Spatially-modulated Superfluid States in Fermionic Optical Ladder Systems with Repulsive Interactions

We investigate two-component ultracold fermionic atoms with repulsive interactions trapped in an optical lattice with a ladder structure. By applying the Bogoliubov-de Gennes equations to an effective t-J model in the strong correlation limit, we discuss how the spatially-modulated spin-singlet pairs with d-wave like symmetry are formed in the systems with trapping potentials. Furthermore, a close examination of the condensation energy as well as the local average of potential, kinetic and exchange energies by means of the variational Monte Carlo method elucidates that local particle correlations enhance the stability of the superfluid state via substantial energy gain due to singlet pairing in the high particle density region.Comment: 8 pages, 5 figure

Cubic Rashba spin-orbit interaction of two-dimensional hole gas in strained-Ge/SiGe quantum well

The spin-orbit interaction (SOI) of the two-dimensional hole gas in the inversion symmetric semiconductor Ge is studied in a strained-Ge/SiGe quantum well structure. We observed weak anti-localization (WAL) in the magnetoconductivity measurement, revealing that the WAL feature can be fully described by the k-cubic Rashba SOI theory. Furthermore, we demonstrated electric field control of the Rashba SOI. Our findings reveal that the heavy hole (HH) in strained-Ge is a purely cubic-Rashba-system, which is consistent with the spin angular momentum mj = +-3/2 nature of the HH wave function.Comment: To be published in Phys. Rev. Let

Infrared Absorption and Its Sources of CdZnTe at Cryogenic Temperature

To reveal the causes of infrared absorption in the wavelength region between electronic and lattice absorptions, we measured the temperature dependence of the absorption coefficient of p-type low-resistivity (∼102 Ωcm) CdZnTe crystals. We measured the absorption coefficients of CdZnTe crystals in four wavelength bands (λ=6.45, 10.6, 11.6, 15.1 μm) over the temperature range of T=8.6-300 K with an originally developed system. The CdZnTe absorption coefficient was measured to be α=0.3-0.5 cm−1 at T=300 K and α=0.4-0.9 cm−1 at T=8.6 K in the investigated wavelength range. With an absorption model based on transitions of free holes and holes trapped at an acceptor level, we conclude that the absorption due to free holes at T=150-300 K and that due to trapped-holes at T<50 K are dominant absorption causes in CdZnTe. We also discuss a method to predict the CdZnTe absorption coefficient at cryogenic temperature based on the room-temperature resistivity

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell's native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a novel Bayesian method to estimate and remove contamination in individual cells. DecontX accurately predicts contamination levels in a mouse-human mixture dataset and removes aberrant expression of marker genes in PBMC datasets. We also compare the contamination levels between four different scRNA-seq protocols. Overall, DecontX can be incorporated into scRNA-seq workflows to improve downstream analyses.R01 LM013154 - NLM NIH HHS; U01 CA220413 - NCI NIH HHS; R01LM013154-01 - NLM NIH HHSPublished versio

Switching and Emergence of CTL Epitopes in HIV-1 Infection

Background Human Leukocyte Antigen (HLA) class I restricted Cytotoxic T Lymphocytes (CTLs) exert substantial evolutionary pressure on HIV-1, as evidenced by the reproducible selection of HLA-restricted immune escape mutations in the viral genome. An escape mutation from tyrosine to phenylalanine at the 135th amino acid (Y135F) of the HIV-1 nef gene is frequently observed in patients with HLA-A*24:02, an HLA Class I allele expressed in ~70% of Japanese persons. The selection of CTL escape mutations could theoretically result in the de novo creation of novel epitopes, however, the extent to which such dynamic “CTL epitope switching” occurs in HIV-1 remains incompletely known. Results Two overlapping epitopes in HIV-1 nef, Nef126-10 and Nef134-10, elicit the most frequent CTL responses restricted by HLA-A*24:02. Thirty-five of 46 (76%) HLA-A*24:02-positive patients harbored the Y135F mutation in their plasma HIV-1 RNA. Nef codon 135 plays a crucial role in both epitopes, as it represents the C-terminal anchor for Nef126-10 and the N-terminal anchor for Nef134-10. While the majority of patients with 135F exhibited CTL responses to Nef126-10, none harboring the “wild-type” (global HIV-1 subtype B consensus) Y135 did so, suggesting that Nef126-10 is not efficiently presented in persons harboring Y135. Consistent with this, peptide binding and limiting dilution experiments confirmed F, but not Y, as a suitable C-terminal anchor for HLA-A*24:02. Moreover, experiments utilizing antigen specific CTL clones to recognize endogenously-expressed peptides with or without Y135F indicated that this mutation disrupted the antigen expression of Nef134-10. Critically, the selection of Y135F also launched the expression of Nef126-10, indicating that the latter epitope is created as a result of escape within the former. Conclusions Our data represent the first example of the de novo creation of a novel overlapping CTL epitope as a direct result of HLA-driven immune escape in a neighboring epitope. The robust targeting of Nef126-10 following transmission (or in vivo selection) of HIV-1 containing Y135F may explain in part the previously reported stable plasma viral loads over time in the Japanese population, despite the high prevalence of both HLA-A*24:02 and Nef-Y135F in circulating HIV-1 sequences