bluuebunny/crossref_metadata_2025_split huggingface dataset:
GfaViz: flexible and interactive visualization of GFA sequence graphs
Authors: Gonnella Giorgio , Niehus Niklas , Kurtz Stefan 
Published: December 2018

Abstract

Summary
The graphical fragment assembly (GFA) formats are emerging standard formats for the representation of sequence graphs. Although GFA 1 was primarily targeting assembly graphs, the newer GFA 2 format introduces several features, which makes it suitable for representing other kinds of information, such as scaffolding graphs, variation graphs, alignment graphs and colored metagenomic graphs. Here, we present GfaViz, an interactive graphical tool for the visualization of sequence graphs in GFA format. The software supports all new features of GFA 2 and introduces conventions for their visualization. The user can choose between two different layouts and multiple styles for representing single elements or groups. All customizations can be stored in custom tags of the GFA format itself, without requiring external configuration files. Stylesheets are supported for storing standard configuration options for groups of files. The visualizations can be exported to raster and vector graphics formats. A command line interface allows for batch generation of images.

Availability and implementation
GfaViz is available at https://github.com/ggonnella/gfaviz

Supplementary information
Supplementary data are available at Bioinformatics online.
Linking sequence patterns and functionality of alpha-helical antimicrobial peptides
Authors: Eliseev Igor E , Terterov Ivan N , Yudenko Anna N , Shamova Olga V 
Published: December 2018

Abstract

Motivation
The rational design of antimicrobial peptides (AMPs) with increased therapeutic potential requires deep understanding of the determinants of their activities. Inspired by the computational linguistic approach, we hypothesized that sequence patterns may encode the functional features of AMPs.

Results
We found that α-helical and β-sheet peptides have non-intersecting pattern sets and therefore constructed new sequence templates using only helical patterns. Designed peptides adopted an α-helical conformation upon binding to lipids, confirming that the method captures structural and biophysical properties. In the antimicrobial assay, 5 of 7 designed peptides exhibited activity against Gram(+) and Gram(–) bacteria, with most potent candidate comparable to best natural peptides. We thus conclude that sequence patterns comprise the structural and functional features of α-helical AMPs and guide their efficient design.

Supplementary information
Supplementary data are available at Bioinformatics online.
An empirical analysis of Minsky regimes in the US economy
Authors: Davis Leila E , de Souza Joao Paulo A , Hernandez Gonzalo 
Published: December 2018

Abstract
In this paper, we analyse Minskian dynamics in the US economy via an empirical application of Minsky’s financing regime classifications to a panel of nonfinancial corporations. First, we map Minsky’s definitions of hedge, speculative and Ponzi finance onto firm-level data to describe the evolution of Minskian regimes. We highlight striking growth in the share of Ponzi firms in the post-1970 US, concentrated among small corporations. This secular growth in the incidence of Ponzi firms is consistent with the possibility of a long wave of increasingly fragile finance in the US economy. Second, we explore the possibility of short-run Minskian dynamics at a business cycle frequency. Using linear probability models relating firms’ probability of being Ponzi to the aggregate output gap, which captures short-term macroeconomic fluctuations exogenous to individual firms, we find that the relationship between aggregate downturns and the probability of being Ponzi is statistically significant, but very small (almost zero). This result is corroborated by quantile regressions using a continuous measure of financial fragility, the interest coverage ratio, which identify almost zero effects of short-term fluctuations on financial fragility across the interest coverage distribution. Together, these results speak to an important question in the theoretical literature on financial fragility regarding the duration of Minskian cycles, and lend support, in particular, to the contention that Minskian dynamics may take the form of long waves, but do not operate at business cycle frequencies.
Consumer perceptions of health IT utilization and benefits
Authors: Feldman Sue S , Bhavsar Grishma P , Schooley Benjamin L 
Published: December 2018

AbstractObjectivesThe objective of this article is to examine consumer perceptions of health information technology (health IT) utilization and benefits through an integrated conceptual framework.Materials and MethodsThis article employs an integrated conceptual framework to examine consumer perceptions of health IT. A consumer survey yielded 1125 completed responses. A factor-based scale was developed for each sub-construct. Bivariate analysis using χ2 tests was performed to determine differences in the percentage of respondents who agreed with each sub-construct based on whether their physician used an electronic health record (EHR) system. Multivariable logistic regression that controlled for demographic characteristics of respondents was performed to determine adjusted odds of agreeing with selected opinions of health information exchange (HIE).ResultsResults indicate that respondents whose physicians used an EHR system were significantly more likely to agree that there was a perceived benefit with HIE and to care provided; that the patient should have control over the record; that they trust the physician and security of the medical information; that they understand the need for HIE, and that HIE must be easy to use.DiscussionThe results suggest that consumers who have experienced the use of one technology in the healthcare setting can recognize the potential benefit of another technology. Race/ethnicity, gender, and education played some role in respondents’ views of EHRs and HIE, more specifically, non-Hispanic African American participants indicated lower levels of trust in HIE when compared with non-Hispanic Whites.ConclusionThis cross-sectional survey indicated that physician use of EHRs significantly increases the odds of consumers’ seeing perceived benefits of HIE and understanding the need for HIE.
A novel case of late left ventricular outflow tract obstruction post mitral valve surgery
Authors: Jones Andrew , Livesey Steven 
Published: December 2018

Abstract
Left ventricular outflow tract (LVOT) obstruction (LVOTO) is a rare but recognized complication of mitral valve surgery. Concomitant factors can cause significant clinical deterioration which requires urgent intervention. We present the case of a female patient who underwent closed valvotomy at age 20 for mitral stenosis secondary to rheumatic heart disease. Seventeen years later, a re-stenosed valve prompted mitral valve replacement (MVR) with a Carbomedics mechanical prosthesis. 8 years later, she re-presented with increasing dyspnoea. On echocardiogram a frond-like structure was visible in the LVOT, the valve housing was protruding into the LVOT and she had marked septal hypertrophy. The LVOT gradient was 72 mmHg. This is a novel case of mechanical MVR associated LVOTO due to at least three discrete factors. This case demonstrates how multiple factors can amalgamate to result in significant clinical deterioration. Over an 8-year period, all three distinct factors contributed to the development of severe LVOTO.
Menopausal hormone therapy trends before versus after 2002: impact of the Women's Health Initiative Study Results
Authors: Crawford Sybil L. , Crandall Carolyn J. , Derby Carol A. , Khoudary Samar R. El , Waetjen L. Elaine , Fischer Mary , Joffe Hadine 
Published: December 2018

Abstract

Objective:
To better understand how to educate patients and providers about study findings relevant to treatment guidelines, we assessed pre- versus post-Women's Health Initiative (WHI) differences in menopausal hormone therapy (MHT) initiation and continuation and their correlates, and in women's reasons for initiation and discontinuation.

Methods:
We analyzed survey data from up to 14 approximately annual visits over 17 years (1996-2013) from 3,018 participants in the Study of Women's Health Across the Nation, a prospective cohort study. We used logistic regression to compare pre- versus post-WHI associations of covariates with MHT initiation and continuation, and to compare pre- versus post-WHI reasons for initiation and continuation.

Results:
MHT initiation dropped from 8.6% pre-WHI to 2.8% post-WHI (P < 0.0001), and the corresponding decrease in MHT continuation was 84.0% to 62.0% (P < 0.0001). Decreases in MHT initiation and continuation occurred across a range of participant subgroups, consistent with wide dissemination of post-WHI recommendations. However, contrary to current guidelines, we found large declines in MHT use in subgroups for whom MHT is often recommended, that is, younger women and those with more vasomotor symptoms. Post-WHI, women's reasons for MHT initiation and discontinuation reflected concerns highlighted by WHI results. The largest declines in initiation reasons were for reducing risks of osteoporosis and heart disease, whereas the largest increases in discontinuation reasons were for media reports and provider advice.

Conclusions:
Immediate post-WHI recommendations for MHT use were widely adopted. MHT risks documented in older women, however, may have led younger symptomatic women to forgo MHT for symptom relief.
Medical Radiation Exposure in the United States: 2006–2016 Trends
Authors: Mettler Fred A. 
Published: December 2018

Abstract
The use of radiation in medicine and the associated population dose grew very rapidly from 1980–2006 predominantly as a result of computed tomography and nuclear medicine. Over the last decade there have been significant changes in image detectors and processing with almost complete elimination of film use. Economic and reimbursement issues have also had a significant effect on usage. After about 2010, the volume of computed tomography and interventional techniques has been fairly level, plain radiography has declined slightly, and noninterventional fluoroscopy has declined dramatically. Nuclear medicine procedures have also declined significantly. Cone-beam computed tomography has expanded particularly in dental radiography. The use of several complex types of image-guided radiotherapy has increased significantly. National Council on Radiation Protection and Measurements’ Scientific Committee 4-9 is currently conducting a full assessment for 2016 of collective and per caput effective dose. The report is expected to be completed in 2019, and preliminary work suggests a decrease in collective and per caput effective dose from that previously estimated for 2006.
Communicating Radiation Risk: The Power of Planned, Persuasive Messaging
Authors: Wieder Jessica S. 
Published: December 2018

Abstract
Every day, health physicists and physicians are expected to communicate effectively with concerned people, but rarely (if ever) are they given training on how to effectively communicate. In an age of social media, this paper presents the relevance of teachings from an ancient Greek philosopher. Aristotle’s Rhetoric is still considered one of the most influential works on persuasive messaging. He puts the onus of effective communications on the people with the “true” and “just” information to communicate that information clearly to the audience. By communicating with intention—using the persuasive appeals of ethos, pathos, logos, and storytelling—radiation professionals can speak to their expertise in radiation science, while adapting their instructions, presentations, and communication styles to meet the needs of each type of audience: from scientists to concerned citizens, from doctors to first responders, and beyond.
Radiopharmaceutical Therapy
Authors: Sgouros George 
Published: December 2018

Abstract
Radiopharmaceutical therapy involves the use of radionuclides that are either conjugated to tumor-targeting agents (e.g., nanoscale constructs, antibodies, peptides, and small molecules) or that concentrate in tumors through natural physiological mechanisms that occur predominantly in neoplastic cells. In the latter category, radioiodine therapy of thyroid cancer is the prototypical and most widely implemented radiopharmaceutical therapy. In the category of radionuclide-ligand conjugates, antibody and peptide conjugates have been studied extensively. The efficacy of radiopharmaceutical therapy relies on the ability to deliver cytotoxic radiation to tumor cells without causing prohibitive normal tissue toxicity. After some 30 y of preclinical and clinical research, a number of recent developments suggest that radiopharmaceutical therapy is poised to emerge as an important and widely recognized therapeutic modality. These developments include the substantial investment in antibodies by the pharmaceutical industry and the compelling rationale to build upon this already existing and widely tested platform. In addition, the growing recognition that the signaling pathways responsible for tumor cell survival and proliferation are less easily and durably inhibited than originally envisioned has also provided a rationale for identifying agents that are cytotoxic rather than inhibitory. A number of radiopharmaceutical agents are currently undergoing clinical trial investigation; these include beta-particle emitters, such as 177Lu, that are being used to label antisomatostatin receptor peptides for neuroendocrine cancers and also prostate-specific membrane antigen targeting small molecules for prostate cancer. Alpha-particle-emitting radionuclides have also been studied for radiopharmaceutical therapy; these include 211At for glioblastoma, 225Ac for leukemias and prostate cancer, 212Pb for breast cancer, and 223Ra for prostate cancer. The alpha emitters have tended to show particular promise, and there is substantial interest in further developing these agents for therapy of cancers that are particularly difficult to treat.
Uses of Effective Dose: The Good, the Bad, and the Future
Authors: Bushberg Jerrold T. 
Published: December 2018

Abstract
Effective dose (E) is a risk-adjusted dosimetric quantity developed by the International Commission on Radiological Protection. It is a key metric for practical management of the risk of stochastic health effects in a comprehensive radiation protection program. The International Commission on Radiological Protection and others have emphasized repeatedly that E is not intended to represent an actual radiation dose and should not be used as a risk-related metric for a specific person or population. The cancer risk uncertainties in the low-dose range and the underlying approximations, simplifications, and sex- and age-averaging used in generating E make it unsuitable for this purpose. However, in practice, medical imaging professionals and authors of peer-reviewed medical publications frequently and incorrectly use E as a surrogate for whole-body dose in order to calculate cancer risk estimates for specific patients or patient populations. This frequent misuse has popularized E for uses for which it was neither designed nor intended. Alternatives to E have been proposed that attempt to account for known age and sex differences in radiation sensitivity. E has also been proposed as a general indicator for communicating radiation risk to patients, if its limitations are kept in mind. Forthcoming guidance from the International Commission on Radiological Protection will likely clarify if, when, and how some form of E may be used as a rough indicator of the risk of a stochastic effect, possibly with some modifications for the substantial variations in risk known to exist with respect to age, sex, and population group.
Recent Epidemiologic Studies and the Linear No-Threshold Model For Radiation Protection—Considerations Regarding NCRP Commentary 27
Authors: Shore Roy E. , Beck Harold L. , Boice John D. , Caffrey Emily A. , Davis Scott , Grogan Helen A. , Mettler Fred A. , Preston R. Julian , Till John E. , Wakeford Richard , Walsh Linda , Dauer Lawrence T. 
Published: December 2018

Abstract
National Council on Radiation Protection and Measurements Commentary 27 examines recent epidemiologic data primarily from low-dose or low dose-rate studies of low linear-energy-transfer radiation and cancer to assess whether they support the linear no-threshold model as used in radiation protection. The commentary provides a critical review of low-dose or low dose-rate studies, most published within the last 10 y, that are applicable to current occupational, environmental, and medical radiation exposures. The strengths and weaknesses of the epidemiologic methods, dosimetry assessments, and statistical modeling of 29 epidemiologic studies of total solid cancer, leukemia, breast cancer, and thyroid cancer, as well as heritable effects and a few nonmalignant conditions, were evaluated. An appraisal of the degree to which the low-dose or low dose-rate studies supported a linear no-threshold model for radiation protection or on the contrary, demonstrated sufficient evidence that the linear no-threshold model is inappropriate for the purposes of radiation protection was also included. The review found that many, though not all, studies of solid cancer supported the continued use of the linear no-threshold model in radiation protection. Evaluations of the principal studies of leukemia and low-dose or low dose-rate radiation exposure also lent support for the linear no-threshold model as used in protection. Ischemic heart disease, a major type of cardiovascular disease, was examined briefly, but the results of recent studies were considered too weak or inconsistent to allow firm conclusions regarding support of the linear no-threshold model. It is acknowledged that the possible risks from very low doses of low linear-energy-transfer radiation are small and uncertain and that it may never be possible to prove or disprove the validity of the linear no-threshold assumption by epidemiologic means. Nonetheless, the preponderance of recent epidemiologic data on solid cancer is supportive of the continued use of the linear no-threshold model for the purposes of radiation protection. This conclusion is in accord with judgments by other national and international scientific committees, based on somewhat older data. Currently, no alternative dose-response relationship appears more pragmatic or prudent for radiation protection purposes than the linear no-threshold model.
Medical Physics 3.0: Ensuring Quality and Safety in Medical Imaging
Authors: Samei Ehsan 
Published: December 2018

Abstract
Medical imaging often involves radiation and thus radiation protection. Radiation protection in medicine is only one component of the broader calling of health care professionals: fostering human health. As such, radiation risk needs to be put into the context of the larger mandate of improved outcomes in health care. Medical physicists, according to the new vision of Medical Physics 3.0, make a significant contribution to this mandate as they engage proactively and meaningfully in patient care. Facing the new realities of value-based, personalized, and evidence-based practice, Medical Physics 3.0 is an initiative to make physics inform every patient’s care by fostering new skills and expanding horizons for the medical physics profession. It provides a framework by which medical physicists can maintain and improve their integral roles in, and contributions to, health care, its innovation, and its precision. One way that Medical Physics 3.0 will manifest itself in medical imaging practice is by engaging physicists to ensure the precise and optimized use of radiation. Optimization takes place through knowing the defining attributes of the technology in use, the specifics of the patient’s situation, and the goals of the imaging and/or intervention. The safety as well as the quality of the procedure is ascertained quantitatively and optimized prospectively, ensuring a proper balance between quality and safety to offer maximum potential benefit to the patient. The results of procedures across the health care operation are then retrospectively analyzed to ensure that each procedure has, in actuality, delivered the targeted quality and safety objectives. Characterizing quality and safety in quantitative terms, objectively optimizing them in the practice of personalized care, and analyzing the results from clinical operations all require the unique combination of precision and innovation that physicists bring to the development and practice of medicine.
Projection X-ray Imaging: Radiography, Mammography, Fluoroscopy
Authors: Seibert James Anthony 
Published: December 2018

Abstract
Recent advances in digital detector technology for medical radiography and fluoroscopy have resulted in improved workflow efficiency, operational flexibility, image quality, and diagnostic accuracy. This is attributed to the implementation of portable flat-panel x-ray detector devices able to provide real-time readout, processing, and display of medical images. As a result, digital radiography flat-panel detectors are rapidly replacing computed radiography passive detectors for projection imaging exams and image intensifier detectors for dynamic fluoroscopy exams. Advanced exam capabilities now include digital tomosynthesis and dual-energy radiography; the former is based on rapid acquisition of multiple angle-dependent image projections to synthesize tomographic slabs at selectable depths within the patient, and the latter is based on rapid back-to-back acquisition of the same anatomy at low and high x-ray energies to generate separate soft tissue and bone images. In both situations, superimposition of anatomy is reduced or eliminated, with the possibility of enhanced diagnostic confidence. Increased x-ray absorption efficiency and lower electronic noise of digital radiography detectors compared to computed radiography detectors enable equal image quality at lower patient dose; however, because of a disconnect between image appearance and radiation dose, lower patient dose is not always achieved. Education, training, and implementation of standards such as the International Electrotechnical Commission 62494-1 Digital Radiography Exposure Index are needed to ensure image quality at the lowest appropriate radiation dose. The National Council on Radiation Protection and Measurements can contribute to radiation responsibility in medical imaging by providing guidance on use of digital radiography, including recommendations for acquisition protocols and exposure index standards, for development of radiographic exam diagnostic reference levels, and for oversight of retake and reject analysis.
Benefits and Risks in Medical Imaging
Authors: Zanzonico Pat B. 
Published: December 2018

Abstract
Ionizing radiation has contributed enormously to dramatic improvements in medical care. The potential risks of radiation-based medical imaging have, however, drawn considerable attention in recent years. Although such concern is beneficial in terms of critical evaluation and optimization of imaging procedures, it can create the misconception that radiation is the only risk of medical imaging. In contrast to expression of radiation risks, quantitative estimates of the benefits of medical imaging are notably lacking. Expression of benefit in purely qualitative terms vs. expression of risk in quantitative, and thus apparently more concrete, terms may contribute to a biased judgement of the relative benefits and risks of medical imaging among health care professionals as well as the public. This paper, therefore, quantitatively compares the benefits of diagnostic imaging in several cases, based on actual mortality or morbidity data if ionizing radiation were not employed, with the linear no-threshold model derived (i.e., theoretical) estimates of radiogenic cancer mortality and illustrates the large benefit-to-risk ratios typical of medical imaging procedures.