Recent Progress of the Computational 2D Materials Database (C2DB)

The C2DB is a highly curated open database organizing a wealth of computed properties for more than 4000 atomically thin two-dimensional (2D) materials. Here we report on new materials and properties that were added to the database since its first release in 2018. The set of new materials comprise several hundred monolayers exfoliated from experimentally known layered bulk materials, (homo)bilayers in various stacking configurations, native point defects in semiconducting monolayers, and chalcogen/halogen Janus monolayers. The new properties include exfoliation energies, Bader charges, spontaneous polarisations, Born charges, infrared polarisabilities, piezoelectric tensors, band topology invariants, exchange couplings, Raman- and second harmonic generation spectra. We also describe refinements of the employed material classification schemes, upgrades of the computational methodologies used for property evaluations, as well as significant enhancements of the data documentation and provenance. Finally, we explore the performance of Gaussian process-based regression for efficient prediction of mechanical and electronic materials properties. The combination of open access, detailed documentation, and extremely rich materials property data sets make the C2DB a unique resource that will advance the science of atomically thin materials.Comment: 30 pages, 26 figure

GPAW: open Python package for electronic-structure calculations

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE) providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation (BSE), variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support of GPU acceleration has been achieved with minor modifications of the GPAW code thanks to the CuPy library. We end the review with an outlook describing some future plans for GPAW

Staphylococcal enterotoxin A (SEA) stimulates STAT3 activation and IL-17 expression in cutaneous T-cell lymphoma

Cutaneous T-cell lymphoma (CTCL) is characterized by proliferation of malignant T cells in a chronic inflammatory environment. With disease progression, bacteria colonize the compromised skin barrier and half of CTCL patients die of infection rather than from direct organ involvement by the malignancy. Clinical data indicate that bacteria play a direct role in disease progression, but little is known about the mechanisms involved. Here, we demonstrate that bacterial isolates containing staphylococcal enterotoxin A (SEA) from the affected skin of CTCL patients, as well as recombinant SEA, stimulate activation of signal transducer and activator of transcription 3 (STAT3) and upregulation of interleukin (IL)-17 in immortalized and primary patient-derived malignant and nonmalignant T cells. Importantly, SEA induces STAT3 activation and IL-17 expression in malignant T cells when cocultured with nonmalignant T cells, indicating an indirect mode of action. In accordance, malignant T cells expressing an SEA-nonresponsive T-cell receptor variable region β chain are nonresponsive to SEA in monoculture but display strong STAT3 activation and IL-17 expression in cocultures with SEA-responsive nonmalignant T cells. The response is induced via IL-2 receptor common γ chain cytokines and a Janus kinase 3 (JAK3)-dependent pathway in malignant T cells, and blocked by tofacitinib, a clinical-grade JAK3 inhibitor. In conclusion, we demonstrate that SEA induces cell cross talk-dependent activation of STAT3 and expression of IL-17 in malignant T cells, suggesting a mechanism whereby SEA-producing bacteria promote activation of an established oncogenic pathway previously implicated in carcinogenesis

Malignant inflammation in cutaneous T-cell lymphoma: a hostile takeover

Cutaneous T-cell lymphomas (CTCL) are characterized by the presence of chronically inflamed skin lesions containing malignant T cells. Early disease presents as limited skin patches or plaques and exhibits an indolent behavior. For many patients, the disease never progresses beyond this stage, but in approximately one third of patients, the disease becomes progressive, and the skin lesions start to expand and evolve. Eventually, overt tumors develop and the malignant T cells may disseminate to the blood, lymph nodes, bone marrow, and visceral organs, often with a fatal outcome. The transition from early indolent to progressive and advanced disease is accompanied by a significant shift in the nature of the tumor-associated inflammation. This shift does not appear to be an epiphenomenon but rather a critical step in disease progression. Emerging evidence supports that the malignant T cells take control of the inflammatory environment, suppressing cellular immunity and anti-tumor responses while promoting a chronic inflammatory milieu that fuels their own expansion. Here, we review the inflammatory changes associated with disease progression in CTCL and point to their wider relevance in other cancer contexts. We further define the term "malignant inflammation" as a pro-tumorigenic inflammatory environment orchestrated by the tumor cells and discuss some of the mechanisms driving the development of malignant inflammation in CTCL

Quality of Endoscopic Surveillance of Barrett’s Esophagus in Denmark

<p><b>Objectives:</b> The aim of this study was to evaluate adherence to Barrett’s esophagus (BE) surveillance guidelines in Denmark.</p> <p><b>Methods:</b> The Danish Pathology Registry was used to identify 3692 patients. A total of 300 patients were included by drawing a simple random sample. Description of the BE segment, biopsy protocol, communication with the pathologist and planned follow-up endoscopy, was evaluated.</p> <p><b>Results:</b> Thirty-one patients were excluded due to missing reports and 83 patients (28%) due to no endoscopic evidence of BE. Endoscopists suspected BE in 186 patients (62%) and these patients were included. Prague C&M classification was used in 34% of the endoscopy reports. The median number of biopsies was 4 (interquartile range (IQR), 3–6). The BE segment was stratified by lengths of 1–5, 6–10 and 11–15 cm and endoscopists obtained a sufficient number of biopsies in 12, 8 and 0% of cases, respectively. 28% of endoscopists described the exact location of the biopsy site in the pathology requisition. Patients with nondysplastic BE had endoscopic surveillance performed after a median of 24 months (IQR, 6–24).</p> <p><b>Conclusions:</b> Adherence to the Danish guidelines was poor. This may be associated with insufficient quality of BE surveillance. Lack of endoscopic evidence of BE in the Danish Pathology Registry may have underestimated the incidence of adenocarcinoma in BE patients in previous studies.</p

Quality of endoscopic surveillance of Barrett’s esophagus

<p><b>Objectives:</b> The aim of this study was to evaluate adherence to Barrett’s esophagus (BE) surveillance guidelines in Denmark.</p> <p><b>Methods:</b> The Danish Pathology Registry was used to identify 3692 patients. A total of 300 patients were included by drawing a simple random sample. Description of the BE segment, biopsy protocol, communication with the pathologist and planned follow-up endoscopy, was evaluated.</p> <p><b>Results:</b> Thirty-one patients were excluded due to missing reports and 83 patients (28%) due to no endoscopic evidence of BE. Endoscopists suspected BE in 186 patients (62%) and these patients were included. Prague C&M classification was used in 34% of the endoscopy reports. The median number of biopsies was 4 (interquartile range (IQR), 3–6). The BE segment was stratified by lengths of 1–5, 6–10 and 11–15 cm and endoscopists obtained a sufficient number of biopsies in 12, 8 and 0% of cases, respectively. 28% of endoscopists described the exact location of the biopsy site in the pathology requisition. Patients with nondysplastic BE had endoscopic surveillance performed after a median of 24 months (IQR, 6–24).</p> <p><b>Conclusions:</b> Adherence to the Danish guidelines was poor. This may be associated with insufficient quality of BE surveillance. Lack of endoscopic evidence of BE in the Danish Pathology Registry may have underestimated the incidence of adenocarcinoma in BE patients in previous studies.</p