Decoupling the scholarly journal

Although many observers have advocated the reform of the scholarly publishing system, improvements to functions like peer review have been adopted sluggishly. We argue that this is due to the tight coupling of the journal system: the system's essential functions of archiving, registration, dissemination, and certification are bundled together and siloed into tens of thousands of individual journals. This tight coupling makes it difficult to change any one aspect of the system, choking out innovation. We suggest that the solution is the “decoupled journal (DcJ).” In this system, the functions are unbundled and performed as services, able to compete for patronage and evolve in response to the market. For instance, a scholar might deposit an article in her institutional repository, have it copyedited and typeset by one company, indexed for search by several others, self-marketed over her own social networks, and peer reviewed by one or more stamping agencies that connect her paper to external reviewers. The DcJ brings publishing out of its current seventeenth-century paradigm, and creates a Web-like environment of loosely joined pieces—a marketplace of tools that, like the Web, evolves quickly in response to new technologies and users' needs. Importantly, this system is able to evolve from the current one, requiring only the continued development of bolt-on services external to the journal, particularly for peer review

Comparison of Navigation Techniques for Large Digital Images

Medical images are examined on computer screens in a variety of contexts. Frequently, these images are larger than computer screens, and computer applications support different paradigms for user navigation of large images. The paper reports on a systematic investigation of what interaction techniques are the most effective for navigating images larger than the screen size for the purpose of detecting small image features. An experiment compares five different types of geometrically zoomable interaction techniques, each at two speeds (fast and slow update rates) for the task of finding a known feature in the image. There were statistically significant performance differences between several groupings of the techniques. The fast versions of the ArrowKey, Pointer, and ScrollBar performed the best. In general, techniques that enable both intuitive and systematic searching performed the best at the fast speed, while techniques that minimize the number of interactions with the image were more effective at the slow speed. Additionally, based on a postexperiment questionnaire and qualitative comparison, users expressed a clear preference for the Pointer technique, which allowed them to more freely and naturally interact with the image

AnnotationOne: A global annotation system

Our study presents a web‐based annotation tool, AnnotationOne, developed to facilitate the easier creation and global sharing of annotations. Our aim is to create conversations around scholarly content benefitting everyone and forging new connections between scholars. Using this tool, users can read and make globally accessible annotations shared with a large scale of users. User studies were conducted to investigate the utility of this universal annotations system. Subjects completed tasks including making annotations, initial reading with annotations and re‐reading with annotations on our prototype system. Both observations and interviews were conducted to explore whether and how this annotation tool would be beneficial for scholarly communication. Moreover, we also collected subjects' suggestions to improve this tool's usability

Image presentation in digital radiology: perspectives on the emerging DICOM display function standard and its application

DICOM (Digital Imaging and Communications in Medicine) Working Group XI, formerly called ACR/NEMA (American College of Radiology/National Electrical Manufacturers' Association) Working Group XI, is currently developing a display function standard. The main objective of the standard is to define mathematically a display function for all image presentation systems. As a secondary objective, the standard aims at providing similarity in gray-scale perception for a given image between display systems of different luminance and at facilitating efficient utilization of the available digital input levels of a display system. The design of the display function incorporates the concept of perceptual linearization. The proposed standard applies to monochrome image presentation devices such as cathode ray tube monitor-display controller systems and digital laser image printers. The standard does not eliminate the use of application-specific display functions but rather ensures their effectiveness. Neither does the standard guarantee equal information transfer between image presentation devices with different physical properties; it does, however, from the basis for applying image processing to compensate for such differences

Mining connections between chemicals, proteins, and diseases extracted from Medline annotations

The biomedical literature is an important source of information about the biological activity and effects of chemicals. We present an application that extracts terms indicating biological activity of chemicals from Medline records, associates them with chemical name and stores the terms in a repository called ChemoText. We describe the construction of ChemoText and then demonstrate its utility in drug research by employing Swanson’s ABC discovery paradigm. We reproduce Swanson’s discovery of a connection between magnesium and migraine in a novel approach that uses only proteins as the intermediate B terms. We validate our methods by using a cutoff date and evaluate them by calculating precision and recall. In addition to magnesium, we have identified valproic acid and nitric oxide as chemicals which developed links to migraine. We hypothesize, based on protein annotations, that zinc and retinoic acid may play a role in migraine. The ChemoText repository has promise as a data source for drug discovery

Global science discussed in local altmetrics: Weibo and its comparison with Twitter

Local altmetrics is currently an integral part of the altmetrics landscape. This paper aims to investigate the characteristics of microblog altmetrics of the Chinese microblog platform, Weibo, to shed light on cultural differences and draw attention to local altmetrics in developing countries. The analysis is based on 4.4 million records provided by Altmetric.com. Data collected are from March 2014 to July 2015. It is found that Weibo users discuss global science, more actively compared with several international altmetrics sources. Statistical results show strong evidence of the immediacy advantage of metrics based on Weibo as well as Twitter and the general altmetrics over citations. Distribution of Weibo altmetrics on the article level, source level and discipline level are highly skewed. Overall, compared with Twitter, Weibo altmetrics present similar distributions, with some minor variations. To better understand how and why Weibo users discuss global scientific articles, the top weiboed articles, sources and disciplines are identified and further explored. Our content analysis shows that the common motivation of scientific weibos is to disseminate or discuss the articles because they are interesting, surprising, academically useful or practically useful. Conclusion of articles is the most frequently mentioned element in scientific weibos. In addition, different from Twitter, Weibo users have a preference for traditional prestigious journals

Contrast Limited Adaptive Histogram Equalization image processing to improve the detection of simulated spiculations in dense mammograms

The purpose of this project was to determine whether Contrast Limited Adaptive Histogram Equalization (CLAHE) improves detection of simulated spiculations in dense mammograms. Lines simulating the appearance of spiculations, a common marker of malignancy when visualized with masses, were embedded in dense mammograms digitized at 50 micron pixels, 12 bits deep. Film images with no CLAHE applied were compared to film images with nine different combinations of clip levels and region sizes applied. A simulated spiculation was embedded in a background of dense breast tissue, with the orientation of the spiculation varied. The key variables involved in each trial included the orientation of the spiculation, contrast level of the spiculation and the CLAHE settings applied to the image. Combining the 10 CLAHE conditions, 4 contrast levels and 4 orientations gave 160 combinations. The trials were constructed by pairing 160 combinations of key variables with 40 backgrounds. Twenty student observers were asked to detect the orientation of the spiculation in the image. There was a statistically significant improvement in detection performance for spiculations with CLAHE over unenhanced images when the region size was set at 32 with a clip level of 2, and when the region size was set at 32 with a clip level of 4. The selected CLAHE settings should be tested in the clinic with digital mammograms to determine whether detection of spiculations associated with masses detected at mammography can be improved

Assessment of Real-Time 3D Visualization for Cardiothoracic Diagnostic Evaluation and Surgery Planning

RATIONALE AND OBJECTIVES: Three-dimensional (3D) real-time volume rendering has demonstrated improvements in clinical care for several areas of radiological imaging. We test whether advanced real-time rendering techniques combined with an effective user interface will allow radiologists and surgeons to improve their performance for cardiothoracic surgery planning and diagnostic evaluation. MATERIAL AND METHODS: An interactive combination 3D and 2D visualization system developed at the University of North Carolina at Chapel Hill was compared against standard tiled 2D slice presentation on a viewbox. The system was evaluated for 23 complex cardiothoracic computed tomographic (CT) cases including heart-lung and lung transplantation, tumor resection, airway stent placement, repair of congenital heart defects, aortic aneurysm repair, and resection of pulmonary arteriovenous malformation. Radiologists and surgeons recorded their impressions with and without the use of the interactive visualization system. RESULTS: The cardiothoracic surgeons reported positive benefits to using the 3D visualizations. The addition of the 3D visualization changed the surgical plan (65% of cases), increased the surgeon's confidence (on average 40% per case), and correlated well with the anatomy found at surgery (95% of cases). The radiologists reported fewer and less major changes than the surgeons in their understanding of the case due to the 3D visualization. They found new findings or additional information about existing findings in 66% of the cases; however, they changed their radiology report in only 14% of the cases. CONCLUSION: With the appropriate choice of 3D real-time volume rendering and a well-designed user interface, both surgeons and radiologists benefit from viewing an interactive 3D visualization in addition to 2D images for surgery planning and diagnostic evaluation of complex cardiothoracic cases. This study finds that 3D visualization is especially helpful to the surgeon in understanding the case, and in communicating and planning the surgery. These results suggest that including real-time 3D visualization would be of clinical benefit for complex cardiothoracic CT cases

Does intensity windowing improve the detection of simulated calcifications in dense mammograms?

This study attempts to determine whether intensity windowing (IW) improves detection of simulated calcifications in dense mammograms. Clusters of five simulated calcifications were embedded in dense mammograms digitized at 50-microns pixels, 12 bits deep. Film images with no windowing applied were compared with film images with nine different window widths and levels applied. A simulated cluster was embedded in a realistic background of dense breast tissue, with the position of the cluster varied. The key variables involved in each trial included the position of the cluster, contrast level of the cluster, and the IW settings applied to the image. Combining the ten IW conditions, four contrast levels and four quadrant positions gave 160 combinations. The trials were constructed by pairing 160 combinations of key variables with 160 backgrounds. The entire experiment consisted of 800 trials. Twenty student observers were asked to detect the quadrant of the image in which the mass was located. There was a statistically significant improvement in detection performance for clusters of calcifications when the window width was set at 1024 with a level of 3328, and when the window width was set at 1024 with a level of 3456. The selected IW settings should be tested in the clinic with digital mammograms to determine whether calcification detection performance can be improved

Interpretation of CT studies: single-screen workstation versus film alternator

A prototype single-screen workstation with a 2,048 x 2,560-pixel high-brightness monitor, 0.11-second image display time, and simple ergonomic design was compared to a conventional horizontal film alternator in diagnostic interpretation of chest computed tomography (CT) studies. Four radiologists used either the workstation or film alternator in interpretation of studies obtained in 10 patients. A counterbalanced within-subject repeated measures experimental design was used. Response times were analyzed for both methods of interpretation. Grades of excellent, acceptable, and unacceptable were assigned by a blinded "grader" to reports of the radiologists. The average time needed for an interpretation at the workstation was 5.65 minutes. No interpretations were graded unacceptable. Retrospective power analysis showed that 16 observers rather than four would have been required to show that use of the workstation was faster than the alternator. With this 95% confidence interval, the workstation interpretation time is clinically equivalent to that with the alternator. These data show that this type of workstation has practical application in interpretation of CT, magnetic resonance imaging, and ultrasound studies