Software Citation in HEP: Current State and Recommendations for the Future

In November 2022, the HEP Software Foundation (HSF) and the Institute for Research and Innovation for Software in High-Energy Physics (IRIS-HEP) organized a workshop on the topic of Software Citation and Recognition in HEP. The goal of the workshop was to bring together different types of stakeholders whose roles relate to software citation and the associated credit it provides in order to engage the community in a discussion on: the ways HEP experiments handle citation of software, recognition for software efforts that enable physics results disseminated to the public, and how the scholarly publishing ecosystem supports these activities. Reports were given from the publication board leadership of the ATLAS, CMS, and LHCb experiments and HEP open source software community organizations (ROOT, Scikit-HEP, MCnet), and perspectives were given from publishers (Elsevier, JOSS) and related tool providers (INSPIRE, Zenodo). This paper summarizes key findings and recommendations from the workshop as presented at the 26th International Conference on Computing In High Energy and Nuclear Physics (CHEP 2023).Comment: 7 pages, 2 listings. Contribution to the Proceedings of the 26th International Conference on Computing In High Energy and Nuclear Physics (CHEP 2023

Software Citation in HEP: Current State and Recommendations for the Future

In November 2022, the HEP Software Foundation and the Institute for Research and Innovation for Software in High-Energy Physics organized a workshop on the topic of Software Citation and Recognition in HEP. The goal of the workshop was to bring together different types of stakeholders whose roles relate to software citation, and the associated credit it provides, in order to engage the community in a discussion on: the ways HEP experiments handle citation of software, recognition for software efforts that enable physics results disseminated to the public, and how the scholarly publishing ecosystem supports these activities. Reports were given from the publication board leadership of the ATLAS, CMS, and LHCb experiments and HEP open source software community organizations (ROOT, Scikit-HEP, MCnet), and perspectives were given from publishers (Elsevier, JOSS) and related tool providers (INSPIRE, Zenodo). This paper summarizes key findings and recommendations from the workshop as presented at the 26th International Conference on Computing in High Energy and Nuclear Physics (CHEP 2023)

ManyDogs Project: A Big Team Science Approach to Investigating Canine Behavior and Cognition

Dogs have a special place in human history as the first domesticated species and play important roles in many cultures around the world. However, their role in scientific studies has been relatively recent. With a few notable exceptions (e.g., Darwin, Pavlov, Scott, and Fuller), domestic dogs were not commonly the subject of rigorous scientific investigation of behavior until the late 1990s. Although the number of canine science studies has increased dramatically over the last 20 years, most research groups are limited in the inferences they can draw because of the relatively small sample sizes used, along with the exceptional diversity observed in dogs (e.g., breed, geographic location, experience). To this end, we introduce the ManyDogs Project, an international consortium of researchers interested in taking a big team science approach to understanding canine behavioral science. We begin by discussing why studying dogs provides valuable insights into behavior and cognition, evolutionary processes, human health, and applications for animal welfare. We then highlight other big team science projects that have previously been conducted in canine science and emphasize the benefits of our approach. Finally, we introduce the ManyDogs Project and our mission: (a) replicating important findings, (b) investigating moderators that need a large sample size such as breed differences, (c) reaching methodological consensus, (d) investigating cross-cultural differences, and (e) setting a standard for replication studies in general. In doing so, we hope to address previous limitations in individual lab studies and previous big team science frameworks to deepen our understanding of canine behavior and cognition

The Rewiring of Ubiquitination Targets in a Pathogenic Yeast Promotes Metabolic Flexibility, Host Colonization and Virulence

Funding: This work was funded by the European Research Council [http://erc.europa.eu/], AJPB (STRIFE Advanced Grant; C-2009-AdG-249793). The work was also supported by: the Wellcome Trust [www.wellcome.ac.uk], AJPB (080088, 097377); the UK Biotechnology and Biological Research Council [www.bbsrc.ac.uk], AJPB (BB/F00513X/1, BB/K017365/1); the CNPq-Brazil [http://cnpq.br], GMA (Science without Borders fellowship 202976/2014-9); and the National Centre for the Replacement, Refinement and Reduction of Animals in Research [www.nc3rs.org.uk], DMM (NC/K000306/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Acknowledgments We thank Dr. Elizabeth Johnson (Mycology Reference Laboratory, Bristol) for providing strains, and the Aberdeen Proteomics facility for the biotyping of S. cerevisiae clinical isolates, and to Euroscarf for providing S. cerevisiae strains and plasmids. We are grateful to our Microscopy Facility in the Institute of Medical Sciences for their expert help with the electron microscopy, and to our friends in the Aberdeen Fungal Group for insightful discussions.Peer reviewedPublisher PD

Biased M1-muscarinic-receptor-mutant mice inform the design of next-generation drugs

Cholinesterase inhibitors, the current frontline symptomatic treatment for Alzheimer’s disease (AD), are associated with low efficacy and adverse effects. M1 muscarinic acetylcholine receptors (M1 mAChRs) represent a potential alternate therapeutic target; however, drug discovery programs focused on this G protein-coupled receptor (GPCR) have failed, largely due to cholinergic adverse responses. Employing novel chemogenetic and phosphorylation-deficient, G protein-biased, mouse models, paired with a toolbox of probe molecules, we establish previously unappreciated pharmacologically targetable M1 mAChR neurological processes, including anxiety-like behaviors and hyper-locomotion. By mapping the upstream signaling pathways regulating these responses, we determine the importance of receptor phosphorylation-dependent signaling in driving clinically relevant outcomes and in controlling adverse effects including ‘epileptic-like’ seizures. We conclude that M1 mAChR ligands that promote receptor phosphorylation-dependent signaling would protect against cholinergic adverse effects in addition to driving beneficial responses such as learning and memory and anxiolytic behavior relevant for the treatment of AD

Measurement of the Lifetime Difference Between B_s Mass Eigenstates

We present measurements of the lifetimes and polarization amplitudes for B_s --> J/psi phi and B_d --> J/psi K*0 decays. Lifetimes of the heavy (H) and light (L) mass eigenstates in the B_s system are separately measured for the first time by determining the relative contributions of amplitudes with definite CP as a function of the decay time. Using 203 +/- 15 B_s decays, we obtain tau_L = (1.05 +{0.16}/-{0.13} +/- 0.02) ps and tau_H = (2.07 +{0.58}/-{0.46} +/- 0.03) ps. Expressed in terms of the difference DeltaGamma_s and average Gamma_s, of the decay rates of the two eigenstates, the results are DeltaGamma_s/Gamma_s = (65 +{25}/-{33} +/- 1)%, and DeltaGamma_s = (0.47 +{0.19}/-{0.24} +/- 0.01) inverse ps.Comment: 8 pages, 3 figures, 2 tables; as published in Physical Review Letters on 16 March 2005; revisions are for length and typesetting only, no changes in results or conclusion

Development and Validation of a Surgical Workload Measure: The Surgery Task Load Index (SURG-TLX)

Background: The purpose of the present study was to develop and validate a multidimensional, surgery-specific workload measure (the SURG-TLX), and to determine its utility in providing diagnostic information about the impact of various sources of stress on the perceived demands of trained surgical operators. As a wide range of stressors have been identified for surgeons in the operating room, the current approach of considering stress as a unidimensional construct may not only limit the degree to which underlying mechanisms may be understood but also the degree to which training interventions may be successfully matched to particular sources of stress. Methods: The dimensions of the SURG-TLX were based on two current multidimensional workload measures and developed via focus group discussion. The six dimensions were defined as mental demands, physical demands, temporal demands, task complexity, situational stress, and distractions. Thirty novices were trained on the Fundamentals of Laparoscopic Surgery (FLS) peg transfer task and then completed the task under various conditions designed to manipulate the degree and source of stress experienced: task novelty, physical fatigue, time pressure, evaluation apprehension, multitasking, and distraction. Results: The results were supportive of the discriminant sensitivity of the SURG-TLX to different sources of stress. The sub-factors loaded on the relevant stressors as hypothesized, although the evaluation pressure manipulation was not strong enough to cause a significant rise in situational stress. Conclusions: The present study provides support for the validity of the SURG-TLX instrument and also highlights the importance of considering how different stressors may load surgeons. Implications for categorizing the difficulty of certain procedures, the implementation of new technology in the operating room (man-machine interface issues), and the targeting of stress training strategies to the sources of demand are discussed. Modifications to the scale to enhance clinical utility are also suggested. © 2011 The Author(s).published_or_final_versionSpringer Open Choice, 21 Feb 201

American Society of Hematology 2021 guidelines for management of venous thromboembolism: prevention and treatment in patients with cancer

Background: Venous thromboembolism (VTE) is a common complication among patients with cancer. Patients with cancer and VTE are at a markedly increased risk for morbidity and mortality. Objective: These evidence-based guidelines of the American Society of Hematology (ASH) are intended to support patients, clinicians, and other health care professionals in their decisions about the prevention and treatment of VTE in patients with cancer. Methods: ASH formed a multidisciplinary guideline panel balanced to minimize potential bias from conflicts of interest. The guideline development process was supported by updated or new systematic evidence reviews. The Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach was used to assess evidence and make recommendations. Results: Recommendations address mechanical and pharmacological prophylaxis in hospitalized medical patients with cancer, those undergoing a surgical procedure, and ambulatory patients receiving cancer chemotherapy. The recommendations also address the use of anticoagulation for the initial, short-term, and long-term treatment of VTE in patients with cancer. Conclusions: Strong recommendations include not using thromboprophylaxis in ambulatory patients receiving cancer chemotherapy at low risk of VTE and to use low-molecular-weight heparin (LMWH) for initial treatment of VTE in patients with cancer. Conditional recommendations include using thromboprophylaxis in hospitalized medical patients with cancer, LMWH or fondaparinux for surgical patients with cancer, LMWH or direct oral anticoagulants (DOAC) in ambulatory patients with cancer receiving systemic therapy at high risk of VTE and LMWH or DOAC for initial treatment of VTE, DOAC for the short-term treatment of VTE, and LMWH or DOAC for the long-term treatment of VTE in patients with cancer