTS

Our analysis presented the enrichment of functional genomic alterations in antigen-presentation machinery (APM). Associative analysis of neoantigens indicated the generation of immune escape mechanisms via HLA alterations. Multiregion analysis revealed the clonal acquisition of driver mutations and subclonal accumulation of APM defects in MSI-H CRCs. Examination of variant allele frequencies demonstrated that subclonal mutations tend to be subjected to selective sweep. Computational simulations of tumour progression with the interaction of immune cells successfully verified the subclonal accumulation of immune escape mutations and suggested the efficacy of early initiation of an immune checkpoint inhibitor (ICI) -based treatment.

CONCLUSIONS

Our results demonstrate the heterogeneous acquisition of immune escape mechanisms in MSI-H CRCs by Darwinian selection, providing novel insights into ICI-based treatment strategies.

Rectangular tapered short stem excellently preserves proximal bone mineral density preservation than tapered wedge short stem

Fitmore stem is a rectangular, tapered, short, cementless stem. A characteristic feature of this stem is that it provides rotational stability due to the high medullary occupancy achieved by its rectangular cross-section and thick antero- posterior width. We aimed to investigate the differences in periprosthetic bone remodelling between a rectangular- tapered short stem and a short tapered-wedge stem. Eighty patients who underwent primary total hip arthroplasty using a rectangular-tapered short stem (Fitmore) or a short tapered-wedge stem (Tri-Lock BPS) were enrolled in this study. Bone mineral densities (BMDs) in the seven Gruen zones were evaluated using dual-energy X-ray absorptiometry at baseline, and at 6 and 24 months postoperatively. Peri-prosthetic BMD and clinical factors were assessed and compared. In addition, correlations between periprosthetic BMD changes and stem anteversion error were analyzed using Pearson's correlation coefficient in the two groups. A significantly better postoperative periprosthetic BMD change was found in zones 1 and 7 in the rectangular-tapered group. Additionally, no significant correlation was observed between stem anteversion error and periprosthetic BMD changes in the rectangular-tapered groups. However, in the tapered-wedge group, there were significant negative correlations between the stem anteversion error and BMD changes at 6 months and 24 months in zones 1 and 7. In the rectangular-tapered group, a significantly better postoperative periprosthetic BMD change was found particularly in the region proximal to the stem. Rectangular-tapered short stem can be more resistant to rotation due to higher medullary occupancy and may lead to better periprosthetic BMD than the tapered-wedge short stem, especially in the proximal region of the stem.

Topological data analysis of protein structure and inter/intra-molecular interaction changes attributable to amino acid mutations

The presence of some amino acid mutations in the amino acid sequence that determines a protein's structure can significantly affect that 3D structure and its biological function. However, the effects upon structural and functional changes differ for each displaced amino acid, and it is very difficult to predict these changes in advance. Although computer simulations are very effective at predicting conformational changes, they struggle to determine whether the amino acid mutation of interest induces sufficient conformational changes, unless the researcher is a specialist in molecular structure calculations. Therefore, we created a framework that efficiently utilizes molecular dynamics and persistent homology methods to identify amino acid mutations that induce structural changes. We show that this framework can be used not only to predict conformational changes produced by amino acid mutations but also to extract groups of mutations that significantly alter similar molecular interactions, by capturing the resultant protein-protein interaction changes.

Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer

The cellular interactions in the tumor microenvironment of colorectal cancer (CRC) are poorly understood, hindering patient treatment. In the current study, we investigate whether events occurring at the invasion front are of particular importance for CRC treatment strategies. To this end, we analyze CRC tissues by combining spatial transcriptomics from patients with a public single-cell transcriptomic atlas to determine cell-cell interactions at the invasion front. We show that CRC cells are localized specifically at the invasion front. These cells induce human leukocyte antigen G (HLA-G) to produce secreted phosphoprotein 1 (SPP1)+ macrophages while conferring CRC cells with anti-tumor immunity, as well as proliferative and invasive properties. Taken together, these findings highlight the signaling between CRC cell populations and stromal cell populations at the cellular level.

Analyzing Antibody Repertoire Using Next-Generation Sequencing and Machine Learning

Advances in high-throughput sequencing technologies have enabled comprehensive sequencing of the immune repertoire. Since repertoire analysis can help to explain the relationship between the immune system and diseases, several methods have been developed for repertoire analysis. Here, using simulated and real-world datasets, we describe how to use DeepRC, a method that applies cutting-edge machine learning techniques.

Nucleic acid-triggered tumoral immunity propagates pH-selective therapeutic antibodies through tumor-driven epitope spreading

Important roles of humoral tumor immunity are often pointed out; however, precise profiles of dominant antigens and developmental mechanisms remain elusive. We systematically investigated the humoral antigens of dominant intratumor immunoglobulin clones found in human cancers. We found that approximately half of the corresponding antigens were restricted to strongly and densely negatively charged polymers, resulting in simultaneous reactivities of the antibodies to both densely sulfated glycosaminoglycans (dsGAGs) and nucleic acids (NAs). These anti-dsGAG/NA antibodies matured and expanded via intratumoral immunological driving force of innate immunity via NAs. These human cancer-derived antibodies exhibited acidic pH-selective affinity across both antigens and showed specific reactivity to diverse spectrums of human tumor cells. The antibody-drug conjugate exerted therapeutic effects against multiple cancers in vivo by targeting cell surface dsGAG antigens. This study reveals that intratumoral immunological reactions propagate tumor-oriented immunoglobulin clones and demonstrates a new therapeutic modality for the universal treatment of human malignancies.

Hypertriton Production in p-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The study of nuclei and antinuclei production has proven to be a powerful tool to investigate the formation mechanism of loosely bound states in high-energy hadronic collisions. The first measurement of the production of _{Λ}^{3}H in p-Pb collisions at sqrt[s_{NN}]=5.02  TeV is presented in this Letter. Its production yield measured in the rapidity interval -1<y<0 for the 40% highest-multiplicity p-Pb collisions is dN/dy=[6.3±1.8(stat)±1.2(syst)]×10^{-7}. The measurement is compared with the expectations of statistical hadronization and coalescence models, which describe the nucleosynthesis in hadronic collisions. These two models predict very different yields of the hypertriton in charged particle multiplicity environments relevant to small collision systems such as p-Pb, and therefore the measurement of dN/dy is crucial to distinguish between them. The precision of this measurement leads to the exclusion with a significance larger than 6.9σ of some configurations of the statistical hadronization model, thus constraining the theory behind the production of loosely bound states at hadron colliders.

Polarization of Λ and Λ[over ¯] Hyperons along the Beam Direction in Pb-Pb Collisions at sqrt[s]_{NN}=5.02 TeV

The polarization of the Λ and Λ[over ¯] hyperons along the beam (z) direction, P_{z}, has been measured in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV recorded with ALICE at the Large Hadron Collider (LHC). The main contribution to P_{z} comes from elliptic flow-induced vorticity and can be characterized by the second Fourier sine coefficient P_{z,s2}=⟨P_{z}sin(2φ-2Ψ_{2})⟩, where φ is the hyperon azimuthal emission angle and Ψ_{2} is the elliptic flow plane angle. We report the measurement of P_{z,s2} for different collision centralities and in the 30%-50% centrality interval as a function of the hyperon transverse momentum and rapidity. The P_{z,s2} is positive similarly as measured by the STAR Collaboration in Au-Au collisions at sqrt[s_{NN}]=200  GeV, with somewhat smaller amplitude in the semicentral collisions. This is the first experimental evidence of a nonzero hyperon P_{z} in Pb-Pb collisions at the LHC. The comparison of the measured P_{z,s2} with the hydrodynamic model calculations shows sensitivity to the competing contributions from thermal and the recently found shear-induced vorticity, as well as to whether the polarization is acquired at the quark-gluon plasma or the hadronic phase.

Measurement of the Groomed Jet Radius and Momentum Splitting Fraction in pp and Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

This article presents groomed jet substructure measurements in pp and Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV with the ALICE detector. The soft drop grooming algorithm provides access to the hard parton splittings inside a jet by removing soft wide-angle radiation. We report the groomed jet momentum splitting fraction, z_{g}, and the (scaled) groomed jet radius, θ_{g}. Charged-particle jets are reconstructed at midrapidity using the anti-k_{T} algorithm with resolution parameters R=0.2 and R=0.4. In heavy-ion collisions, the large underlying event poses a challenge for the reconstruction of groomed jet observables, since fluctuations in the background can cause groomed parton splittings to be misidentified. By using strong grooming conditions to reduce this background, we report these observables fully corrected for detector effects and background fluctuations for the first time. A narrowing of the θ_{g} distribution in Pb-Pb collisions compared to pp collisions is seen, which provides direct evidence of the modification of the angular structure of jets in the quark-gluon plasma. No significant modification of the z_{g} distribution in Pb-Pb collisions compared to pp collisions is observed. These results are compared with a variety of theoretical models of jet quenching, and provide constraints on jet energy-loss mechanisms and coherence effects in the quark-gluon plasma.

A preliminary study of the safety and effectiveness of isoproterenol loading transesophageal echocardiography in atrial fibrillation

Funding Acknowledgements

Type of funding sources: None.

Background

In patients with sludge or severe spontaneous echo contrast (SEC) in the left atrial appendage (LAA), isoproterenol loading transesophageal echocardiography (ISP-TEE) has been reported to check the presence of thrombus in the LAA, as the sludge or severe SEC disappears (Figure 1).

Purpose

The aim of this study was to assess the safety of ISP-TEE for the identification of LAA thrombus and the hemodynamic changes in the LAA caused by ISP loading.

Methods

We prospectively enrolled 25 patients with atrial fibrillation (AF) and sludge or SEC in the LAA who underwent ISP-TEE from April 2020 to July 2021. ISP was administered intravenously to achieve the target heart rate (HR) defined as follows: Max HR [beats per minutes: bpm] = 220 – age (years), Target HR [bpm] = Max HR × 0.8. Patients with tachycardia exceeding Max HR before ISP administration, hemodynamic instability, and other contraindications to ISP were excluded from the study. To assess the safety of ISP-TEE, we evaluated patients’ condition, changes in systolic blood pressure (sBP) and HR before and after ISP loading. We also assessed the presence or absence of worsening heart failure, new arrhythmias other than atrial fibrillation, and cerebral infarction or transient ischemic attack during the examination, and after 24 hours. Hemodynamic evaluation was performed using LAA blood flow velocity, LAA tissue Doppler imaging (TDI) velocity, and LAA volume fraction (LAAVF) defined as follows: LAAVF (%) = (Max LAA volume – Min LAA volume) / Max LAA volume × 100. Quantification of LAA volume was performed using the stacked-contour method of a 3-dimensional TEE full-volume acquisition.

Results

Among 25 patients, 13 patients had sludge or grade3 SEC, 7 patients had grade2 SEC, 5 patients had grade1 SEC. HR after ISP loading was significantly higher than before loading, but sBP did not change significantly before and after ISP loading. No complications due to ISP loading were observed during examination and after 24 hours. After ISP loading, there were 18 patients with grade 1 SEC or no SEC (classified as Group1), 7 patients had residual sludge or grade 2 to 3 SEC (classified as Group2). The differences in LAA blood flow velocity between before and after ISP loading was faster in Group1 than in Group2: 13.0 ± 10.5 vs 2.6 ± 4.2. p = 0.019. The differences in TDI velocity was also faster in Group1 than in Group2: 1.46 ± 1.14 vs 0.19 ± 0.50, p = 0.010. The differences in LAAVF was higher in Group1 than in Group2: 13.7 ± 10.3 vs 2.2 ± 2.0, p = 0.009.

Conclusions

In our study, no complications were observed in ISP-TEE for the identification of LAA thrombus. Patients with grade 1 SEC or no SEC, the LAA function was increased by ISP loading. These results may provide insights into the mechanisms of ISP loading on SEC in the LAA. Abstract Figure.

Measurement of Prompt D^{0}, Λ_{c}^{+}, and Σ_{c}^{0,++}(2455) Production in Proton-Proton Collisions at sqrt[s]=13 TeV

The p_{T}-differential production cross sections of prompt D^{0}, Λ_{c}^{+}, and Σ_{c}^{0,++}(2455) charmed hadrons are measured at midrapidity (|y|<0.5) in pp collisions at sqrt[s]=13  TeV. This is the first measurement of Σ_{c}^{0,++} production in hadronic collisions. Assuming the same production yield for the three Σ_{c}^{0,+,++} isospin states, the baryon-to-meson cross section ratios Σ_{c}^{0,+,++}/D^{0} and Λ_{c}^{+}/D^{0} are calculated in the transverse momentum (p_{T}) intervals 2<p_{T}<12 and 1<p_{T}<24  GeV/c. Values significantly larger than in e^{+}e^{-} collisions are observed, indicating for the first time that baryon enhancement in hadronic collisions also extends to the Σ_{c}. The feed-down contribution to Λ_{c}^{+} production from Σ_{c}^{0,+,++} is also reported and is found to be larger than in e^{+}e^{-} collisions. The data are compared with predictions from event generators and other phenomenological models, providing a sensitive test of the different charm-hadronization mechanisms implemented in the models.

Measurement of the Cross Sections of Ξ_{c}^{0} and Ξ_{c}^{+} Baryons and of the Branching-Fraction Ratio BR(Ξ_{c}^{0}→Ξ^{-}e^{+}ν_{e})/BR(Ξ_{c}^{0}→Ξ^{-}π^{+}) in pp Collisions at sqrt[s]=13 TeV

The p_{T}-differential cross sections of prompt charm-strange baryons Ξ_{c}^{0} and Ξ_{c}^{+} were measured at midrapidity (|y|<0.5) in proton-proton (pp) collisions at a center-of-mass energy sqrt[s]=13  TeV with the ALICE detector at the LHC. The Ξ_{c}^{0} baryon was reconstructed via both the semileptonic decay (Ξ^{-}e^{+}ν_{e}) and the hadronic decay (Ξ^{-}π^{+}) channels. The Ξ_{c}^{+} baryon was reconstructed via the hadronic decay (Ξ^{-}π^{+}π^{+}) channel. The branching-fraction ratio BR(Ξ_{c}^{0}→Ξ^{-}e^{+}ν_{e})/BR(Ξ_{c}^{0}→Ξ^{-}π^{+})=1.38±0.14(stat)±0.22(syst) was measured with a total uncertainty reduced by a factor of about 3 with respect to the current world average reported by the Particle Data Group. The transverse momentum (p_{T}) dependence of the Ξ_{c}^{0}- and Ξ_{c}^{+}-baryon production relative to the D^{0} meson and to the Σ_{c}^{0,+,++}- and Λ_{c}^{+}-baryon production are reported. The baryon-to-meson ratio increases toward low p_{T} up to a value of approximately 0.3. The measurements are compared with various models that take different hadronization mechanisms into consideration. The results provide stringent constraints to these theoretical calculations and additional evidence that different processes are involved in charm hadronization in electron-positron (e^{+}e^{-}) and hadronic collisions.

Λ_{c}^{+} Production and Baryon-to-Meson Ratios in pp and p-Pb Collisions at sqrt[s_{NN}]=5.02 TeV at the LHC

The prompt production of the charm baryon Λ_{c}^{+} and the Λ_{c}^{+}/D^{0} production ratios were measured at midrapidity with the ALICE detector in pp and p-Pb collisions at sqrt[s_{NN}]=5.02  TeV. These new measurements show a clear decrease of the Λ_{c}^{+}/D^{0} ratio with increasing transverse momentum (p_{T}) in both collision systems in the range 2<p_{T}<12  GeV/c, exhibiting similarities with the light-flavor baryon-to-meson ratios p/π and Λ/K_{S}^{0}. At low p_{T}, predictions that include additional color-reconnection mechanisms beyond the leading-color approximation, assume the existence of additional higher-mass charm-baryon states, or include hadronization via coalescence can describe the data, while predictions driven by charm-quark fragmentation processes measured in e^{+}e^{-} and e^{-}p collisions significantly underestimate the data. The results presented in this Letter provide significant evidence that the established assumption of universality (colliding-system independence) of parton-to-hadron fragmentation is not sufficient to describe charm-baryon production in hadronic collisions at LHC energies.

Experimental Evidence for an Attractive p-ϕ Interaction

This Letter presents the first experimental evidence of the attractive strong interaction between a proton and a ϕ meson. The result is obtained from two-particle correlations of combined p-ϕ⊕ p[over ¯]-ϕ pairs measured in high-multiplicity pp collisions at sqrt[s]=13  TeV by the ALICE Collaboration. The spin-averaged scattering length and effective range of the p-ϕ interaction are extracted from the fully corrected correlation function employing the Lednický-Lyuboshits approach. In particular, the imaginary part of the scattering length vanishes within uncertainties, indicating that inelastic processes do not play a prominent role for the p-ϕ interaction. These data demonstrate that the interaction is dominated by elastic p-ϕ scattering. Furthermore, an analysis employing phenomenological Gaussian- and Yukawa-type potentials is conducted. Under the assumption of the latter, the N-ϕ coupling constant is found to be g_{N-ϕ}=0.14±0.03(stat)±0.02(syst). This work provides valuable experimental input to accomplish a self-consistent description of the N-ϕ interaction, which is particularly relevant for the more fundamental studies on partial restoration of chiral symmetry in nuclear medium.

Multiharmonic Correlations of Different Flow Amplitudes in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV

The event-by-event correlations between three flow amplitudes are measured for the first time in Pb-Pb collisions, using higher-order symmetric cumulants. We find that different three-harmonic correlations develop during the collective evolution of the medium when compared to correlations that exist in the initial state. These new results cannot be interpreted in terms of previous lower-order flow measurements since contributions from two-harmonic correlations are explicitly removed in the new observables. A comparison to Monte Carlo simulations provides new and independent constraints for the initial conditions and system properties of nuclear matter created in heavy-ion collisions.

Plasmonic mode coupling and thin film sensing in metal-insulator-metal structures

Optical sensors based on surface plasmon resonance (SPR) in the attenuated total reflection (ATR) configuration in layered media have attracted considerable attention over the past decades owing to their ability of label free sensing in biomolecular interaction analysis, and highly sensitive detection of changes in refractive index and thickness, i.e. the optical thickness, of thin film adsorbates (thin film sensing). Furthermore, SPR is highly sensitive to the refractive index of the medium adjacent to the bare metal, and it allows for bulk sensing as well. When deposited at the metal/air interface, an adsorbed layer disturbs the highly localized, i.e. bound, wave at this interface and changes the plasmon resonance to allow for sensing in angular or wavelength interrogation and intensity measurement modes. A high degree of sensitivity is required for precise and efficient sensing, especially for biomolecular interaction analysis for early stage diagnostics; and besides conventional SPR (CSPR), several other configurations have been developed in recent years targeting sensitivity, including long-range SPR (LRSPR) and waveguide-coupled SPR (WGSPR) observed in MIM structures, referred here to by MIM modes, resulting from the coupling of SPRs at I/M interfaces, and Fano-type resonances occurring from broad and sharp modes coupling in layered structures. In our previous research, we demonstrated that MIM is better than CSPR for bulk sensing, and in this paper, we show that CSPR is better than MIM for thin film sensing for thicknesses of the sensing layer (SL) larger than 10 nm. We discuss and compare the sensitivity of CSPR and MIM for thin film sensing by using both experiments and theoretical calculations based on rigorous electromagnetic (EM) theory. We discuss in detail MIM modes coupling and anti-crossing, and we show that when a thin film adsorbate, i.e. a SL), is deposited on top of the outermost-layer of an optimized MIM structure, it modifies the characteristics of the coupled modes of the structure, and it reduces the electric field, both inside the SL and at the SL/air interface, and as a result, it decreases the sensitivity of the MIM versus the CSPR sensor. Our work is of critical importance to plasmonic mode coupling using MIM configurations, as well as to optical bio- and chemical-sensing.

Soft-Dielectron Excess in Proton-Proton Collisions at sqrt[s]=13 TeV

A measurement of dielectron production in proton-proton (pp) collisions at sqrt[s]=13  TeV, recorded with the ALICE detector at the CERN LHC, is presented in this Letter. The data set was recorded with a reduced magnetic solenoid field. This enables the investigation of a kinematic domain at low dielectron (ee) invariant mass m_{ee} and pair transverse momentum p_{T,ee} that was previously inaccessible at the LHC. The cross section for dielectron production is studied as a function of m_{ee}, p_{T,ee}, and event multiplicity dN_{ch}/dη. The expected dielectron rate from hadron decays, called hadronic cocktail, utilizes a parametrization of the measured η/π^{0} ratio in pp and proton-nucleus collisions, assuming that this ratio shows no strong dependence on collision energy at low transverse momentum. Comparison of the measured dielectron yield to the hadronic cocktail at 0.15<m_{ee}<0.6  GeV/c^{2} and for p_{T,ee}<0.4  GeV/c indicates an enhancement of soft dielectrons, reminiscent of the "anomalous" soft-photon and soft-dilepton excess in hadron-hadron collisions reported by several experiments under different experimental conditions. The enhancement factor over the hadronic cocktail amounts to 1.61±0.13(stat)±0.17(syst,data)±0.34(syst,cocktail) in the ALICE acceptance. Acceptance-corrected excess spectra in m_{ee} and p_{T,ee} are extracted and compared with calculations of dielectron production from hadronic bremsstrahlung and thermal radiation within a hadronic many-body approach.

Antimony from brake dust to the combined sewer collection system via road effluent under rainy conditions

Abrasion of the brake lining of automobiles is one of the main antimony (Sb) sources on the road. Therefore, the road effluent possibly supplies Sb to the combined sewer collection system. However, Sb in road-sewer systems has attracted little concern, although heavy metals such as copper (Cu), zinc (Zn), cadmium (Cd), and lead (Pb) in sewer water have been studied by many previous authors. We investigated the effect of road effluent on Sb in the combined sewer water by collecting road effluent, road dust, and sewer water under rainy and dry weather conditions. Sb in road effluent showed a significantly higher concentration than the other types of samples, and the Sb concentration in sewer during wet weather was significantly higher than that during dry weather. Furthermore, the Sb concentration in sewer water decreased with time during a wash-off event. Clear positive relationships between Sb and Cu and between Sb and Ba in both road effluent and road dust extract indicate the effect of brake abrasion because the brake lining contains Cu, Sb, and Ba in high concentrations. Approximately 42% of Sb load occurred during the wash-off event, while the loads of Cu and Ba were much less. Unlike Cu and Ba, we conclude that Sb in combined sewer water largely depends on road effluent in wet weather due to the wash-off of road dust, which is probably associated with brake lining abrasion.

Elliptic Flow of Electrons from Beauty-Hadron Decays in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The elliptic flow of electrons from beauty hadron decays at midrapidity (|y|<0.8) is measured in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the LHC. The azimuthal distribution of the particles produced in the collisions can be parametrized with a Fourier expansion, in which the second harmonic coefficient represents the elliptic flow, v_{2}. The v_{2} coefficient of electrons from beauty hadron decays is measured for the first time in the transverse momentum (p_{T}) range 1.3-6  GeV/c in the centrality class 30%-50%. The measurement of electrons from beauty-hadron decays exploits their larger mean proper decay length cτ≈500  μm compared to that of charm hadrons and most of the other background sources. The v_{2} of electrons from beauty hadron decays at midrapidity is found to be positive with a significance of 3.75  σ. The results provide insights into the degree of thermalization of beauty quarks in the medium. A model assuming full thermalization of beauty quarks is strongly disfavored by the measurement at high p_{T}, but is in agreement with the results at low p_{T}. Transport models including substantial interactions of beauty quarks with an expanding strongly interacting medium describe the measurement within uncertainties.

Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens

SUMMARY

It is known that some mutant peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T cells on the surface of a tumor cell. These peptides are termed neoantigen, and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package termed Neoantimon that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions and structural variants. Beyond the existing applications, Neoantimon is capable of attaching and reflecting several additional information, e.g. wild-type binding capability, allele specific RNA expression levels, single nucleotide polymorphism information and combinations of mutations to filter out infeasible peptides as neoantigen.

AVAILABILITY AND IMPLEMENTATION

The R package is available at http://github/hase62/Neoantimon.

Measurement of the Low-Energy Antideuteron Inelastic Cross Section

In this Letter, we report the first measurement of the inelastic cross section for antideuteron-nucleus interactions at low particle momenta, covering a range of 0.3≤p<4  GeV/c. The measurement is carried out using p-Pb collisions at a center-of-mass energy per nucleon-nucleon pair of sqrt[s_{NN}]=5.02  TeV, recorded with the ALICE detector at the CERN LHC and utilizing the detector material as an absorber for antideuterons and antiprotons. The extracted raw primary antiparticle-to-particle ratios are compared to the results from detailed ALICE simulations based on the geant4 toolkit for the propagation of (anti)particles through the detector material. The analysis of the raw primary (anti)proton spectra serves as a benchmark for this study, since their hadronic interaction cross sections are well constrained experimentally. The first measurement of the inelastic cross section for antideuteron-nucleus interactions averaged over the ALICE detector material with atomic mass numbers ⟨A⟩=17.4 and 31.8 is obtained. The measured inelastic cross section points to a possible excess with respect to the Glauber model parametrization used in geant4 in the lowest momentum interval of 0.3≤p<0.47  GeV/c up to a factor 2.1. This result is relevant for the understanding of antimatter propagation and the contributions to antinuclei production from cosmic ray interactions within the interstellar medium. In addition, the momentum range covered by this measurement is of particular importance to evaluate signal predictions for indirect dark-matter searches.

Development and growth of the foot lumbricalis muscle: a histological study using human fetuses

Our group has shown early development of the hand lumbricalis and hypothesized that, at midterm, the lumbricalis (LU) bundles flexor tendons to provide a configuration of "one tendon per one finger" (Folia Morphologica 2012; 71:154). However, the study concentrated on the hand and contained no sections of near-term fetuses. The present examination of paraffin-embedded tangential sections along the planta from 25 embryos and fetuses at 6-40 weeks (15-320 mm crown-rump length or CRL) demonstrated that, at 8 weeks, the initial foot LU appeared in the proximal side of the common tendinous plate of all five deep tendons. After midterm, a drastic three phase change occurred at the muscle origin: 1) the LU originated from each of the flexor digitorum longus tendon (FDLT), but abundant tenocyte candidates separated the muscle fiber from the tendon collagen bundle; 2) the LU arose from the covering fascia depending on increased thickness of the muscle; and 3) the LU muscle fibers intermingled with tendon collagen bundles and partly surrounded the tendon. Simultaneously, a dividing site of the FDLT migrated distally to accelerate the changes at the LU origin. These phases did not always correspond to the size of fetus after 30 weeks. Consequently, in contrast to the hand LU, the delayed changes in the foot were characterized by involvement of the LU origin into a single common part of the FDLT. The quadratus plantae muscle fibers did not attach to the LU at any phase, and connected with the fourth and fifth toe tendons.

Probing the Effects of Strong Electromagnetic Fields with Charge-Dependent Directed Flow in Pb-Pb Collisions at the LHC

The first measurement at the LHC of charge-dependent directed flow (v_{1}) relative to the spectator plane is presented for Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV. Results are reported for charged hadrons and D^{0} mesons for the transverse momentum intervals p_{T}>0.2  GeV/c and 3<p_{T}<6  GeV/c in the 5%-40% and 10%-40% centrality classes, respectively. The difference between the positively and negatively charged hadron v_{1} has a positive slope as a function of pseudorapidity η, dΔv_{1}/dη=[1.68±0.49(stat)±0.41(syst)]×10^{-4}. The same measurement for D^{0} and D[over ¯]^{0} mesons yields a positive value dΔv_{1}/dη=[4.9±1.7(stat)±0.6(syst)]×10^{-1}, which is about 3 orders of magnitude larger than the one of the charged hadrons. These measurements can provide new insights into the effects of the strong electromagnetic field and the initial tilt of matter created in noncentral heavy ion collisions on the dynamics of light (u, d, and s) and heavy (c) quarks. The large difference between the observed Δv_{1} of charged hadrons and D^{0} mesons may reflect different sensitivity of the charm and light quarks to the early time dynamics of a heavy ion collision. These observations challenge some recent theoretical calculations, which predicted a negative and an order of magnitude smaller value of dΔv_{1}/dη for both light flavor and charmed hadrons.