Human Chromosomes: Evaluation of Processing Techniques for Scanning Electron Microscopy

Methods for scanning electron microscopy (SEM) of chromosomes have been developed in the last two decades. Technical limitations in the study of human chromosomes, however, have hindered the routine use of SEM in clinical and experimental human cytogenetics. We compared different methodologies, including metal impregnation, air drying and specimen coating. SEM preparation of human chromosomes in which osmium impregnation is mediated by tannic acid, yielded more reproducible results when compared with osmium impregnation protocols previously described. The level of osmium impregnation was systematically evaluated by imaging chromosomes in the backscattering mode. Critical point drying and a light gold-palladium coating were essential for appropriate secondary electron imaging of chromosomes. With this method, and in a preliminary quantitative analysis, we show that our SEM technique is mere sensitive than light microscopy for the detection of aphidicolin-induced fragile sites. This technical approach is useful for chromosomal studies requiring resolution higher than that obtained by light microscopy. Also, it allows the use of clinical and archival chromosomal samples prepared by routine cytogenetic techniques

Interface Depinning in the Absence of External Driving Force

We study the pinning-depinning phase transition of interfaces in the quenched Kardar-Parisi-Zhang model as the external driving force $F$ goes towards zero. For a fixed value of the driving force we induce depinning by increasing the nonlinear term coefficient $\lambda$, which is related to lateral growth, up to a critical threshold. We focus on the case in which there is no external force applied (F=0) and find that, contrary to a simple scaling prediction, there is a finite value of $\lambda$ that makes the interface to become depinned. The critical exponents at the transition are consistent with directed percolation depinning. Our results are relevant for paper wetting experiments, in which an interface gets moving with no external driving force.Comment: 4 pages, 3 figures included, uses epsf. Submitted to PR

Universality of Level Spacing Distributions in Classical Chaos

We suggest that random matrix theory applied to a classical action matrix can be used in classical physics to distinguish chaotic from non-chaotic behavior. We consider the 2-D stadium billiard system as well as the 2-D anharmonic and harmonic oscillator. By unfolding of the spectrum of such matrix we compute the level spacing distribution, the spectral auto-correlation and spectral rigidity. We observe Poissonian behavior in the integrable case and Wignerian behavior in the chaotic case. We present numerical evidence that the action matrix of the stadium billiard displays GOE behavior and give an explanation for it. The findings present evidence for universality of level fluctuations - known from quantum chaos - also to hold in classical physics

Thermal effects on atomic friction

We model friction acting on the tip of an atomic force microscope as it is dragged across a surface at non-zero temperatures. We find that stick-slip motion occurs and that the average frictional force follows $|\ln v|^{2/3}$, where $v$ is the tip velocity. This compares well to recent experimental work (Gnecco et al, PRL 84, 1172), permitting the quantitative extraction of all microscopic parameters. We calculate the scaled form of the average frictional force's dependence on both temperature and tip speed as well as the form of the friction-force distribution function.Comment: Accepted for publication, Physical Review Letter

Post-Prior discrepancies in CDW-EIS calculations for ion impact ionization fully differential cross sections

In this work we present fully differential cross sections (FDCSs) calculations using post and prior version of CDW--EIS theory for helium single ionization by 100 MeV C$^{6+}$ amu$^{-1}$ and 3.6 MeV amu$^{-1}$ Au$^{24+}$ and Au$^{53+}$ ions. We performed our calculations for different momentum transfer and ejected electron energies. The influence of internuclear potential on the ejected electron spectra is taken into account in all cases. We compare our calculations with absolute experimental measurements. It is shown that prior version calculations give better agreement with experiments in almost all studied cases.Comment: 9 pages, 7 figure

Enhanced detection of antigen-specific T cells by a multiplexed AIM assay.

Broadly applicable methods to identify and characterize antigen-specific CD4 <sup>+</sup> and CD8 <sup>+</sup> T cells are key to immunology research, including studies of vaccine responses and immunity to infectious diseases. We developed a multiplexed activation-induced marker (AIM) assay that presents several advantages compared to single pairs of AIMs. The simultaneous measurement of four AIMs (CD69, 4-1BB, OX40, and CD40L) creates six AIM pairs that define CD4 <sup>+</sup> T cell populations with partial and variable overlap. When combined in an AND/OR Boolean gating strategy for analysis, this approach enhances CD4 <sup>+</sup> T cell detection compared to any single AIM pair, while CD8 <sup>+</sup> T cells are dominated by CD69/4-1BB co-expression. Supervised and unsupervised clustering analyses show differential expression of the AIMs in defined T helper lineages and that multiplexing mitigates phenotypic biases. Paired and unpaired comparisons of responses to infections (HIV and cytomegalovirus [CMV]) and vaccination (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) validate the robustness and versatility of the method

Spontaneous HIV expression during suppressive ART is associated with the magnitude and function of HIV-specific CD4+ and CD8+ T cells.

Spontaneous transcription and translation of HIV can persist during suppressive antiretroviral therapy (ART). The quantity, phenotype, and biological relevance of this spontaneously "active" reservoir remain unclear. Using multiplexed single-cell RNAflow-fluorescence in situ hybridization (FISH), we detect active HIV transcription in 14/18 people with HIV on suppressive ART, with a median of 28/million CD4 <sup>+</sup> T cells. While these cells predominantly exhibit abortive transcription, p24-expressing cells are evident in 39% of participants. Phenotypically diverse, active reservoirs are enriched in central memory T cells and CCR6- and activation-marker-expressing cells. The magnitude of the active reservoir positively correlates with total HIV-specific CD4 <sup>+</sup> and CD8 <sup>+</sup> T cell responses and with multiple HIV-specific T cell clusters identified by unsupervised analysis. These associations are particularly strong with p24-expressing active reservoir cells. Single-cell vDNA sequencing shows that active reservoirs are largely dominated by defective proviruses. Our data suggest that these reservoirs maintain HIV-specific CD4 <sup>+</sup> and CD8 <sup>+</sup> T responses during suppressive ART

Ethics of HIV cure research: an unfinished agenda

Background: The pursuit of a cure for HIV is a high priority for researchers, funding agencies, governments and people living with HIV (PLWH). To date, over 250 biomedical studies worldwide are or have been related to discovering a safe, effective, and scalable HIV cure, most of which are early translational research and experimental medicine. As HIV cure research increases, it is critical to identify and address the ethical challenges posed by this research. Methods: We conducted a scoping review of the growing HIV cure research ethics literature, focusing on articles published in English peer-reviewed journals from 2013 to 2021. We extracted and summarized key developments in the ethics of HIV cure research. Twelve community advocates actively engaged in HIV cure research provided input on this summary and suggested areas warranting further ethical inquiry and foresight via email exchange and video conferencing. Discussion: Despite substantial scholarship related to the ethics of HIV cure research, additional attention should focus on emerging issues in six categories of ethical issues: (1) social value (ongoing and emerging biomedical research and scalability considerations); (2) scientific validity (study design issues, such as the use of analytical treatment interruptions and placebos); (3) fair selection of participants (equity and justice considerations); (4) favorable benefit/risk balance (early phase research, benefit-risk balance, risk perception, psychological risks, and pediatric research); (5) informed consent (attention to language, decision-making, informed consent processes and scientific uncertainty); and (6) respect for enrolled participants and community (perspectives of people living with HIV and affected communities and representation). Conclusion: HIV cure research ethics has an unfinished agenda. Scientific research and bioethics should work in tandem to advance ethical HIV cure research. Because the science of HIV cure research will continue to rapidly advance, ethical considerations of the major themes we identified will need to be revisited and refined over time