Characterizing quantum dynamics with initial system-environment correlations

We fully characterize the reduced dynamics of an open quantum system initially correlated with its environment. Using a photonic qubit coupled to a simulated environment we tomographically reconstruct a superchannel---a generalised channel that treats preparation procedures as inputs---from measurement of the system alone, despite its coupling to the environment. We introduce novel quantitative measures for determining the strength of initial correlations, and to allow an experiment to be optimised in regards to its environment.Comment: 10 pages, 15 figure

Cellular milieu in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is globally the most prevalent renal cancer. The cells of origin in ccRCC have been identified as proximal tubular epithelial cells (PTEC); however, the transcriptomic pathways resulting in the transition from normal to malignant PTEC state have remained unclear. Immunotherapy targeting checkpoints have revolutionized the management of ccRCC, but a sustained clinical response is achieved in only a minority of ccRCC patients. This indicates that our understanding of the mechanisms involved in the malignant transition and resistance to immune checkpoint therapy in ccRCC is unclear. This review examines recent single-cell transcriptomics studies of ccRCC to clarify the transition of PTEC in ccRCC development, and the immune cell types, states, and interactions that may limit the response to targeted immune therapy, and finally suggests stromal cells as key drivers in recurrent and locally invasive ccRCC. These and future single-cell transcriptomics studies will continue to clarify the cellular milieu in the ccRCC microenvironment, thus defining actional clinical, therapeutic, and prognostic characteristics of ccRCC

Operating at the extreme: Estimating the upper yield boundary of winter wheat production in commercial practice

© 2020 The Authors. Wheat farming provides 28.5% of global cereal production. After steady growth in average crop yield from 1950 to 1990, wheat yields have generally stagnated, which prompts the question of whether further improvements are possible. Statistical studies of agronomic parameters such as crop yield have so far exclusively focused on estimating parameters describing the whole of the data, rather than the highest yields specifically. These indicators include the mean or median yield of a crop, or finding the combinations of agronomic traits that are correlated with increasing average yields. In this paper, we take an alternative approach and consider high yields only. We carry out an extreme value analysis of winter wheat yield data collected in England and Wales between 2006 and 2015. This analysis suggests that, under current climate and growing conditions, there is indeed a finite upper bound for winter wheat yield, whose value we estimate to be 17.60 tonnes per hectare. We then refine the analysis for strata defined by either location or level of use of agricultural inputs. We find that there is no statistical evidence for variation of maximal yield depending on location, and neither is there statistical evidence that maximum yield levels are improved by high levels of crop protection and fertilizer use

Intermolecular Interaction Energies in Transition Metal Coordination Compounds

The PIXEL method has been parameterised and validated for transition metals, extending its applicability from ~40% to ~85% of all published crystal structures.</p

Hybridization and Back-Crossing in Giant Petrels (Macronectes giganteus and M. halli) at Bird Island, South Georgia, and a Summary of Hybridization in Seabirds

Hybridization in natural populations provides an opportunity to study the evolutionary processes that shape divergence and genetic isolation of species. The emergence of pre-mating barriers is often the precursor to complete reproductive isolation. However, in recently diverged species, pre-mating barriers may be incomplete, leading to hybridization between seemingly distinct taxa. Here we report results of a long-term study at Bird Island, South Georgia, of the extent of hybridization, mate fidelity, timing of breeding and breeding success in mixed and conspecific pairs of the sibling species, Macronectes halli (northern giant petrel) and M . giganteus (southern giant petrel). The proportion of mixed-species pairs varied annually from 0.4-2.4% (mean of 1.5%), and showed no linear trend with time. Mean laying date in mixed-species pairs tended to be later than in northern giant petrel, and always earlier than in southern giant petrel pairs, and their breeding success (15.6%) was lower than that of conspecific pairs. By comparison, mixed-species pairs at both Marion and Macquarie islands always failed before hatching. Histories of birds in mixed-species pairs at Bird Island were variable; some bred previously or subsequently with a conspecific partner, others subsequently with a different allospecific partner, and some mixed-species pairs remained together for multiple seasons. We also report the first verified back-crossing of a hybrid giant petrel with a female northern giant petrel. We discuss the potential causes and evolutionary consequences of hybridization and back-crossing in giant petrels and summarize the incidence of back-crossing in other seabird species

Multi-color Optical and NIR Light Curves of 64 Stripped-Envelope Core-Collapse Supernovae

We present a densely-sampled, homogeneous set of light curves of 64 low redshift (z < 0.05) stripped-envelope supernovae (SN of type IIb, Ib, Ic and Ic-bl). These data were obtained between 2001 and 2009 at the Fred L. Whipple Observatory (FLWO) on Mt. Hopkins in Arizona, with the optical FLWO 1.2-m and the near-infrared PAIRITEL 1.3-m telescopes. Our dataset consists of 4543 optical photometric measurements on 61 SN, including a combination of UBVRI, UBVr'i', and u'BVr'i', and 2142 JHKs near-infrared measurements on 25 SN. This sample constitutes the most extensive multi-color data set of stripped-envelope SN to date. Our photometry is based on template-subtracted images to eliminate any potential host galaxy light contamination. This work presents these photometric data, compares them with data in the literature, and estimates basic statistical quantities: date of maximum, color, and photometric properties. We identify promising color trends that may permit the identification of stripped-envelope SN subtypes from their photometry alone. Many of these SN were observed spectroscopically by the CfA SN group, and the spectra are presented in a companion paper (Modjaz et al. 2014). A thorough exploration that combines the CfA photometry and spectroscopy of stripped-envelope core-collapse SN will be presented in a follow-up paper.Comment: 26 pages, 17 figures, 8 tables. Revised version resubmitted to ApJ Supplements after referee report. Additional online material is available through http://cosmo.nyu.edu/SNYU

Investigating the effects of irrational and rational self-statements on motor-skill and hazard-perception performance

Rational Emotive Behavior Therapy (REBT) is a psychotherapeutic approach based on the premise that when faced with adversity irrational beliefs determine unhealthy negative emotions and maladaptive behaviors, whereas rational beliefs lead to healthy and adaptive alternatives. The detrimental effects of irrational beliefs on psychological health are established, however less is known about the deleterious effects on human behavior and performance. In the present study we examined the effects of irrational and rational self-statements on motor-skill performance (Experiment 1), performance effectiveness, and efficiency during a modified hazard perception task, and task persistence during a breath-holding task (Experiment 2). Using a repeated measures counter balanced design, two cohorts of 35 undergraduate university students were recruited for Experiment 1 and 2, each participating in no self-statement, irrational, and rational self-statement conditions. Data indicated no differences in motor-skill and task performance, performance efficiency, task persistence, mental effort, and pre-performance anxiety between irrational and rational self-statement conditions. In contrast to previous research the findings provide insight into a juxtaposition that irrational beliefs hinder psychological health, yet may help performance, highlighting important distinctions in factual and practical rationality that have been overlooked within the extant literature. The findings have important practical implications for practitioners that may look to REBT to enhance the psychological health and performance for individuals who operate in high performance contexts. Further, the short and long-term effects of irrational and rational beliefs on performance and psychological health warrants greater investigation

Chimpanzees demonstrate individual differences in social information use

Studies of transmission biases in social learning have greatly informed our understanding of how behaviour patterns may diffuse through animal populations, yet within-species inter-individual variation in social information use has received little attention and remains poorly understood. We have addressed this question by examining individual performances across multiple experiments with the same population of primates. We compiled a dataset spanning 16 social learning studies (26 experimental conditions) carried out at the same study site over a 12-year period, incorporating a total of 167 chimpanzees. We applied a binary scoring system to code each participant’s performance in each study according to whether they demonstrated evidence of using social information from conspecifics to solve the experimental task or not (Social Information Score—‘SIS’). Bayesian binomial mixed effects models were then used to estimate the extent to which individual differences influenced SIS, together with any effects of sex, rearing history, age, prior involvement in research and task type on SIS. An estimate of repeatability found that approximately half of the variance in SIS was accounted for by individual identity, indicating that individual differences play a critical role in the social learning behaviour of chimpanzees. According to the model that best fit the data, females were, depending on their rearing history, 15–24% more likely to use social information to solve experimental tasks than males. However, there was no strong evidence of an effect of age or research experience, and pedigree records indicated that SIS was not a strongly heritable trait. Our study offers a novel, transferable method for the study of individual differences in social learning

A Screen for Retrotransposed Imprinted Genes Reveals an Association between X Chromosome Homology and Maternal Germ-Line Methylation

Imprinted genes undergo epigenetic modifications during gametogenesis, which lead to transcriptional silencing of either the maternally or the paternally derived allele in the subsequent generation. Previous work has suggested an association between imprinting and the products of retrotransposition, but the nature of this link is not well defined. In the mouse, three imprinted genes have been described that originated by retrotransposition and overlap CpG islands which undergo methylation during oogenesis. Nap1l5, U2af1-rs1, and Inpp5f_v2 are likely to encode proteins and share two additional genetic properties: they are located within introns of host transcripts and are derived from parental genes on the X chromosome. Using these sequence features alone, we identified Mcts2, a novel candidate imprinted retrogene on mouse Chromosome 2. Mcts2 has been validated as imprinted by demonstrating that it is paternally expressed and undergoes promoter methylation during oogenesis. The orthologous human retrogenes NAP1L5, INPP5F_V2, and MCTS2 are also shown to be paternally expressed, thus delineating novel imprinted loci on human Chromosomes 4, 10, and 20. The striking correlation between imprinting and X chromosome provenance suggests that retrotransposed elements with homology to the X chromosome can be selectively targeted for methylation during mammalian oogenesis

Loss of Atrx Affects Trophoblast Development and the Pattern of X-Inactivation in Extraembryonic Tissues

ATRX is an X-encoded member of the SNF2 family of ATPase/helicase proteins thought to regulate gene expression by modifying chromatin at target loci. Mutations in ATRX provided the first example of a human genetic disease associated with defects in such proteins. To better understand the role of ATRX in development and the associated abnormalities in the ATR-X (alpha thalassemia mental retardation, X-linked) syndrome, we conditionally inactivated the homolog in mice, Atrx, at the 8- to 16-cell stage of development. The protein, Atrx, was ubiquitously expressed, and male embryos null for Atrx implanted and gastrulated normally but did not survive beyond 9.5 days postcoitus due to a defect in formation of the extraembryonic trophoblast, one of the first terminally differentiated lineages in the developing embryo. Carrier female mice that inherit a maternal null allele should be affected, since the paternal X chromosome is normally inactivated in extraembryonic tissues. Surprisingly, however, some carrier females established a normal placenta and appeared to escape the usual pattern of imprinted X-inactivation in these tissues. Together these findings demonstrate an unexpected, specific, and essential role for Atrx in the development of the murine trophoblast and present an example of escape from imprinted X chromosome inactivation