Classifying the saline seeps of a region into best-management groupings

Non-Peer Reviewedover 60 salinity investigations have been completed within a 9 township area near Avonlea, Saskatchewan. This level of study has provided detailed information on a large number of seeps. These have been grouped according to their common features and general landscape position, creating 3 seep classes: Uplands/Side-hill; Plains Transitional; and Bedrock Controlled. Recommendations from detailed farmer reports and local hydrogeologic test sites have been used to derive "best management" strategies for each seep class. This approach will provide direction toward the treatment of future salinity requests, while promoting the realistic management of existing seeps

In-situ spectroscopy of intrinsic Bi2Te3 topological insulator thin films and impact of extrinsic defects

Combined in-situ x-ray photoemission spectroscopy, scanning tunnelling spectroscopy and angle resolved photoemission spectroscopy of molecular beam epitaxy grown Bi2Te3 on lattice mismatched substrates reveal high quality stoichiometric thin films with topological surface states without a contribution from the bulk bands at the Fermi energy. The absence of bulk states at the Fermi energy is achieved without counter doping. We observe that the surface morphology and electronic band structure of Bi2Te3 are not affected by in-vacuo storage and exposure to oxygen, whereas major changes are observed when exposed to ambient conditions. These films help define a pathway towards intrinsic topological devices.Comment: 8 pages, 5 figure

Strong Pinning in High Temperature Superconductors

Detailed measurements of the critical current density jc of YBa2Cu3O7 films grown by pulsed laser deposition reveal the increase of jc as function of the filmthickness. Both this thickness dependence and the field dependence of the critical current are consistently described using a generalization of the theory of strong pinning of Ovchinnikov and Ivlev [Phys. Rev. B 43, 8024 (1991)]. From the model, we deduce values of the defect density (10^21 m^-3) and the elementary pinning force, which are in good agreement with the generally accepted values for Y2O3-inclusions. In the absence of clear evidence that the critical current is determined by linear defects or modulations of the film thickness, our model provides an alternative explanation for the rather universal field dependence of the critical current density found in YBa2Cu3O7 films deposited by different methods.Comment: 11 pages; 8 Figures; Published Phys. Rev. B 66, 024523 (2002

Improving diagnostic precision, care and syndrome definitions using comprehensive next-generation sequencing for the inherited bone marrow failure syndromes

Background Phenotypic overlap among the inherited bone marrow failure syndromes (IBMFSs) frequently limits the ability to establish a diagnosis based solely on clinical features. \u3e70 IBMFS genes have been identified, which often renders genetic testing prolonged and costly. Since correct diagnosis, treatment and cancer surveillance often depend on identifying the mutated gene, strategies that enable timely genotyping are essential. Methods To overcome these challenges, we developed a next-generation sequencing assay to analyse a panel of 72 known IBMFS genes. Cases fulfilling the clinical diagnostic criteria of an IBMFS but without identified causal genotypes were included. Results The assay was validated by detecting 52 variants previously found by Sanger sequencing. A total of 158 patients with unknown mutations were studied. Of 75 patients with known IBMFS categories (eg, Fanconi anaemia), 59% had causal mutations. Among 83 patients with unclassified IBMFSs, we found causal mutations and established the diagnosis in 18% of the patients. The assay detected mutant genes that had not previously been reported to be associated with the patient phenotypes. In other cases, the assay led to amendments of diagnoses. In 20% of genotype cases, the results indicated a cancer surveillance programme. Conclusions The novel assay is efficient, accurate and has a major impact on patient care

The impact of category, cytopathology and cytogenetics on development and progression of clonal and malignant myeloid transformation in inherited bone marrow failure syndromes

Inherited bone marrow failure syndromes are a group of rare, heterogeneous genetic disorders with a risk of clonal and malignant myeloid transformation including clonal marrow cytogenetic abnormalities, myelodysplastic syndrome and acute myeloid leukemia. The clinical characteristics, risk classification, prognostic factors and outcome of clonal and malignant myeloid transformation associated with inherited bone marrow failure syndromes are largely unknown. The aims of this study were to determine the impact of category, cytopathology and cytogenetics, the three components of the “Category Cytology Cytogenetics” classification of pediatric myelodysplastic syndrome, on the outcome of clonal and malignant myeloid transformation associated with inherited bone marrow failure. We used data from the Canadian Inherited Marrow Failure Registry. Among 327 patients with inherited bone marrow failure syndrome enrolled in the registry, the estimated risk of clonal and malignant myeloid transformation by the age of 18 years was 37%. The risk of clonal and malignant myeloid transformation varied according to the type of inherited bone marrow failure syndrome but was highest in Fanconi anemia. The development of clonal and malignant myeloid transformation significantly affected overall survival. Mortality varied based on cytopathological group. The largest group of patients had refractory cytopenia. Clonal marrow cytogenetic abnormalities were identified in 87% of patients with clonal and malignant myeloid transformation, and different cytogenetic groups had different impacts on disease progression. We conclude that category, cytopathology and cytogenetics in cases of clonal and malignant myeloid transformation associated with inherited bone marrow failure syndromes have an important impact on outcome and that the classification of such cases should incorporate these factors

Moiré-modulated band gap and van Hove singularities in twisted bilayer germanene

Twisting bilayers of two-dimensional topological insulators has the potential to create unique quantum states of matter. Here, we successfully synthesized a twisted bilayer of germanene on Ge2Pt(101) with a 21.8° twist angle, corresponding to a commensurate (√7×√7) structure. Using scanning tunneling microscopy and spectroscopy, we unraveled the structural and electronic properties of this configuration, revealing a moiré-modulated band gap and a well-defined edge state. This band gap opens at AB/BA stacked sites and closes at AA stacked sites, a phenomenon attributed to the electric field induced by the scanning tunneling microscopy tip. Our study further revealed two van Hove singularities at −0.8 eV and +1.04 eV, resulting in a Fermi velocity of (8 ± 1) × 105 m s−1. Our tight-binding results uncover a unique quantum state, where the topological properties could be regulated through an electric field, potentially triggering two topological phase transitions.</p

Reanalysing genomic data by normalized coverage values uncovers CNVs in bone marrow failure gene panels

Inherited bone marrow failure syndromes (IBMFSs) are genetically heterogeneous disorders with cytopenia. Many IBMFSs also feature physical malformations and an increased risk of cancer. Point mutations can be identified in about half of patients. Copy number variation (CNVs) have been reported; however, the frequency and spectrum of CNVs are unknown. Unfortunately, current genome-wide methods have major limitations since they may miss small CNVs or may have low sensitivity due to low read depths. Herein, we aimed to determine whether reanalysis of NGS panel data by normalized coverage value could identify CNVs and characterize them. To address this aim, DNA from IBMFS patients was analyzed by a NGS panel assay of known IBMFS genes. After analysis for point mutations, heterozygous and homozygous CNVs were searched by normalized read coverage ratios and specific thresholds. Of the 258 tested patients, 91 were found to have pathogenic point variants. NGS sample data from 165 patients without pathogenic point mutations were re-analyzed for CNVs; 10 patients were found to have deletions. Diamond Blackfan anemia genes most commonly exhibited heterozygous deletions, and included RPS19, RPL11, and RPL5. A diagnosis of GATA2-related disorder was made in a patient with myelodysplastic syndrome who was found to have a heterozygous GATA2 deletion. Importantly, homozygous FANCA deletion were detected in a patient who could not be previously assigned a specific syndromic diagnosis. Lastly, we identified compound heterozygousity for deletions and pathogenic point variants in RBM8A and PARN genes. All deletions were validated by orthogonal methods. We conclude that careful analysis of normalized coverage values can detect CNVs in NGS panels and should be considered as a standard practice prior to do further investigations

Hydrogen atom moving across a strong magnetic field: analytical approximations

Analytical approximations are constructed for binding energies, quantum-mechanical sizes and oscillator strengths of main radiative transitions of hydrogen atoms arbitrarily moving in magnetic fields 10^{12}-10^{13} G. Examples of using the obtained approximations for determination of maximum transverse velocity of an atom and for evaluation of absorption spectra in magnetic neutron star atmospheres are presented.Comment: 17 pages, 3 figures, 5 tables, LaTeX with IOP style files (included). In v.2, Fig.1 and Table 5 have been corrected. In v.3, a misprint in the fit for oscillator strengths, Eq.(21), has been correcte

Vortex pinning by natural defects in thin films of YBa2Cu3O7−δ

Although vortex pinning in laser-ablated YBa2Cu3O7−δ films on (100) SrTiO3 is dominated by threading dislocations, many other natural pinning sites are present. To identify the contribution from twin planes, surface corrugations and point defects, we manipulate the relative densities of all defects by post-annealing films with various as-grown dislocation densities, ndisl. While a universal magnetic field B dependence of the transport current density js(B, T) is observed (independently of ndisl, temperature T and the annealing treatment), the defect structure changes considerably. Correlating the microstructure to js(B, T), it becomes clear that surface roughness, twins and point defects are not important at low magnetic fields compared to linear defect pinning. Transmission electron microscopy indicates that threading dislocations are not part of grain boundaries nor are they related to the twin domain structure. We conclude that js(B, T) is essentially determined by pinning along threading dislocations, naturally induced during the growth process. Even in high magnetic fields, where the vortex density outnumbers ndisl, it appears that linear defects stabilize the vortex lattice by means of the vortex–vortex interaction.

Personalized surveillance and aftercare for non-metastasized breast cancer:the NABOR study protocol of a multiple interrupted time series design

Background: Follow-up of curatively treated primary breast cancer patients consists of surveillance and aftercare and is currently mostly the same for all patients. A more personalized approach, based on patients’ individual risk of recurrence and personal needs and preferences, may reduce patient burden and reduce (healthcare) costs. The NABOR study will examine the (cost-)effectiveness of personalized surveillance (PSP) and personalized aftercare plans (PAP) on patient-reported cancer worry, self-rated and overall quality of life and (cost-)effectiveness.Methods: A prospective multicenter multiple interrupted time series (MITs) design is being used. In this design, 10 participating hospitals will be observed for a period of eighteen months, while they -stepwise- will transit from care as usual to PSPs and PAPs. The PSP contains decisions on the surveillance trajectory based on individual risks and needs, assessed with the ‘Breast Cancer Surveillance Decision Aid’ including the INFLUENCE prediction tool. The PAP contains decisions on the aftercare trajectory based on individual needs and preferences and available care resources, which decision-making is supported by a patient decision aid. Patients are non-metastasized female primary breast cancer patients (N = 1040) who are curatively treated and start follow-up care. Patient reported outcomes will be measured at five points in time during two years of follow-up care (starting about one year after treatment and every six months thereafter). In addition, data on diagnostics and hospital visits from patients’ Electronical Health Records (EHR) will be gathered. Primary outcomes are patient-reported cancer worry (Cancer Worry Scale) and overall quality of life (as assessed with EQ-VAS score). Secondary outcomes include health care costs and resource use, health-related quality of life (as measured with EQ5D-5L/SF-12/EORTC-QLQ-C30), risk perception, shared decision-making, patient satisfaction, societal participation, and cost-effectiveness. Next, the uptake and appreciation of personalized plans and patients’ experiences of their decision-making process will be evaluated. Discussion: This study will contribute to insight in the (cost-)effectiveness of personalized follow-up care and contributes to development of uniform evidence-based guidelines, stimulating sustainable implementation of personalized surveillance and aftercare plans. Trial registration: Study sponsor: ZonMw. Retrospectively registered at ClinicalTrials.gov (2023), ID: NCT05975437.</p