Atomic Fermi gas in the trimerized Kagom\'e lattice at the filling 2/3

We study low temperature properties of an atomic spinless interacting Fermi gas in the trimerized Kagom\'e lattice for the case of two fermions per trimer. The system is described by a quantum spin 1/2 model on the triangular lattice with couplings depending on bonds directions. Using exact diagonalizations we show that the system exhibits non-standard properties of a {\it quantum spin-liquid crystal}, combining a planar antiferromagnetic order with an exceptionally large number of low energy excitations.Comment: 4 pages & 4 figures + 2 tables, better version of Fig.

Atomic Bose-Fermi mixtures in an optical lattice

A mixture of ultracold bosons and fermions placed in an optical lattice constitutes a novel kind of quantum gas, and leads to phenomena, which so far have been discussed neither in atomic physics, nor in condensed matter physics. We discuss the phase diagram at low temperatures, and in the limit of strong atom-atom interactions, and predict the existence of quantum phases that involve pairing of fermions with one or more bosons, or, respectively, bosonic holes. The resulting composite fermions may form, depending on the system parameters, a normal Fermi liquid, a density wave, a superfluid liquid, or an insulator with fermionic domains. We discuss the feasibility for observing such phases in current experiments.Comment: 4 pages, 1 eps figure, misprints correcte

Robust metabolic transcriptional components in 34,494 patient-derived cancer-related samples and cell lines

BACKGROUND: Patient-derived bulk expression profiles of cancers can provide insight into the transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. However, consensus independent component analyses (c-ICA) can capture statistically independent transcriptional footprints of both subtle and more pronounced metabolic processes. METHODS: We performed c-ICA with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. Gene set enrichment analysis with 608 gene sets that describe metabolic processes was performed to identify the transcriptional components enriched for metabolic processes (mTCs). The activity of these mTCs was determined in all samples to create a metabolic transcriptional landscape. RESULTS: A set of 555 mTCs was identified of which many were robust across different datasets, platforms, and patient-derived tissues and cell lines. We demonstrate how the metabolic transcriptional landscape defined by the activity of these mTCs in samples can be used to explore the associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. CONCLUSIONS: To facilitate the use of our transcriptional metabolic landscape, we have provided access to all data via a web portal (www.themetaboliclandscapeofcancer.com). We believe this resource will contribute to the formulation of new hypotheses on how to metabolically engage the tumor or its (immune) microenvironment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40170-021-00272-7

Immune microenvironment composition in non-small cell lung cancer and its association with survival

Objectives In non-small cell lung cancer (NSCLC), the immune system and possibly its composition affect survival. In thisin silicostudy, the immune infiltrate composition in NSCLC patients was evaluated. Methods Gene expression data of tumors from early NSCLC patients were obtained from Gene Expression Omnibus (GEO). With CIBERSORT, 22 immune cell fractions were estimated. Results The immune infiltrate of 1430 pretreatment NSCLC patients contained mostly plasma cells, macrophages and CD8 T cells. Higher fractions of resting mast and CD4 T-helper cells were associated with longer overall survival (OS) (HR = 0.95,P <0.01; HR = 0.98, = 0.04, respectively) and higher fractions of M2 macrophages and active dendritic cells with shorter survival (HR = 1.02,P = 0.03; HR = 1.03,P = 0.05, respectively). Adenocarcinoma patients with survival data (n = 587) showed higher fractions of resting mast and resting CD4 T cells, and lower M0 macrophages than squamous cell carcinoma (n = 254), which were associated with OS (HR = 0.95,P = 0.04; HR = 0.97,P = 0.01; HR = 1.03,P = 0.01, respectively). Fractions of memory B cells, naive CD4 T cells and neutrophils had different associations with survival depending on the subtype. Smokers had had higher fractions of regulatory T cell, follicular helper T cell, neutrophil and M2 macrophage, which were associated with shorter survival (HR = 1.3,P <0.01; HR = 1.13,P = 0.02; HR = 1.09,P = 0.03; HR = 1.04,P = 0.02, respectively). Conclusion Pretreatment differences in immune cell composition in NSCLC are associated with survival and depend on smoking status and histological subtype. Smokers' immune composition is associated with lower survival

Quantum gases in trimerized kagom\'e lattices

We study low temperature properties of atomic gases in trimerized optical kagom\'{e} lattices. The laser arrangements that can be used to create these lattices are briefly described. We also present explicit results for the coupling constants of the generalized Hubbard models that can be realized in such lattices. In the case of a single component Bose gas the existence of a Mott insulator phase with fractional numbers of particles per trimer is verified in a mean field approach. The main emphasis of the paper is on an atomic spinless interacting Fermi gas in the trimerized kagom\'{e} lattice with two fermions per site. This system is shown to be described by a quantum spin 1/2 model on the triangular lattice with couplings that depend on the bond directions. We investigate this model by means of exact diagonalization. Our key finding is that the system exhibits non-standard properties of a quantum spin-liquid crystal: it combines planar antiferromagnetic order in the ground state with an exceptionally large number of low energy excitations. The possibilities of experimental verification of our theoretical results are critically discussed.Comment: 19 pages/14 figures, version to appear in Phys. Rev. A., numerous minor corrections with respect to former lanl submissio

Genome-wide association study of cardiovascular disease in testicular cancer patients treated with platinum-based chemotherapy

Genetic variation may mediate the increased risk of cardiovascular disease (CVD) in chemotherapy-treated testicular cancer (TC) patients compared to the general population. Involved single nucleotide polymorphisms (SNPs) might differ from known CVD-associated SNPs in the general population. We performed an explorative genome-wide association study (GWAS) in TC patients. TC patients treated with platinum-based chemotherapy between 1977 and 2011, age ≤55 years at diagnosis, and ≥3 years relapse-free follow-up were genotyped. Association between SNPs and CVD occurrence during treatment or follow-up was analyzed. Data-driven Expression Prioritized Integration for Complex Trait (DEPICT) provided insight into enriched gene sets, i.e., biological themes. During a median follow-up of 11 years (range 3-37), CVD occurred in 53 (14%) of 375 genotyped patients. Based on 179 SNPs associated at p ≤ 0.001, 141 independent genomic loci associated with CVD occurrence. Subsequent, DEPICT found ten biological themes, with the RAC2/RAC3 network (linked to endothelial activation) as the most prominent theme. Biology of this network was illustrated in a TC cohort (n = 60) by increased circulating endothelial cells during chemotherapy. In conclusion, the ten observed biological themes highlight possible pathways involved in CVD in chemotherapy-treated TC patients. Insight in the genetic susceptibility to CVD in TC patients can aid future intervention strategies