Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology.Comment: Minor update

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology

Reversible Tuning of Collinear versus Chiral Magnetic Order by Chemical Stimulus

The Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction mediates collinear magnetic interactions via the conduction electrons of a non-magnetic spacer, resulting in a ferro- or antiferromagnetic magnetization in magnetic multilayers. The resulting spin-polarized charge transport effects have found numerous applications. Recently it has been discovered that heavy non-magnetic spacers are able to mediate an indirect magnetic coupling that is non-collinear and chiral. This Dzyaloshinskii-Moriya-enhanced RKKY (DME-RKKY) interaction causes the emergence of a variety of interesting magnetic structures, such as skyrmions and spin spirals. Applications using these magnetic quasi-particles require a thorough understanding and fine-tuning of the balance between the Dzyaloshinskii-Moriya interaction and other magnetic interactions, e.g., the exchange interaction and magnetic anisotropy contributions. Here, we show by spin-polarized scanning tunneling microscopy that the spin structure of manganese oxide chains on Ir(001) can reproducibly be switched from chiral to collinear antiferromagnetic interchain interactions by increasing the oxidation state of MnO$_2$ while the reverse process can be induced by thermal reduction. The underlying structural change is revealed by low-energy electron diffraction intensity data (LEED-IV) analysis. Density functional theory calculations suggest that the magnetic transition may be caused by a significant increase of the Heisenberg exchange upon oxidation.Comment: 6 pages, 3 figure

Charge diffusion in the field-free region of charge-coupled devices

The potential well in back-illuminated charge-coupled devices (CCDs) does not reach all the way to the back surface. Hence, light that is absorbed in the field-free region generates electrons that can diffuse into neighboring pixels and thus decreases the spatial resolution of the sensor. We present data for the charge diffusion from a near point source by measuring the response of a back-illuminated CCD to light emitted from a submicron diameter glass fiber tip. The diffusion of electrons into neighboring pixels is analyzed for different wavelengths of light ranging from 430 to 780 nm. To find out how the charge spreading into other pixels depends on the location of the light spot; the fiber tip could be moved with a piezoelectric translation stage. The experimental data are compared to Monte Carlo simulations and an analytical model of electron diffusion in the field-free region. The presented analysis can be used to predict the charge diffusion in other back-illuminated sensors, and the experiment is universally applicable to measure any type of sensors

Effects of Homophobic versus Nonhomophobic Victimization on School Commitment and the Moderating Effect of Teacher Attitudes in Brazilian Public Schools

This study investigated homophobic victimization, teacher support, and school commitment in Brazilian schools. Participants were 339 students, ages 11 to 18 years old, in two public schools in Brazil. Data were obtained using the Brazil Preventing School Harassment Survey. Structural equation modeling revealed that both homophobic and nonhomophobic victimization were negatively related to school commitment but that homophobic victimization was a stronger predictor. Results supported the hypothesis that supportive teachers can moderate the relationship between victimization and school commitment. Finally, the moderating effect of teacher support was stronger in instances of frequent homophobic victimization

Changes in epithelial proportions and transcriptional state underlie major premenopausal breast cancer risks

The human breast undergoes lifelong remodeling in response to estrogen and progesterone, but hormone exposure also increases breast cancer risk. Here, we use single-cell analysis to identify distinct mechanisms through which breast composition and cell state affect hormone signaling. We show that prior pregnancy reduces the transcriptional response of hormone-responsive (HR+) epithelial cells, whereas high body mass index (BMI) reduces overall HR+ cell proportions. These distinct changes both impact neighboring cells by effectively reducing the magnitude of paracrine signals originating from HR+ cells. Because pregnancy and high BMI are known to protect against hormone-dependent breast cancer in premenopausal women, our findings directly link breast cancer risk with person-to-person heterogeneity in hormone responsiveness. More broadly, our findings illustrate how cell proportions and cell state can collectively impact cell communities through the action of cell-to-cell signaling networks

Electrically driven photon emission from individual atomic defects in monolayer WS2.

Quantum dot-like single-photon sources in transition metal dichalcogenides (TMDs) exhibit appealing quantum optical properties but lack a well-defined atomic structure and are subject to large spectral variability. Here, we demonstrate electrically stimulated photon emission from individual atomic defects in monolayer WS2 and directly correlate the emission with the local atomic and electronic structure. Radiative transitions are locally excited by sequential inelastic electron tunneling from a metallic tip into selected discrete defect states in the WS2 bandgap. Coupling to the optical far field is mediated by tip plasmons, which transduce the excess energy into a single photon. The applied tip-sample voltage determines the transition energy. Atomically resolved emission maps of individual point defects closely resemble electronic defect orbitals, the final states of the optical transitions. Inelastic charge carrier injection into localized defect states of two-dimensional materials provides a powerful platform for electrically driven, broadly tunable, atomic-scale single-photon sources

Long-Range Exciton Diffusion in Two-Dimensional Assemblies of Cesium Lead Bromide Perovskite Nanocrystals

F\"orster Resonant Energy Transfer (FRET)-mediated exciton diffusion through artificial nanoscale building block assemblies could be used as a new optoelectronic design element to transport energy. However, so far nanocrystal (NC) systems supported only diffusion length of 30 nm, which are too small to be useful in devices. Here, we demonstrate a FRET-mediated exciton diffusion length of 200 nm with 0.5 cm2/s diffusivity through an ordered, two-dimensional assembly of cesium lead bromide perovskite nanocrystals (PNC). Exciton diffusion was directly measured via steady-state and time-resolved photoluminescence (PL) microscopy, with physical modeling providing deeper insight into the transport process. This exceptionally efficient exciton transport is facilitated by PNCs high PL quantum yield, large absorption cross-section, and high polarizability, together with minimal energetic and geometric disorder of the assembly. This FRET-mediated exciton diffusion length matches perovskites optical absorption depth, opening the possibility to design new optoelectronic device architectures with improved performances, and providing insight into the high conversion efficiencies of PNC-based optoelectronic devices