Generating Peptide Mass Spectrometry Ground Truth Data

Very few quantitative evaluations exist for precursor mass spectrometry data due to the lack of tools for enabling the manual feature finding necessary to generate this data. Other lacks the ability to capture, edit, save, and view precursor mass spectrometry data. We present JS-MS 2.0, a software suite that provides a dependency-free, browser-based, one click, cross-platform solution for creating precursor ground truth. The software retains the first version’s capacity for loading, viewing, and navigating MS1 data in 2- and 3-D, and adds tools for capturing, editing, saving and viewing isotopic envelope and extracted isotopic chromatogram features. The software can also be used to view and explore the results of feature finding algorithms. JS-MS 2.0 enables faster creation and inspection of precursor mass spectrometry ground truth data. It is publicly available with a GPL 2.0 license at github.com/optimusmoose/jsms

Exploring root rot pathogens in wheat-pea rotations in Kansas

In 2018, over 277,000 bushels of wheat were produced on 7.7 million acres of land in Kansas alone. Based on the price of wheat by the end of 2018, this accounted for $1.44 million. This wheat is normally rotated with soybeans or fallow, but recent interest has arisen regarding the growth of peas in northern Kansas. As of 2019, there are both research and commercial growing operations underway. Many plant diseases have been especially prevalent during the summer because of the high rainfall and heat. In order to assess the severity of pea disease in Kansas, as well as explore potential interconnectivity between wheat and pea pathogens, a survey was conducted, and efforts were made to isolate and culture fungal pathogens of both wheat and pea

A cohort study of the recovery of health and wellbeing following colorectal cancer (CREW study): protocol paper

Background: the number of people surviving colorectal cancer has doubled in recent years. While much of the literature suggests that most people return to near pre-diagnosis status following surgery for colorectal cancer, this literature has largely focused on physical side effects. Longitudinal studies in colorectal cancer have either been small scale or taken a narrow focus on recovery after surgery. There is a need for a comprehensive, long-term study exploring all aspects of health and wellbeing in colorectal cancer patients. The aim of this study is to establish the natural history of health and wellbeing in people who have been treated for colorectal cancer. People have different dispositions, supports and resources, likely resulting in individual differences in restoration of health and wellbeing. The protocol described in this paper is of a study which will identify who is most at risk of problems, assess how quickly people return to a state of subjective health and wellbeing, and will measure factors which influence the course of recovery. Methods: this is a prospective, longitudinal cohort study following 1000 people with colorectal cancer over a period of two years, recruiting from 30 NHS cancer treatment centres across the UK. Questionnaires will be administered prior to surgery, and 3, 9, 15 and 24 months after surgery, with the potential to return to this cohort to explore on-going issues related to recovery after cancer. Discussion: outcomes will help inform health care providers about what helps or hinders rapid and effective recovery from cancer, and identify areas for intervention development to aid this process. Once established the cohort can be followed up for longer periods and be approached to participate in related projects as appropriate and subject to funding<br/

Discovery of a Metal-Line Absorber Associated with a Local Dwarf Starburst Galaxy

We present optical and near-infrared images, H I 21 cm emission maps, optical spectroscopy, and Hubble Space Telescope/Space Telescope Imaging Spectrograph ultraviolet spectroscopy of the QSO/galaxy pair SBS 1122+594/IC 691. The QSO sight line lies at a position angle of 27 degrees from the minor axis of the nearby dwarf starburst galaxy IC 691 (cz_gal = 1204+-3 km/s, L_B ~ 0.09 L*, current star formation rate = 0.08-0.24 solar masses per year) and 33 kpc (6.6 arcmin) from its nucleus. We find that IC 691 has an H I mass of M_HI = (3.6+-0.1) x 10^8 solar masses and a dynamical mass of M_dyn = (3.1+-0.5) x 10^10 solar masses. The UV spectrum of SBS 1122+594 shows a metal-line (Ly-alpha + C IV) absorber near the redshift of IC 691 at cz_abs = 1110+-30 km/s. Since IC 691 is a dwarf starburst and the SBS 1122+594 sight line lies in the expected location for an outflowing wind, we propose that the best model for producing this metal-line absorber is a starburst wind from IC 691. We place consistent metallicity limits on IC 691 ([Z/Zsun] ~ -0.7) and the metal-line absorber ([Z/Zsun] < -0.3). We also find that the galaxy's escape velocity at the absorber location is v_esc = 80+-10 km/s and derive a wind velocity of v_w = 160+-50 km/s. Thus, the evidence suggests that IC 691 produces an unbound starburst wind that escapes from its gravitational potential to transport metals and energy to the surrounding intergalactic medium.Comment: 31 pages, 8 figures; AJ in press; a version with high resolution figures can be downloaded from http://casa.colorado.edu/~keeney/research/papers/IC691.pd

Arctic fires re-emerging

Underground smouldering fires resurfaced early in 2020, contributing to the unprecedented wildfires that tore through the Arctic this spring and summer. An international effort is needed to manage a changing fire regime in the vulnerable Arctic

Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans -Acting Modifiers

Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation

Parity at a Price: The Emerging Professional Liability of Mental Health Providers

This Article considers the issues associated with emerging professional liability claims against mental health care providers. Part II supplies background information regarding this liability, including the elements of these claims. Part III details the decreasing stigma associated with obtaining mental health services and its impact on professional liability, while Part IV summarizes advancements in mental health treatment that have enhanced the functional capacities of potential litigants. The remaining Parts explore changes in the delivery of mental health care where litigation may be focused, including the increasing use of psychotropic medications (Part V), the expanding role of primary care physicians and other health care providers with limited training and experience pertaining to the treatment of mental illness (Part VI), the surge in pediatric psychotropic prescriptions (Part VII), the emergence of the informed consent doctrine and psychiatric advance directives (Part VIII), and the continuing development of Tarasoff-related liability (Part IX)

Engaging Rural and Urban Appalachians in Research using a Community-Based Participatory Research Approach

Appalachians are particularly vulnerable to chronic diseases as documented by recent national studies that have identified disproportionally higher rates of cancer, diabetes, heart disease and premature mortality for this population. Evidence-based interventions to reduce rates of diabetes and obesity among adults and children have been ineffective among Appalachians where multiple factors including poor living conditions, limited health information, lifestyle behaviors, and lack of access to health care interact to increase the prevalence of these problems. However, there is growing evidence that Community-Based Participatory Research (CBPR) conducted through community-academic partnerships can lead to significant health and social impact in communities faced with seemingly intractable health disparities. Framed in the guiding principles of the CBPR approach, this paper describes the development of two academic-community partnerships that took root in Appalachian communities, one urban and one rural. Both partnerships aimed to identify community health needs, develop a community-led intervention to promote positive health outcomes, and evaluate that work iteratively. Although the initial focus for each community was to address obesity and diabetes risk, adherence to the CBPR approach led to different community identified prioritized needs and different pilot projects. The CBPR approach resulted in strong partnerships, each with improved capacity to address Appalachian health disparities in their communities

Individual Differences in Personality Predict Externalizing Versus Internalizing Outcomes Following Sexual Assault

For some women, the experience of being sexually assaulted leads to increases in externalizing behaviors, such as problem drinking and drug use; for other women, the experience of being assaulted leads to increases in internalizing distress, such as depression or anxiety. It is possible that preassault personality traits interact with sexual assault to predict externalizing or internalizing distress. We tested whether concurrent relationships among personality, sexual assault, and distress were consistent with such a model. We surveyed 750 women just prior to their freshman year at a large public university. Consistent with our hypotheses, at low levels of negative urgency (the tendency to act rashly when distressed), sexual assault exposure had little relationship to problem drinking and drug use. At high levels of negative urgency, being sexually assaulted was highly associated with those externalizing behaviors. At low levels of internalizing personality traits, being assaulted had little relationship to depression and anxiety symptoms; at high levels of the traits, assault experience was highly related to those symptoms. Personality assessment could lead to more person-specific postassault interventions