The ground state of a spin-1/2 neutral particle with anomalous magnetic moment in a Aharonov-Casher configuration

We determine the (bound) ground state of a spin 1/2 chargless particle with anomalous magnetic moment in certain Aharonov-Casher configurations. We recast the description of the system in a supersymmetric form. Then the basic physical requirements for unbroken supersymmetry are established. We comment on the possibility of neutron trapping in these systems

Linearly independent pure-state decomposition and quantum state discrimination

We put the pure-state decomposition mathematical property of a mixed state to a physical test. We begin by characterizing all the possible decompositions of a rank-two mixed state by means of the complex overlap between two involved states. The physical test proposes a scheme of quantum state recognition of one of the two linearly independent states which arise from the decomposition. We find that the two states associated with the balanced pure-state decomposition have the smaller overlap modulus and therefore the smallest probability of being discriminated conclusively, while in the nonconclusive scheme they have the highest probability of having an error. In addition, we design an experimental scheme which allows to discriminate conclusively and optimally two nonorthogonal states prepared with different a priori probabilities. Thus, we propose a physical implementation for this linearly independent pure-state decomposition and state discrimination test by using twin photons generated in the process of spontaneous parametric down conversion. The information-state is encoded in one photon polarization state whereas the second single-photon is used for heralded detection.Comment: 6 pages, 5 figures, Submitted to Phys. Rev.

Automated Variance-Based Sensitivity Analysis of a Heterogeneous Atomistic-Continuum System

A fully automated computational tool for the study of the uncertainty in a mathematical-computational model of a heterogeneous multi-scale atomistic-continuum coupling system is implemented and tested in this project. This tool can facilitate quantitative assessments of the model’s overall uncertainty for a given specific range of variables. The computational approach here is based on the polynomial chaos expansion using projection variance, a pseudo-spectral method. It also supports regression variance, a point collocation method with nested quadrature point where the random sampling method takes a dictionary of the names of the parameters which are manually defined to vary with corresponding distributions. The tool in conjunction with an existing platform for verification, validation, and uncertainty quantification offers a scientific simulation environment and data processing workflows that enables the execution of simulation and analysis tasks on a cluster or supercomputing platform with remote submission capabilities

Monkeypox, bioethics and the LGBTQI+ community

The COVID-19 pandemic has been a challenging time for different communities, including the LGBTQI+ (lesbian, gay, bisexual, transgender, queer, intersex, and other gender identities and sexual orientations) community, and has sharpened health inequalities already present before the pandemic. In his report to the United Nations General Assembly of 28 July 2020, the United Nations Independent Expert on protection against violence and discrimination based on sexual orientation and gender identity, Victor Madrigal-Borloz, provided a detailed overview of ways in which the COVID-19 pandemic has affected the LGBTQI+ community [1]. Stay-at-home policies, quarantine and isolation, and social stress have severely increased their risk of victimization, particularly in the case of LGBTQI+ people living with unsupportive family members. In several countries, including, e.g., the United States, Turkey, Georgia, Ghana and Malaysia, powerful religious and political leaders have blamed LGBTQI+ persons for the COVID-19 pandemic, which has led to a sharp rise in (online) hate speech. In Uganda, lockdown policies have been instrumentalised for a crackdown on the LGBTQI+ community [1]. The mental health of many LGBTQI+ persons has also significantly deteriorated in many countries; in the US, for example, 50.0% of LGBTQI+ adult respondents in the US Census Bureau’s March – May 2022 Household Pulse Survey reported symptoms of anxiety (compared to 24.3% of non-LGBTQI+ adults) and 41.6% symptoms of depression (compared to 19.4% of non-LGBTQI+ adults) [2]

Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate

Coupled transcription and translation in bacteria are tightly regulated. Some small RNAs (sRNAs) control aspects of this coupling by modifying ribosome access or inducing degradation of the message. Here, we show that sRNA IsrA (IS61 or McaS) specifically associates with core enzyme of RNAP in vivo and in vitro, independently of σ factor and away from the main nucleic-acids-binding channel of RNAP. We also show that, in the cells, IsrA exists as ribonucleoprotein particles (sRNPs), which involve a defined set of proteins including Hfq, S1, CsrA, ProQ and PNPase. Our findings suggest that IsrA might be directly involved in transcription or can participate in regulation of gene expression by delivering proteins associated with it to target mRNAs through its interactions with transcribing RNAP and through regions of sequence-complementarity with the target. In this eukaryotic-like model only in the context of a complex with its target, IsrA and its associated proteins become active. In this manner, in the form of sRNPs, bacterial sRNAs could regulate a number of targets with various outcomes, depending on the set of associated proteins

Demersal fish assemblages on seamounts and other rugged features in the northeastern Caribbean

© The Author(s), 2017. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part I: Oceanographic Research Papers 123 (2017): 90–104, doi:10.1016/j.dsr.2017.03.009.Recent investigations of demersal fish communities in deepwater (>50 m) habitats have considerably increased our knowledge of the factors that influence the assemblage structure of fishes across mesophotic to deep-sea depths. While different habitat types influence deepwater fish distribution, whether different types of rugged seafloor features provide functionally equivalent habitat for fishes is poorly understood. In the northeastern Caribbean, different types of rugged features (e.g., seamounts, banks, canyons) punctuate insular margins, and thus create a remarkable setting in which to compare demersal fish communities across various features. Concurrently, several water masses are vertically layered in the water column, creating strong stratification layers corresponding to specific abiotic conditions. In this study, we examined differences among fish assemblages across different features (e.g., seamount, canyon, bank/ridge) and water masses at depths ranging from 98 to 4060 m in the northeastern Caribbean. We conducted 26 remotely operated vehicle dives across 18 sites, identifying 156 species of which 42% of had not been previously recorded from particular depths or localities in the region. While rarefaction curves indicated fewer species at seamounts than at other features in the NE Caribbean, assemblage structure was similar among the different types of features. Thus, similar to seamount studies in other regions, seamounts in the Anegada Passage do not harbor distinct communities from other types of rugged features. Species assemblages, however, differed among depths, with zonation generally corresponding to water mass boundaries in the region. High species turnover occurred at depths <1200 m, and may be driven by changes in water mass characteristics including temperature (4.8–24.4 °C) and dissolved oxygen (2.2–9.5 mg per l). Our study suggests the importance of water masses in influencing community structure of benthic fauna, while considerably adding to the knowledge of mesophotic and deep-sea fish biogeography.Funding was provided by NOAA-OER for the 2014 E/V Nautilus cruise and by the USGS Environments and Hazards Program and Ocean Exploration Trust for the 2013 E/V Nautilus 807 cruise.2019-03-1

The ATPase activity of MLH1 is required to orchestrate DNA double-strand breaks and end processing during class switch recombination.

PublishedJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tAntibody diversification through somatic hypermutation (SHM) and class switch recombination (CSR) are similarly initiated in B cells with the generation of U:G mismatches by activation-induced cytidine deaminase but differ in their subsequent mutagenic consequences. Although SHM relies on the generation of nondeleterious point mutations, CSR depends on the production of DNA double-strand breaks (DSBs) and their adequate recombination through nonhomologous end joining (NHEJ). MLH1, an ATPase member of the mismatch repair (MMR) machinery, is emerging as a likely regulator of whether a U:G mismatch progresses toward mutation or DSB formation. We conducted experiments on cancer modeled ATPase-deficient MLH1G67R knockin mice to determine the function that the ATPase domain of MLH1 mediates in SHM and CSR. Mlh1(GR/GR) mice displayed a significant decrease in CSR, mainly attributed to a reduction in the generation of DSBs and diminished accumulation of 53BP1 at the immunoglobulin switch regions. However, SHM was normal in these mice, which distinguishes MLH1 from upstream members of the MMR pathway and suggests a very specific role of its ATPase-dependent functions during CSR. In addition, we show that the residual switching events still taking place in Mlh1(GR/GR) mice display unique features, suggesting a role for the ATPase activity of MLH1 beyond the activation of the endonuclease functions of its MMR partner PMS2. A preference for switch junctions with longer microhomologies in Mlh1(GR/GR) mice suggests that through its ATPase activity, MLH1 also has an impact in DNA end processing, favoring canonical NHEJ downstream of the DSB. Collectively, our study shows that the ATPase domain of MLH1 is important to transmit the CSR signaling cascade both upstream and downstream of the generation of DSBs.Spanish Ministry of Education and ScienceNIHNational Women’s Division of the Albert Einstein College of Medicin

A rapid and simple quantitative method for specific Detection of Smaller Co-terminal RNA by PCR (DeSCo-PCR): Application to the detection of viral subgenomic RNAs

RNAs that are 5’-truncated versions of a longer RNA, but share the same 3’ terminus can be generated by alternative promoters in transcription of cellular mRNAs or by replicating RNA viruses. These truncated RNAs cannot be distinguished from the longer RNA by a simple two-primer RT-PCR because primers that anneal to the cDNA from the smaller RNA also anneal to - and amplify - the longer RNA-derived cDNA. Thus, laborious methods, such as northern blot hybridization, are used to distinguish shorter from longer RNAs. For rapid, low-cost and specific detection of these truncated RNAs, we report Detection of Smaller Co-terminal RNA by PCR (DeSCo-PCR). DeSCo-PCR employs a non-extendable blocking primer (BP), which outcompetes a forward primer (FP) for annealing to longer RNA-derived cDNA, while FP outcompetes BP for annealing to shorter RNA-derived cDNA. In the presence of BP, FP and the reverse primer, only cDNA from the shorter RNA is amplified in a single-tube reaction containing both RNAs. Many positive strand RNA viruses generate 5’-truncated forms of the genomic RNA (gRNA) called subgenomic RNAs (sgRNA), which play key roles in viral gene expression and pathogenicity. We demonstrate that DeSCo-PCR is easily optimized to selectively detect relative quantities of sgRNAs of red clover necrotic mosaic virus from plants and Zika virus from human cells, each infected with viral strains that generate different amounts of sgRNA. This technique should be readily adaptable to other sgRNA-producing viruses, and for quantitative detection of any truncated or alternatively spliced RNA

Quantum phase transitions in an effective Hamiltonian: fast and slow systems

An effective Hamiltonian describing interaction between generic "fast" and a "slow" systems is obtained in the strong interaction limit. The result is applied for studying the effect of quantum phase transition as a bifurcation of the ground state of the "slow subsystem" in the thermodynamic limit. Examples as atom-field and atom-atom interactions are analyzed in detail