Finding the most relevant fragments in networks

We study a point pattern detection problem on networks, motivated by applications in geographical analysis, such as crime hotspot detection. Given a network N (a connected graph with non-negative edge lengths) together with a set of sites, which lie on the edges or vertices of N, we look for a connected subnetwork F of N of small total length that contains many sites. The edges of F can form parts of the edges of N. We consider different variants of this problem where N is either a general graph or restricted to a tree, and the subnetwork F that we are looking for is either a simple path or a tree. We give polynomial-time algorithms, NP-hardness and NP-completeness proofs, approximation algorithms, and also fixed-parameter tractable algorithms

Absence of stable collinear configurations in Ni(001)ultrathin films: canted domain structure as ground state

Brillouin light scattering (BLS) measurements were performed for (17-120) Angstrom thick Cu/Ni/Cu/Si(001) films. A monotonic dependence of the frequency of the uniform mode on an in-plane magnetic field H was observed both on increasing and on decreasing H in the range (2-14) kOe, suggesting the absence of a metastable collinear perpendicular ground state. Further investigation by magneto-optical vector magnetometry (MOKE-VM) in an unconventional canted-field geometry provided evidence for a domain structure where the magnetization is canted with respect to the perpendicular to the film. Spin wave calculations confirm the absence of stable collinear configurations.Comment: 6 pages, 3 figures (text, appendix and 1 figure added

Effect of anisotropic impurity scattering in superconductors

We discuss the weak-coupling BCS theory of a superconductor with the impurities, accounting for their anisotropic momentum-dependent potential. The impurity scattering process is considered in the t-matrix approximation and its influence on the superconducting critical temperature is studied in the Born and unitary limit for a d- and (d+s)-wave superconductors. We observe a significant dependence of the pair-breaking strength on the symmetry of the scattering potential and classify the impurity potentials according to their ability to alter T_c. A good agreement with the experimental data for Zn doping and oxygen irradiation in the overdoped cuprates is found.Comment: 31 pages, RevTex, 15 PostScript figure

Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction

Activation-induced deaminase (AID) initiates antibody diversification in germinal center B cells by deaminating cytosines, leading to somatic hypermutation and class-switch recombination. Loss-of-function mutations in AID lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. AID-mediated deamination has been proposed as leading to active demethylation of 5-methycytosines in the DNA, although evidence both supports and casts doubt on such a role. In this study, using whole-genome bisulfite sequencing of HIGM2 B cells, we investigated direct AID involvement in active DNA demethylation. HIGM2 naïve and memory B cells both display widespread DNA methylation alterations, of which ∼25% are attributable to active DNA demethylation. For genes that undergo active demethylation that is impaired in HIGM2 individuals, our analysis indicates that AID is not directly involved. We demonstrate that the widespread alterations in the DNA methylation and expression profiles of HIGM2 naïve B cells result from premature overstimulation of the B-cell receptor prior to the germinal center reaction. Our data support a role for AID in B cell central tolerance in preventing the expansion of autoreactive cell clones, affecting the correct establishment of DNA methylation patterns

A distinct CD38+CD45RA+ population of CD4+, CD8+, and double-negative T cells is controlled by FAS.

The identification and characterization of rare immune cell populations in humans can be facilitated by their growth advantage in the context of specific genetic diseases. Here, we use autoimmune lymphoproliferative syndrome to identify a population of FAS-controlled TCRαβ+ T cells. They include CD4+, CD8+, and double-negative T cells and can be defined by a CD38+CD45RA+T-BET- expression pattern. These unconventional T cells are present in healthy individuals, are generated before birth, are enriched in lymphoid tissue, and do not expand during acute viral infection. They are characterized by a unique molecular signature that is unambiguously different from other known T cell differentiation subsets and independent of CD4 or CD8 expression. Functionally, FAS-controlled T cells represent highly proliferative, noncytotoxic T cells with an IL-10 cytokine bias. Mechanistically, regulation of this physiological population is mediated by FAS and CTLA4 signaling, and its survival is enhanced by mTOR and STAT3 signals. Genetic alterations in these pathways result in expansion of FAS-controlled T cells, which can cause significant lymphoproliferative disease

Targeted Gene Panel Sequencing for Early-onset Inflammatory Bowel Disease and Chronic Diarrhea

Background: In contrast to adult-onset inflammatory bowel disease (IBD), where many genetic loci have been shown to be involved in complex disease etiology, early-onset IBD (eoIBD) and associated syndromes can sometimes present as monogenic conditions. As a result, the clinical phenotype and ideal disease management in these patients often differ from those in adult-onset IBD. However, due to high costs and the complexity of data analysis, high-throughput screening for genetic causes has not yet become a standard part of the diagnostic work-up of eoIBD patients. Methods: We selected 28 genes of interest associated with monogenic IBD and performed targeted panel sequencing in 71 patients diagnosed with eoIBD or early-onset chronic diarrhea to detect causative variants. We compared these results to whole-exome sequencing (WES) data available for 25 of these patients. Results: Target coverage was significantly higher in the targeted gene panel approach compared with WES, whereas the cost of the panel was considerably lower (approximately 25% of WES). Disease-causing variants affecting protein function were identified in 5 patients (7%), located in genes of the IL10 signaling pathway (3), WAS (1), and DKC1 (1). The functional effects of 8 candidate variants in 5 additional patients (7%) are under further investigation. WES did not identify additional causative mutations in 25 patients. Conclusions: Targeted gene panel sequencing is a fast and effective screening method for monogenic causes of eoIBD that should be routinely established in national referral centers.info:eu-repo/semantics/publishedVersio

Mobility Data Science (Dagstuhl Seminar 22021)

This report documents the program and the outcomes of Dagstuhl Seminar 22021 "Mobility Data Science". This seminar was held January 9-14, 2022, including 47 participants from industry and academia. The goal of this Dagstuhl Seminar was to create a new research community of mobility data science in which the whole is greater than the sum of its parts by bringing together established leaders as well as promising young researchers from all fields related to mobility data science. Specifically, this report summarizes the main results of the seminar by (1) defining Mobility Data Science as a research domain, (2) by sketching its agenda in the coming years, and by (3) building a mobility data science community. (1) Mobility data science is defined as spatiotemporal data that additionally captures the behavior of moving entities (human, vehicle, animal, etc.). To understand, explain, and predict behavior, we note that a strong collaboration with research in behavioral and social sciences is needed. (2) Future research directions for mobility data science described in this report include a) mobility data acquisition and privacy, b) mobility data management and analysis, and c) applications of mobility data science. (3) We identify opportunities towards building a mobility data science community, towards collaborations between academic and industry, and towards a mobility data science curriculum

Hematopoietic cell transplantation in severe combined immunodeficiency : The SCETIDE 2006-2014 European cohort

Publisher Copyright: © 2021 The AuthorsBackground: Hematopoietic stem cell transplantation (HSCT) represents a curative treatment for patients with severe combined immunodeficiency (SCID), a group of monogenic immune disorders with an otherwise fatal outcome. Objective: We performed a comprehensive multicenter analysis of genotype-specific HSCT outcome, including detailed analysis of immune reconstitution (IR) and the predictive value for clinical outcome. Methods: HSCT outcome was studied in 338 patients with genetically confirmed SCID who underwent transplantation in 2006-2014 and who were registered in the SCETIDE registry. In a representative subgroup of 152 patients, data on IR and long-term clinical outcome were analyzed. Results: Two-year OS was similar with matched family and unrelated donors and better than mismatched donor HSCT (P 0.5 × 10e3/μL at +1 year were identified as independent predictors of favorable clinical and immunologic outcome. Conclusion: Recent advances in HSCT in SCID patients have resulted in improved OS and EFS in all genotypes and donor types. To achieve a favorable long-term outcome, treatment strategies should aim for optimal naive CD4 T lymphocyte regeneration.Peer reviewe