bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of process safety performance measurement, reporting and management
Authors: Baby Binu , Sproston Chris , Jones Huw , Ramos Marc Ocampo
Published: May 2023

Beach Energy Limited (referred as Beach Energy or Beach) is an ASX-listed exploration and production company headquartered in Adelaide, South Australia. Founded in 1961, Beach produces oil and gas from five onshore and offshore basins across Australia and New Zealand. During its most recent growth phase, Beach added a number of assets to its portfolio that were originally developed and operated by companies with different management systems, standards and reporting requirements. Over the past 5 years Beach has been – and continues to be – on a journey of learning, developing and refining its systems and standards for reporting process safety performance and integrating these within a ‘one Beach’ philosophy. This paper describes the current stage of this evolution in measuring, reporting and managing process safety performance at Beach, presents some of the key learnings to date, in addition to outlining the next steps Beach is taking on this journey. The paper covers the following: (1) experience with IOGP RP 456 Tier KPI model and current main KPIs in use; (2) application to projects, drilling campaigns and operating assets; (3) challenges in gathering data and event classification; (4) importance of getting safety critical equipment selection right; (5) communicating large and complex KPIs to a varied audience; (6) learning and improving process safety performance and systems based on KPIs; (7) new approaches to reporting health of process safety barriers aligned to IOGP RP544 categories using simplified bowtie Major Accident Event dashboards; and (8) integration of process safety management within the Beach Operations Excellence Management System. The key conclusions are that measuring process safety performance requires dedicated effort and consensus across all stakeholders on the most appropriate way to measure performance. Reporting needs a positive and collaborative culture to have the right impact. Managing performance must be based on objective evidence and careful analysis of the data. Achieving effective and efficient process safety measurement, reporting and management is a multi-year journey of continual improvement.
Analytical approach for multivariate exploration planning via secondary migration modelling
Authors: Shokrollahi Amin , Borazjani Sara , Mobasher Syeda Sara , Schacht Ulrike , Amrouch Khalid , Bedrikovetsky Pavel
Published: May 2023

Identifying potential petroleum traps in petroleum basins is one of the key challenges in petroleum exploration. Specifically, it is the identification of probable petroleum traps within a set of stratigraphic traps of a particular location of source rock and carrier bed. One solution lies in understanding the behaviour of hydrocarbon flow during secondary migration, and the evaluation of the probability of successful transport from the source rock to the trap. Modern reservoir simulators rely on numerical methods to model the oil/gas secondary migration. Using numerical simulators is, however, cumbersome and requires high volumes of data and computation time, which affects successful decision-making in exploration planning. Yet, analytical models are fast and allow for multivariant analysis of hydrocarbon secondary migration requiring only a moderate amount of geological data. This study presents the analytical modelling of hydrocarbon buoyant transport in petroleum basins by including the (i) areal variation of stringers’ cross-section, (ii) chemical reactions including oil biodegradation and (iii) hydrological water flow. The explicit formula is provided for the first and last moments of hydrocarbon arrival at the trap, describing the dynamics of filling of the trap. Field data from Australian and Chinese basins are used to investigate the effects of the above-mentioned parameters on the first and last moments of hydrocarbon arrival at the trap.
Opportunity of the future: hydrogen as fuel and feedstock
Authors: Walden Matthew , Sarkar Senjit , Mugford Samuel , Wood Thomas
Published: May 2023

Low-emission hydrogen is emerging as an integral building block for the decarbonisation of the global economy, serving as a complementary emission reduction solution to direct electrification and the use of other low emission technologies such as bioenergy. Presently, hydrogen is a key global commodity used within the production of chemicals including ammonia and for refining activities. These existing uses offer an initial demand market for low-emission hydrogen as a replacement for the high-emitting alternative. Furthermore, new applications for low-emission hydrogen are emerging within hard-to-abate industries where other decarbonisation solutions are less technically or commercially viable or have constrained feedstocks. These applications include as an input for steel production and as a fuel for the transport industry, particularly for heavy-duty long-haul road transport as well as the use of hydrogen-derivatives within the maritime and aviation industries. However, for a low-emission hydrogen industry to develop, the disconnect between consumer and producer expectations, high production and end-use technology costs and regulatory challenges must be overcome. Important mechanisms to achieve this include the implementation of targets and mandates for low-emission hydrogen production and uptake, facilitation of product premiums by industry, targeted public funding and financing and revenue support mechanisms.
Towards building a successful CCS hub in Darwin
Authors: Trier Alister , Smith Howard , Anderson-Barr Aiden , Flowers Simon
Published: May 2023

The Northern Territory Government is working with industry, the Australian Government and CSIRO to accelerate development of the Middle Arm of Darwin Harbour into a globally competitive, sustainable industrial development precinct for low-emission hydrocarbons, hydrogen production, carbon capture and storage (CCS) and minerals processing. This project will significantly reduce Northern Territory emissions and catalyse growth of new industries driving low-emissions energy transition and providing a sustainable future Northern Territory economic growth. The Middle Arm Sustainable Development Precinct masterplan provides for a range of development scenarios that incorporate integrated large-scale renewable energy and carbon capture, utilisation and storage (CCUS) infrastructure. Master planning of this greenfields site provides significant benefits including optimising the use of existing and shared infrastructure, resulting in reduced impacts and maximised economic benefits. This provides Industry with greater certainty, reduces the burden of pre-approvals and creates an investment-ready industrial precinct with ready access to key marine, road and rail transport facilities, utilities and other shared services. This provides an advantage over existing precincts around the globe, which may need to be retrofitted at greater cost and impact. When combined with decarbonisation of the existing gas industry at Middle Arm, there is unique opportunity to develop new low-emissions industries within the Northern Territory and supply low-emission energy and products to the Southeast Asian markets. This paper provides an overview of the Middle Arm Sustainable Development Precinct, its integration with the existing Northern Territory gas industry, the minerals industry and renewable energy, and CCS projects.
Minimising the burden of hazardous area inspections
Authors: MacKenzie Iain , Hill Bruce , Dawood Sakeena
Published: May 2023

The requirement for hazardous area inspections is a mandatory, licence to operate, requirement for oil and gas installations and requires a significant resources and maintenance budget. The conventional requirement is to inspect every item of hazardous area electrical equipment once every 4 years. In Woodside Energy’s Australian assets alone, there are over 150 000 items requiring inspection. In some areas where there are issues with having personnel inspecting equipment and where exclusion zones have been put in place, inspection has required us to utilise robotic inspection techniques. This has included use of Boston Dynamic’s Spot, a walking quadrupedal robot and an ExRobotics certified Ex-R2 crawler. Our initial method of close visual inspections was to have an inspector sitting outside the exclusion zone and manipulating the robot until they had a good visual image of the equipment which was recorded as evidence of the inspection. In the case where the equipment item was at high level, a drone was used in the same way. The efficiency gained from using this technique was estimated by the inspection team to be double that of manually inspecting the equipment. While this technique is newly being developed and requires the inspectors to be continually monitoring the inspections, it is hoped that in the future, machine learning would allow the robots to autonomously inspect the equipment items and report anomalies based on changes from previous inspections. To date we have trialled this onshore only, but we do see great potential in utilising this offshore also.
Developing a ‘fit for purpose’ approach to managing methane emissions
Authors: Joynes Ian , Wittwer Mark , Manolas Yvette
Published: May 2023

Gas producers need practical strategies to manage methane emissions within their natural gas supply chains. Methane sources are varied, and in most cases, challenging to identify and quantify due to their temporal and source-specific nature. However, once detected, mitigation is often simple. Complicating this is the diverse and rapidly evolving suite of technology solutions to support measurement and mitigation. As such, a ‘one-size-fits-all’ approach may not provide a complete and cost-effective pathway to mitigate material methane sources. Woodside has taken specific action to reduce methane emissions and worked with stakeholders to improve methane emission management. In this paper, Woodside describes its journey in developing a ‘fit for purpose’ approach to managing methane emissions supporting the identification and prioritisation of projects for decarbonisation. Specifically it explores: (i) the learnings from the activities undertaken to develop methane inventories and the documentation of methane action plans for its facilities; (ii) experience with the measurement technologies deployed and how these technologies have informed a pragmatic basis to prioritise the delivery of mitigation projects; and (iii) the importance of ongoing peer knowledge sharing to unlock cost-effective pathways for sustainable measurement and mitigation technologies being deployed within Australia.
Phosphoinositide regulation of voltage-gated sodium channels
Authors: Short Ben
Published: May 2023

JGP study (Gada et al. 2023. J. Gen. Physiol. https://doi.org/10.1085/jgp.202213255) reveals that the membrane lipid PI(4,5)P2 alters the activity of NaV1.4 channels by modulating their gating behavior.
Neutrino spin-flavour precession in magnetized white dwarf
Authors: Adhikary Jyotismita , Alok Ashutosh Kumar , Mandal Arindam , Sarkar Trisha , Sharma Shreya
Published: May 2023

Due to notoriously small value of the neutrino magnetic moment, the phenomena of neutrino spin flavour precession (SFP) require a very high magnetic field. This makes only a handful of systems suitable to study this phenomenon. By the observation of SFP, the Dirac and Majorana nature of neutrinos is expected to be distinguished. In this work, we point out the potential of the white dwarf (WD) system in studying the spin-flavour oscillation of neutrinos. From recent analysis, it has been found that young isolated WDs may harbour very strong internal magnetic field, even without exhibiting any surface magnetic field. The presence of a magnetic field enhances the cooling process and along with that, renders the spin-flavour oscillation of neutrinos emitted in the neutrino cooling process. Employing the standard WD specifications, we analyse whether a magnetized WD is a suitable environment to distinguish between the Dirac and Majorana nature of the neutrino. Higher value of spin flavour transition probability implies reduced active neutrino flux which is possible to be estimated in terrestrial neutrino detectors. We find that for the current upper bound on the neutrino magnetic moment, the spin flavour transition probability of Dirac neutrinos is much higher in comparison to the Majorana neutrino which converts the active neutrino flavours to sterile in a significant amount. We also examine the sensitivity of the spin flavour transition probability to the neutrino magnetic moment.
Anisotropy in colossal piezoelectricity, giant Rashba effect and ultrahigh carrier mobility in Janus structures of quintuple Bi2X3 (X = S, Se) monolayers
Authors: Tripathy Nilakantha , De Sarkar Abir
Published: May 2023

Due to the asymmetric structures, two-dimensional Janus materials have gained significant attention in research for their intriguing piezoelectric and spintronic properties. In the present work, quintuple Bi2X3 (X = S, Se) monolayers (MLs) have been modified to create stable Janus Bi2X2Y (X ≠ Y = S, Se) MLs that display piezoelectricity in both the planes along with Rashba effect. The out-of-plane piezoelectric constant (d
33) is 41.18 (−173.14) pm V−1, while the in-plane piezoelectric constant (d
22) is 5.23 (6.21) pm V−1 for Janus Bi2S2Se (Bi2Se2S) ML. Including spin–orbit coupling in the Janus MLs results in anisotropic giant Rashba spin splitting (RSS) at the Γ point in the valence band, with RSS proportional to d
33. The Rashba constant along the Γ–K path,

α
R

Γ

−

 K

, is 3.30 (2.27) eV Å, whereas along Γ–M,

α
R

Γ

−

 M

is 3.58 (3.60) eV Å for Janus Bi2S2Se (Bi2Se2S) ML. The MLs exhibit ultrahigh electron mobility (∼5442 cm2V−1s−1) and have electron to hole mobility ratio of more than 2 due to their tiny electron-effective masses. The flexibility of the MLs allows for a signification alteration in its properties, like band gap, piezoelectric coefficient, and Rashba constant, via mechanical (biaxial) strain. For the MLs, band gap and d
33 value are enhanced with compressive strain. The d33 value of Janus Bi2Se2S reaches 4886.51 pm V−1 under compressive strain. The coexistence of anisotropic colossal out-of-plane piezoelectricity, giant RSS, and ultrahigh carrier mobilities in Janus Bi2S2Se and Bi2Se2S MLs showcase their tremendous prospects in nanoelectronic, piezotronics, and spintronics devices.
Study on loose damage monitoring of mortise-tenon joints in traditional wooden structures based on piezoelectric active sensing
Authors: Yang Wenwei , Wang Tongkuai , Meng Huien , Li Weijie
Published: May 2023

In traditional Chinese wooden structural buildings, mortise-tenon joints are used as connection nodes. Under the erosion effects from wind and rain, such nodes are prone to aging and loosening. If they are not tracked and repaired in time, they are likely to cause structural damage when they encounter sudden loads such as earthquakes. In accordance with engineering practice, one mortise-tenon joint specimen with a penetrating straight tenon and one mortise-tenon joint specimen without a penetrating tenon were constructed. Active sensing technology based on piezoelectric ceramics was used to identify the loosening state of tenon and mortise joints. The amplitude of the piezoelectric signal, wavelet packet energy, information entropy, and damage index based on the root mean square deviation were analyzed. It was found that with the increase in loosening damage, the amplitude of the signal gradually decreases, and the information entropy gradually increases. When the damage reaches a certain extent, the changes in the monitoring signal characteristics is limited. The proposed monitoring method can be used to identify the damage state for mortise-tenon joints effectively, and the research results can provide a valuable guideline for the repair of mortise-tenon joints used in traditional wooden structures.
Soliton solutions for a two-component generalized Sasa-Satsuma equation
Authors: Feng Lian-li , Zhu Zuo-nong
Published: May 2023

As is well known, the Sasa-Satsuma equation is an important integrable high order nonlinear Schrödinger equation. In this paper, a two-component generalized Sasa-Satsuma (gSS) equation is investigated. We construct the n-fold Darboux transformation for the two-component gSS equation. Based on the Darboux transformation, we obtain some interesting solutions, such as a breather soliton solution, kink solution, anti-soliton solution and a periodic-like solution.
Analysis and expansion of the quasi-continuous exhaust (QCE) regime in ASDEX Upgrade
Authors: Faitsch M. , Eich T. , Harrer G.F. , Wolfrum E. , Brida D. , David P. , Dunne M. , Gil L. , Labit B. , Stroth U.
Published: May 2023

The quasi-continuous exhaust (QCE) regime, formerly known as either type-II ELM or small ELM regime is studied in ASDEX Upgrade. The regime is a natural type-I ELM-free H-mode. The operational space of QCE discharges in ASDEX Upgrade with respect to their separatrix conditions and their power exhaust capabilities are presented. A significant broadening of the power fall-off length is observed, correlating to an increased separatrix density and pressure. Moreover, the possible reactor relevance of this regime is demonstrated by expanding the operational space to low edge safety factor and demonstrating the benign tungsten impurity behaviour. A discharge without any type-I ELM from start to end reaching a partially detached divertor at high normalised energy confinement time is presented.
A novel porous hydrogel based on hybrid gelation for injectable and tough scaffold implantation and tissue engineering applications
Authors: Hidalgo Carmen , Méndez-Ruette Maxs , Zavala Gabriela , Viafara-García Sergio , Novoa Javier , Díaz-Calderón Paulo , González-Arriagada Wilfredo Alejandro , Cuenca Jimena , Khoury Maroun , Acevedo Juan Pablo
Published: May 2023

Although there have been many advances in injectable hydrogels as scaffolds for tissue engineering or as payload-containing vehicles, the lack of adequate microporosity for the desired cell behavior, tissue integration, and successful tissue generation remains an important drawback. Herein, we describe an effective porous injectable system that allows in vivo formation of pores through conventional syringe injection at room temperature. This system is based on the differential melting profiles of photocrosslinkable salmon gelatin and physically crosslinked porogens of porcine gelatin (PG), in which PG porogens are solid beads, while salmon methacrylamide gelatin remains liquid during the injection procedure. After injection and photocrosslinking, the porogens were degraded in response to the physiological temperature, enabling the generation of a homogeneous porous structure within the hydrogel. The resultant porogen-containing formulations exhibited controlled gelation kinetics within a broad temperature window (18.5 ± 0.5–28.8 ± 0.8 °C), low viscosity (133 ± 1.4–188 ± 16 cP), low force requirements for injectability (17 ± 0.3–39 ± 1 N), robust mechanical properties after photo-crosslinking (100.9 ± 3.4–332 ± 13.2 kPa), and favorable cytocompatibility (>70% cell viability). Remarkably, in vivo subcutaneous injection demonstrated the suitability of the system with appropriate viscosity and swift crosslinking to generate porous hydrogels. The resulting injected porous constructs showed favorable biocompatibility and facilitated cell infiltration for desirable potential tissue remodeling. Finally, the porogen-containing formulations exhibited favorable handling, easy deposition, and good shape fidelity when used as bioinks in 3D bioprinting technology. This injectable porous system serves as a platform for various biomedical applications, thereby inspiring future advances in cell therapy and tissue engineering.
Degradation behavior, cytotoxicity, hemolysis of partially unzipped carbon nanotubes/zinc composites as potential biodegradable bone implants
Authors: Yang Ya , Fan Mei , Zhao Fei
Published: May 2023

Zn with a suitable degradation rate is considered to be a promising candidate biodegradable implant materials. To enhance the mechanical properties of pure Zn and broaden its application in the field of short-term orthopedic surgery, a series of new Zn matrix composites with a high strength are developed by the addition of partially unzipped carbon nanotubes (PUCNTs), and the degradation behavior, cytotoxicity and hemolysis of new PUCNTs/Zn composites are investigated in this paper. The results show that the degradation rate of the PUCNTs/Zn composites with 0, 0.1, 0.2, 0.3 and 0.5 wt.% PUCNTs can meet the standard of clinical biomedical orthopedic implant materials. During cytotoxicity test, the density of living cells rapidly increases with increasing PUCNTs content, and the cell viability of MG-63 cells in the extract with different concentrations is higher than 90%, illustrating an excellent cytocompatibility. For the hematotoxicity assay, the hemolysis percentage of all PUCNTs/Zn composites samples is below the safety threshold of 5.0% for clinical application, exhibiting a good blood compatibility.
Scaling waterbody carbon dioxide and methane fluxes in the arctic using an integrated terrestrial-aquatic approach
Authors: Ludwig Sarah M , Natali Susan M , Schade John D , Powell Margaret , Fiske Greg , Schiferl Luke D , Commane Roisin
Published: May 2023

In the Arctic waterbodies are abundant and rapid thaw of permafrost is destabilizing the carbon cycle and changing hydrology. It is particularly important to quantify and accurately scale aquatic carbon emissions in arctic ecosystems. Recently available high-resolution remote sensing datasets capture the physical characteristics of arctic landscapes at unprecedented spatial resolution. We demonstrate how machine learning models can capitalize on these spatial datasets to greatly improve accuracy when scaling waterbody CO2 and CH4 fluxes across the YK Delta of south-west AK. We found that waterbody size and contour were strong predictors for aquatic CO2 emissions, attributing greater than two-thirds of the influence to the scaling model. Small ponds (<0.001 km2) were hotspots of emissions, contributing fluxes several times their relative area, but were less than 5% of the total carbon budget. Small to medium lakes (0.001–0.1 km2) contributed the majority of carbon emissions from waterbodies. Waterbody CH4 emissions were predicted by a combination of wetland landcover and related drivers, as well as watershed hydrology, and waterbody surface reflectance related to chromophoric dissolved organic matter. When compared to our machine learning approach, traditional scaling methods that did not account for relevant landscape characteristics overestimated waterbody CO2 and CH4 emissions by 26%–79% and 8%–53% respectively. This study demonstrates the importance of an integrated terrestrial-aquatic approach to improving estimates and uncertainty when scaling C emissions in the arctic.
Statistically representative estimators of multi-scale surface topography: example of aluminum blasted rough samples
Authors: Turbil C , Cabrero J , Simonsen I , Vandembroucq D , Gozhyk I
Published: May 2023

The topography of a rough surface determines many of its physical properties, for instance, tribology, contact mechanics, optical properties etc. Nowadays, a deep understanding of such physical phenomena requires the knowledge of the topography at appropriate length scales. Apart from performing multi-scale measurements of the surface topography, it also requires the use of proper statistical estimators for the analysis of such topography maps. Moreover, when dealing with light scattering in the visible spectral range, the scale at which the estimators of local topography properties are defined is extremely important. Here we present a multi-scale and statistical study of the surface topography of blasted aluminum samples which all have rather different visual appearance. Various statistical estimators of surface topography are examined, including estimators related to the height distribution, the lateral correlation and local topology. The combination of these various estimators unveils a scale separation between a micro-scale roughness inherited from the initial cold-rolled aluminum surface and a large scale roughness fully controlled by the blasting process. A special emphasis is given to the crucial importance of length scales in the estimation of local slopes. The present analysis establishes a quantitative link between the statistical properties of the surface topography and the blasting process used to fabricate the samples.
Tumor growth with nutrients: Regularity and stability
Authors: Jacobs Matt , Kim Inwon , Tong Jiajun
Published: May 2023

In this paper, we study a tumor growth model with nutrients. The model presents dynamic patch solutions due to the incompressibility of the tumor cells. We show that when the nutrients do not diffuse and the cells do not die, the tumor density exhibits regularizing dynamics thanks to an unexpected comparison principle. Using the comparison principle, we provide quantitative

L
1

L^1

-contraction estimates and establish the

C

1
,
α

C^{1,\alpha }

-boundary regularity of the tumor patch. Furthermore, whenever the initial nutrient

n
0

n_0

either lies entirely above or entirely below the critical value

n
0

=
1

n_0=1

, we are able to give a complete characterization of the long-time behavior of the system. When

n
0

n_0

is constant, we can even describe the dynamics of the full system in terms of some simpler nutrient-free and parameter-free model problems. These results are in sharp contrast to the observed behavior of the models either with nutrient diffusion or with death rate in tumor cells.
Progression of follicular lymphoma and related entities: Report from the 2021 SH/EAHP Workshop
Authors: Duffield Amy S , Dogan Ahmet , Amador Catalina , Cook James R , Czader Magdalena , Goodlad John R , Nejati Reza , Xiao Wenbin , Happ Lanie , Parker Clay , Thacker Elizabeth , Thakkar Devang , Dave Sandeep S , Wasik Mariusz A , Ott German
Published: May 2023

Objectives

The 2021 Society for Hematopathology and European Association for Haematopathology Workshop addressed the molecular and cytogenetic underpinnings of transformation and transdifferentiation in lymphoid neoplasms.

Methods

Session 4, “Transformations of Follicular Lymphoma,” and session 5, “Transformations of Other B-Cell Lymphomas,” included 45 cases. Gene alteration analysis and expression profiling were performed on cases with submitted formalin-fixed, paraffin embedded tissue.

Results

The findings from session 4 suggest that “diffuse large B-cell lymphoma/high-grade B-cell lymphoma with rearrangements of MYC and BCL2” is a distinct category arising from the constraints of a preexisting BCL2 translocation. TdT expression in aggressive B-cell lymphomas is associated with MYC rearrangements, immunophenotypic immaturity, and a dismal prognosis but must be differentiated from lymphoblastic ­lymphoma. Cases in session 5 illustrated unusual morphologic and immunophenotypic patterns of transformation. Additionally, the findings support the role of cytogenetic abnormalities—specifically, MYC and NOTCH1 rearrangements—as well as single gene alterations, including TP53, in transformation.

Conclusions

Together, these unique cases and their accompanying molecular and cytogenetic data suggest potential mechanisms for and unusual patterns of transformation in B-cell lymphomas and indicate numerous opportunities for further study.
Transdifferentiation, phenotypic infidelity, progression, and transformation in T/NK-cell neoplasms: Report from the 2021 SH/EAHP Workshop
Authors: Amador Catalina , Cook James R , Czader Magdalena , Duffield Amy , Goodlad John , Nejati Reza , Ott German , Xiao Wenbin , Dave Sandeep , Wasik Mariusz A , Dogan Ahmet
Published: May 2023

Objectives

Sessions 8 and 9 of the 2021 Society for Hematopathology and the European Association for Haematopathology Workshop aimed to collect examples of transdifferentiation, lineage infidelity, progression, and transformation in precursor and mature T/natural killer (NK)–cell neoplasms.

Methods

Twenty-eight cases were submitted and analyzed, with whole-exome sequencing and genome-wide RNA expression analysis performed in a subset of the cases.

Results

In session 8, 7 T-lymphoblastic lymphoma/leukemia cases were received that showed transdifferentiation to clonally related mature myeloid hematopoietic neoplasms, including 6 histiocytic/dendritic cell lineage neoplasms and a mast cell sarcoma. Session 9 included 21 mature T-cell neoplasms that were grouped into 3 themes. The first one addressed phenotypic infidelity in mature T-cell lymphomas (TCLs) and included 8 TCLs expressing aberrant antigens, mimicking classic Hodgkin and non-Hodgkin B-cell lymphomas. The second theme addressed disease progression in TCL and included 5 cutaneous T-cell lymphoproliferative disorders and 2 T-cell large granular lymphocyte proliferations with subsequent progression to systemic TCL. The third theme included 6 patients with TCL with T-follicular helper phenotype, mainly angioimmunoblastic T-cell lymphoma, with concurrent/subsequent clonal hematopoiesis or myeloid neoplasms and/or subsequent/concomitant diffuse large B-cell lymphoma.

Conclusions

This cohort of cases allowed us to illustrate, discuss, and review current concepts of transdifferentiation, aberrant antigen expression, and progression in various T/NK-cell neoplasms.
How I Diagnose Rosai-Dorfman Disease
Authors: Ravindran Aishwarya , Rech Karen L
Published: May 2023

Objectives

Rosai-Dorfman disease (RDD) is one of 3 major types of histiocytosis, along with Erdheim-Chester disease and Langerhans cell histiocytosis. While historically, RDD was considered a benign self-limited condition, current data show MAPK/ERK pathway mutations in 30% to 50% of cases, indicative of a clonal process. Rosai-Dorfman disease was incorporated as a histiocytic neoplasm in the fifth edition of the World Health Organization classification of hematopoietic tumors and the International Consensus Classification.

Methods

We discuss the diagnosis of RDD using 2 illustrative cases, interpretative challenges, and a diagnostic algorithm.

Results

Rosai-Dorfman disease involves nodal and extranodal sites, including skin, sinuses, salivary gland, orbit, central nervous system, kidney, and bone. In a subset, RDD can coexist with other neoplasms (lymphomas, other histiocytosis) or autoimmune disease. Morphologically, RDD histiocytes are characterized by enlarged round to oval nuclei, distinct nucleoli, and voluminous cytoplasm with engulfment of inflammatory cells (emperipolesis). By immunohistochemistry, they express CD68, CD163 (majority), S100, OCT2, and cyclin D1. Appropriate use of ancillary studies is important to support the diagnosis of RDD while excluding other histiocytic neoplasms and reactive histiocytic proliferations.

Conclusions

Management of RDD is dependent on the extent of organ involvement and clinical symptoms. In patients who require therapy, next-generation sequencing is recommended to identify MAPK/ERK pathway mutations for targeted therapy.
Heterogeneity and Progression of Chronic Obstructive Pulmonary Disease: Emphysema-Predominant and Non–Emphysema-Predominant Disease
Authors: Castaldi Peter J , Xu Zhonghui , Young Kendra A , Hokanson John E , Lynch David A , Humphries Stephen M , Ross James C , Cho Michael H , Hersh Craig P , Crapo James D , Strand Matthew , Silverman Edwin K
Published: May 2023

While variation in emphysema severity between patients with chronic obstructive pulmonary disease (COPD) is well-recognized, clinically applicable definitions of the emphysema-predominant disease (EPD) and non–emphysema-predominant disease (NEPD) subtypes have not been established. To study the clinical relevance of the EPD and NEPD subtypes, we tested the association of these subtypes with prospective decline in forced expiratory volume in 1 second (FEV1) and mortality among 3,427 subjects with Global Initiative for Chronic Obstructive Lung Disease (GOLD) spirometric grade 2–4 COPD at baseline in the Genetic Epidemiology of COPD (COPDGene) Study, an ongoing national multicenter study that started in 2007. NEPD was defined as airflow obstruction with less than 5% computed tomography (CT) quantitative densitometric emphysema at −950 Hounsfield units, and EPD was defined as airflow obstruction with 10% or greater CT emphysema. Mixed-effects models for FEV1 demonstrated larger average annual FEV1 loss in EPD subjects than in NEPD subjects (−10.2 mL/year; P < 0.001), and subtype-specific associations with FEV1 decline were identified. Cox proportional hazards models showed higher risk of mortality among EPD patients versus NEPD patients (hazard ratio = 1.46, 95% confidence interval: 1.34, 1.60; P < 0.001). To determine whether the NEPD/EPD dichotomy is captured by previously described COPDGene subtypes, we used logistic regression and receiver operating characteristic (ROC) curve analysis to predict NEPD/EPD membership using these previous subtype definitions. The analysis generally showed excellent discrimination, with areas under the ROC curve greater than 0.9. The NEPD and EPD COPD subtypes capture important aspects of COPD heterogeneity and are associated with different rates of disease progression and mortality.
“I think of Chaplin”: Poetry and the Tramp in Cold War America
Authors: Potts George
Published: May 2023

This essay explores how Charlie Chaplin’s tribulations under McCarthyism, which culminated in his exile from the US in 1952, occasioned a minor chorus of poetry on the American Left. Through case studies of Bob Kaufman, Edwin Rolfe, and Louis Zukofsky, this essay explores how radical poets from across different literary groupings were drawn to Chaplin in the Cold War’s early years out of personal and political solidarity, while also finding in him a figure through whom they could collectively register and resist the Left’s broader postwar decline. The article also sheds light on the much longer history of Chaplin’s connections with poetry and poets. It traces his relationship with socialist writers back to the 1910s and suggests how postwar poetry’s imaginative investment in Chaplin as a political figure has a deeper layer of significance, given that the filmmaker had for decades been influenced by his friendships with poets on the Left. The essay proposes that poetry’s unique potentiality as a form through which to oppose Chaplin’s struggles under McCarthyism is a consequence of poets having fostered his political consciousness in the first place.Reading [texts] . . . about Chaplin’s postwar political isolation comparatively and cumulatively, what emerges is a poetry whose shared references bespeak a form of fraught solidarity and whose full force resides in their being understood as a kind of communal response.
134 Occupational Exposure to Different Microbial Species and Endotoxin and Serum Levels of Markers of Inflammation – Across Working Environments
Authors: Mette Madsen Anne , Delsuz Mohammad Seeiar , Al-Saidi Ali , Mølck Sofie M S , Rasmussen Pil Uthaug , Kofoed Victor Carp , Hougaard Karin S , Uhrbrand Katrine , Rui Lu , Frederiksen Margit Wagtberg
Published: May 2023

Occupational exposure to bioaerosols (fungi, bacteria, and endotoxin) may be associated with early signs of health effects of the airways measured as elevated levels of inflammatory markers in serum samples. The aim of this study is to obtain knowledge about the contribution of endotoxin, different fungal and bacterial species, and dust to the inflammatory potential of bioaerosols from different working environments. Using personal samplers, bioaerosols were sampled in the inhalation zone of workers in different occupational settings. Fungal and bacterial species were identified to species level using MALDI-TOF MS. The ability of workers’ exposure to induce production of reactive oxidative species was analysed in a human cell line. Levels of the inflammatory markers C-reactive protein and serum amyloid A were measured in blood samples of the workers. The fungal and bacterial composition as well as species richness and endotoxin exposure level differed between working environments. Among the dominating microorganisms were different Staphylococcus species (work with animals), Stenotrophomonas maltophilia (work with plants), and Aspergillus niger (work with waste). While pigeon house dust was cytotoxic, pig farm dust was highly inflammogenic. The biofilm forming capacity of the exposure correlated with bacterial concentration in high exposure samples. Serum levels of inflammatory markers were associated significantly with occupational exposure to endotoxin for work with plants and waste water. As the next step, we are analysing whether this association is also found for work in other environments and whether it is associated with exposure to different microorganisms.
87 Portuguese Groceries: A Potential Indoor Environment to Be Used as Public Health Sentinel for Fungal and Mycotoxins Contamination
Authors: Viegas Carla , Cervantes Renata , Gomes Bianca , Moreira Silvia , Dias Marta , Pena Pedro , Carolino Elisabete , Twaruzek Magdalena , Kosicki Robert , Caetano Liliana Aranha , Viegas Susana
Published: May 2023

This study aimed to characterize microbial contamination in Portuguese grocery stores. The research was carried out in 15 grocery stores in Cascais, Portugal. Electrostatic dust cloths (EDC) and surface swabs were used on 3 sampling sites: checkout, fruits/vegetable, and warehouse/dispenser. Fungal contamination was characterized by culture-based methods, through the inoculation onto two different culture media: malt extract agar (MEA) supplemented with chloramphenicol (0.05 %) and dichloran-glycerol agar (DG18). Screening of azole resistance was performed by inoculation of EDC extracts´ in azole-supplemented Sabouraud dextrose agar (SDA) media, according to EUCAST guideline. A total of 39 samples were screened for mycotoxins contamination. The highest fungal contamination was obtained from fruits/vegetables in swabs (76 % MEA; 71 % DG18). The most prevalent genera in swabs was Cladosporium sp. (54 % MEA). Regarding EDC, besides Penicillium sp. (63 %) the most prevalent were Aspergillus sections Circumdati (25 %) and Aspergilli (35 %). Penicillium sp. was highly prevalent in the checkout (61 % SDA; 87 % voriconazole), and warehouse/dispenser sectors (73% voriconazole; 52% posaconazole). Circumdati and Fumigati were the most prevalent Aspergillus sections in fruits/vegetables (73 % and 64 % in voriconazole, respectively). Four mycotoxins (fumonisin B1, B2, B3) were detected simultaneously in most of the 36 samples. Identifying the most critical workplaces in groceries concerning fungal and mycotoxins contamination is of upmost importance to human health (workers and consumers) when using a One Health approach.
31 Analysis of the Material Properties of Importance in the Classification of Toxicity of Graphene Nanomaterials.
Authors: Roberts Jenny R , Kodali Vamsi K , Stefaniak Aleksandr B , Boots Theresa E
Published: May 2023

Graphene (Gr) nanomaterials are one of the fastest growing nanotechnology markets with a variety of applications in numerous industries due to a battery of unique physicochemical properties related to two-dimensional structure. Occupational exposure to graphenes by inhalation is a concern. Understanding the relationship of these properties to toxicity is critical for better predicting risk. The goal of this study was to associate material properties of this class of two-dimensional material with parameters of pulmonary toxicity and pathology. In vivo pulmonary exposure studies were previously conducted to compare different graphene nanomaterials [Gr that varied in lateral dimension, graphene oxide (GO), and reduced GO (rGO)] and carbon-based reference nanomaterials [carbon black (CB) and multi-walled carbon nanotubes (MWCNT)]. Size, density, surface area, oxygen content, as well as reactivity, agglomeration size, and zeta potential in delivery vehicle for oropharyngeal aspiration were measured. MWCNT and rGO caused persistent inflammation and a fibrotic response over time whereas inflammatory responses to other materials were transient. A classification Random Forest was used to predict toxicity grouping based on material properties to determine variable importance. Grouping was determined by significant difference from control using lavage and pathology outcomes and incidence. Toxicity ranking was MWCNT=rGO>>Gr5=Gr20=GO=CB≥Gr1. Variable of importance varied by time and toxicity parameter; however, density and mean agglomerate size were critical factors in the highly toxic materials whereas surface area was the most important factor in less toxic groups. This study contributes to understanding the structure-activity of this material class and read-across toxicity assessments of similar emerging materials.
98 Inhalation Exposure to Traffic-Related Air Pollution Accelerates Alzheimer’s Disease-like Pathology in a Murine Model
Authors: Wahle Tina , Sofranko Adriana , Scarcello Eleonora , Masson Isabelle , Albrecht Catrin , Bredeck Gerrit , Busch Mathias , Fokkens Paul , Boere John , Cassee Flemming R , Schins Roel P F
Published: May 2023

A growing number of epidemiological studies has linked exposure to traffic-related air pollution (TRAP) to neurological and neurodegenerative diseases. In a previous study, we showed that subchronic inhalation exposure to diesel engine exhaust, as a model of TRAP, aggravates amyloid-β plaque formation and motor function impairment in the 5xFAD transgenic mouse model of Alzheimer’s disease (AD). To further strengthen the epidemiological association between TRAP and AD we exposed 5xFAD and wildtype littermate mice for 5 h/day, 5 days/week during 2 or 4 consecutive weeks at a representative urban traffic-dominated location to: (I) concentrated ambient particles, (II) particle filtered ambient air or (III) clean air (control).  Our study revealed that repeated inhalation exposure to TRAP accelerates plaque formation in the 5xFAD mice. Data also indicated that the gaseous fraction of the air pollutant mixture probably plays only a minor role in this effect. The major outcome of this study substantiates the role of air pollution in AD and suggests that long-term exposure to traffic-related air pollution particles is a risk factor for this debilitating disease.

Acknowledgements: The work leading to these results has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 814978 (TUBE) and a cross-border grant awarded by the Alzheimer Forschung Initiative (AFI, Germany) and Alzheimer Nederland.
131 Alveolar Macrophage Degranulation Initiates the Spatially Restricted Innate Immune Response During Ventilator-Assisted Nanoparticle Inhalation
Authors: Liu Qiongliang , Yang Lin , Li Chenxi , Schmid Otmar , Stoeger Tobias , Rehberg Markus
Published: May 2023

To visualize and measure in real-time the cellular pulmonary innate immune response elicited by inhaled NPs, we apply state-of-the-art intravital microscopy on the alveolar region of the murine lung.

Fluorescent carboxyl-quantum-dot-NPs (deposited dose of 16 cm2/g) applied via ventilator-assisted inhalation accumulated within seconds as distinct fluorescent spots at the alveolar walls. Already at 30min, cQD-NPs elicited an increase in microvascular neutrophil numbers as compared to controls, which subsequently transmigrated into the alveolar space.

This early immune response was not specific to cQD-NPs, since a comparable increase in neutrophil numbers was also observed upon inhalation of a bioequivalent dose of carbon black NPs, a typical component of urban air pollution. AMs actively accumulated cQD-NPs over time, starting few minutes after inhalation. Significantly more neutrophils were attracted in proximity to cQD-NP-laden AMs, as compared to NP-free AMs or control areas with epithelial associated cQD-NP. Prior airway application of a cellular degranulation inhibitor prevented cQD-NP and CNP induced neutrophil recruitment at 2h and 24 h after inhalation.  Inhibition of Fcγ-receptor mediated AM cQD-NP uptake by prior application of anti-CD64 mAbs or neutralizing of TNFα by anti-TNFα mAbs in the airspace, abolished this early immune response. Importantly, initial ImageStream flow cytometry analysis of BAL samples indicated an increase of macrophage-derived microvesicles upon NP inhalation. Taken together, our data links NP-induced AM degranulation and cytokine release to the rapid and site-specific recruitment of neutrophils, suggesting this process to be a key event in mounting the immune response upon NP inhalation.
TRASH: Tandem Repeat Annotation and Structural Hierarchy
Authors: Wlodzimierz Piotr , Hong Michael , Henderson Ian R
Published: May 2023

Motivation

The advent of long-read DNA sequencing is allowing complete assembly of highly repetitive genomic regions for the first time, including the megabase-scale satellite repeat arrays found in many eukaryotic centromeres. The assembly of such repetitive regions creates a need for their de novo annotation, including patterns of higher order repetition. To annotate tandem repeats, methods are required that can be widely applied to diverse genome sequences, without prior knowledge of monomer sequences.

Results

Tandem Repeat Annotation and Structural Hierarchy (TRASH) is a tool that identifies and maps tandem repeats in nucleotide sequence, without prior knowledge of repeat composition. TRASH analyses a fasta assembly file, identifies regions occupied by repeats and then precisely maps them and their higher order structures. To demonstrate the applicability and scalability of TRASH for centromere research, we apply our method to the recently published Col-CEN genome of Arabidopsis thaliana and the complete human CHM13 genome.

Availability and implementation

TRASH is freely available at:https://github.com/vlothec/TRASH and supported on Linux.
RaPID-Query for fast identity by descent search and genealogical analysis
Authors: Wei Yuan , Naseri Ardalan , Zhi Degui , Zhang Shaojie
Published: May 2023

Motivation

Due to the rapid growth of the genetic database size, genealogical search, a process of inferring familial relatedness by identifying DNA matches, has become a viable approach to help individuals finding missing family members or law enforcement agencies locating suspects. A fast and accurate method is needed to search an out-of-database individual against millions of individuals. Most existing approaches only offer all-versus-all within panel match. Some prototype algorithms offer one-versus-all query from out-of-panel individual, but they do not tolerate errors.

Results

A new method, random projection-based identity-by-descent (IBD) detection (RaPID) query, is introduced to make fast genealogical search possible. RaPID-Query identifies IBD segments between a query haplotype and a panel of haplotypes. By integrating matches over multiple PBWT indexes, RaPID-Query manages to locate IBD segments quickly with a given cutoff length while allowing mismatched sites. A single query against all UK biobank autosomal chromosomes was completed within 2.76 seconds on average, with the minimum length 7 cM and 700 markers. RaPID-Query achieved a 0.016 false negative rate and a 0.012 false positive rate simultaneously on a chromosome 20 sequencing panel having 86 265 sites. This is comparable to the state-of-the-art IBD detection method TPBWT(out-of-sample) and Hap-IBD. The high-quality IBD segments yielded by RaPID-Query were able to distinguish up to fourth degree of the familial relatedness for a given individual pair, and the area under the receiver operating characteristic curve values are at least 97.28%.

Availability and implementation

The RaPID-Query program is available at https://github.com/ucfcbb/RaPID-Query.