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| 2. |
- Cesnik, Anthony J., et al.
(författare)
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Spritz : A Proteogenomic Database Engine
- 2021
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 20:4, s. 1826-1834
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Tidskriftsartikel (refereegranskat)abstract
- Proteoforms are the workhorses of the cell, and subtle differences between their amino acid sequences or post-translational modifications (PTMs) can change their biological function. To most effectively identify and quantify proteoforms in genetically diverse samples by mass spectrometry (MS), it is advantageous to search the MS data against a sample-specific protein database that is tailored to the sample being analyzed, in that it contains the correct amino acid sequences and relevant PTMs for that sample. To this end, we have developed Spritz (https://smith-chem-wisc.github.io/Spritz/), an open-source software tool for generating protein databases annotated with sequence variations and PTMs. We provide a simple graphical user interface for Windows and scripts that can be run on any operating system. Spritz automatically sets up and executes approximately 20 tools, which enable the construction of a proteogenomic database from only raw RNA sequencing data. Sequence variations that are discovered in RNA sequencing data upon comparison to the Ensembl reference genome are annotated on proteins in these databases, and PTM annotations are transferred from UniProt. Modifications can also be discovered and added to the database using bottom-up mass spectrometry data and global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms by searching bottom-up and top-down proteomic data from the Jurkat human T lymphocyte cell line and demonstrate the identification of phosphorylated variant sites with phosphoproteomic data from the U2OS human osteosarcoma cell line.
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| 3. |
- Farinotti, Daniel, et al.
(författare)
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How accurate are estimates of glacier ice thickness? Results from ITMIX, the Ice Thickness Models Intercomparison eXperiment
- 2017
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Ingår i: The Cryosphere. - : Copernicus GmbH. - 1994-0416 .- 1994-0424. ; 11, s. 949-970
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of the ice thickness distribution of glaciers and ice caps is an important prerequisite for many glaciological and hydrological investigations. A wealth of approaches has recently been presented for inferring ice thickness from characteristics of the surface. With the Ice Thickness Models Intercomparison eXperiment (ITMIX) we performed the first coordinated assessment quantifying individual model performance. A set of 17 different models showed that individual ice thickness estimates can differ considerably – locally by a spread comparable to the observed thickness. Averaging the results of multiple models, however, significantly improved the results: on average over the 21 considered test cases, comparison against direct ice thickness measurements revealed deviations on the order of 10 ± 24 % of the mean ice thickness (1σ estimate). Models relying on multiple data sets – such as surface ice velocity fields, surface mass balance, or rates of ice thickness change – showed high sensitivity to input data quality. Together with the requirement of being able to handle large regions in an automated fashion, the capacity of better accounting for uncertainties in the input data will be a key for an improved next generation of ice thickness estimation approaches.
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| 4. |
- Frey, Brian, et al.
(författare)
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Brailletouch : Mobile Texting for the Visually Impaired
- 2011
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Ingår i: Proceedings of the 6th International Conference on Universal Access in Human-computer Interaction. - : ACM Digital Library. - 9783642216657 ; , s. 19-25
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Konferensbidrag (refereegranskat)abstract
- BrailleTouch is an eyes-free text entry application for mobile devices. Currently, there exist a number of hardware and software solutions for eyes-free text entry. Unfortunately, the hardware solutions are expensive and the software solutions do not offer adequate performance. BrailleTouch bridges this gap. We present our design rationale and our explorative evaluation of BrailleTouch with HCI experts and visually impaired users.
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| 5. |
- Frey, Brian, et al.
(författare)
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From Texting App to Braille Literacy
- 2012
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Ingår i: CHI ’12 Extended Abstracts on Human Factors in Computing Systems. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450310161 ; , s. 2495-2500
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Konferensbidrag (refereegranskat)abstract
- We report the results of a pilot study that explores potential uses for BrailleTouch in the instruction of braille literacy for the visually impaired. BrailleTouch is an eyes-free text entry application for smart phones. We conducted individual semi-structured interviews and a focus group with four domain expert participants.
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| 6. |
- Jung, Christian, et al.
(författare)
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A comparison of very old patients admitted to intensive care unit after acute versus elective surgery or intervention
- 2019
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Ingår i: Journal of critical care. - : W B SAUNDERS CO-ELSEVIER INC. - 0883-9441 .- 1557-8615. ; 52, s. 141-148
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Tidskriftsartikel (refereegranskat)abstract
- Background: We aimed to evaluate differences in outcome between patients admitted to intensive care unit (ICU) after elective versus acute surgery in a multinational cohort of very old patients (80 years; VIP). Predictors of mortality, with special emphasis on frailty, were assessed.Methods: In total, 5063 VIPs were induded in this analysis, 922 were admitted after elective surgery or intervention, 4141 acutely, with 402 after acute surgery. Differences were calculated using Mann-Whitney-U test and Wilcoxon test. Univariate and multivariable logistic regression were used to assess associations with mortality.Results: Compared patients admitted after acute surgery, patients admitted after elective surgery suffered less often from frailty as defined as CFS (28% vs 46%; p < 0.001), evidenced lower SOFA scores (4 +/- 5 vs 7 +/- 7; p < 0.001). Presence of frailty (CFS >4) was associated with significantly increased mortality both in elective surgery patients (7% vs 12%; p = 0.01), in acute surgery (7% vs 12%; p = 0.02).Conclusions: VIPs admitted to ICU after elective surgery evidenced favorable outcome over patients after acute surgery even after correction for relevant confounders. Frailty might be used to guide clinicians in risk stratification in both patients admitted after elective and acute surgery.
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| 7. |
- Romero, Mario, 1973-, et al.
(författare)
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BrailleTouch : Designing a Mobile Eyes-free Soft Keyboard
- 2011
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Ingår i: Proceedings of the 13th International Conference on Human Computer Interaction with Mobile Devices and Services. - New York, NY, USA : ACM Digital Library. ; , s. 707-709
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Konferensbidrag (refereegranskat)abstract
- Texting is the essence of mobile communication and connectivity, as evidenced by today's teenagers, tomorrow's workforce. Fifty-four percent of American teens contact each other daily by texting, as compared to face-to-face (33%) and talking on the phone (30%) according to the Pew Research Center's Internet & American Life Project, 2010. Arguably, today's technologies support mobile text input poorly, primarily due to the size constraints of mobile devices. This is the case for everyone, but it is particularly relevant to the visually impaired. According to the World Health Organization, 284 million people are visually impaired worldwide. In order to connect these users to the global mobile community, we need to design effective and efficient methods for eyes-free text input on mobile devices. Furthermore, everyone would benefit from effective mobile texting for safety and speed. This design brief presents BrailleTouch, our working prototype solution for eyes-free mobile text input.
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| 8. |
- Southern, Caleb, et al.
(författare)
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An Evaluation of BrailleTouch : Mobile Touchscreen Text Entry for the Visually Impaired
- 2012
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Ingår i: Proceedings of the 14th International Conference on Human-computer Interaction with Mobile Devices and Services. - New York, NY, USA : Association for Computing Machinery (ACM). ; , s. 317-326
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Konferensbidrag (refereegranskat)abstract
- We present the evaluation of BrailleTouch, an accessible keyboard for blind users on touchscreen smartphones. Based on the standard Perkins Brailler, BrailleTouch implements a six-key chorded braille soft keyboard. Eleven blind participants typed for 165 twenty-minute sessions on three mobile devices: 1) BrailleTouch on a smartphone; 2) a soft braille keyboard on a touchscreen tablet; and 3) a commercial braille keyboard with physical keys. Expert blind users averaged 23.2 words per minute (wpm) on the BrailleTouch smartphone. The fastest participant, a touchscreen novice, achieved 32.1 wpm during his first session. Overall, participants were able to transfer their existing braille typing skills to a touchscreen device within an hour of practice. We report the speed for braille text entry on three mobile devices, an in depth error analysis, and the lessons learned for the design and evaluation of accessible and eyes-free soft keyboards.
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| 9. |
- Southern, Caleb, et al.
(författare)
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Braille Touch : Mobile Touchscreen Text Entry for the Visually Impaired
- 2012
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Ingår i: Proceedings of the 14th International Conference on Human-computer Interaction with Mobile Devices and Services Companion. ; , s. 155-156
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Konferensbidrag (refereegranskat)abstract
- We present a demonstration of BrailleTouch, an accessible keyboard for blind users on a touchscreen smartphone (see Figure 1). Based on the standard Perkins Brailler, BrailleTouch implements a six-key chorded braille soft keyboard [1]. We will briefly introduce audience members to the braille code, and then allow them to hold the BrailleTouch prototype and enter text, with the aid of a visual chart of the braille alphabet.
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| 10. |
- Zimmerman, Brian E, et al.
(författare)
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Multi-centre evaluation of accuracy and reproducibility of planar and SPECT image quantification : An IAEA phantom study
- 2017
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Ingår i: Zeitschrift für Medizinische Physik. - : Elsevier BV. - 1876-4436 .- 0939-3889. ; 27:2, s. 98-112
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Tidskriftsartikel (refereegranskat)abstract
- Accurate quantitation of activity provides the basis for internal dosimetry of targeted radionuclide therapies. This study investigated quantitative imaging capabilities at sites with a variety of experience and equipment and assessed levels of errors in activity quantitation in Single-Photon Emission Computed Tomography (SPECT) and planar imaging. Participants from 9 countries took part in a comparison in which planar, SPECT and SPECT with X ray computed tomography (SPECT-CT) imaging were used to quantify activities of four epoxy-filled cylinders containing 133Ba, which was chosen as a surrogate for 131I. The sources, with nominal volumes of 2, 4, 6 and 23mL, were calibrated for 133Ba activity by the National Institute of Standards and Technology, but the activity was initially unknown to the participants. Imaging was performed in a cylindrical phantom filled with water. Two trials were carried out in which the participants first estimated the activities using their local standard protocols, and then repeated the measurements using a standardized acquisition and analysis protocol. Finally, processing of the imaging data from the second trial was repeated by a single centre using a fixed protocol. In the first trial, the activities were underestimated by about 15% with planar imaging. SPECT with Chang's first order attenuation correction (Chang-AC) and SPECT-CT overestimated the activity by about 10%. The second trial showed moderate improvements in accuracy and variability. Planar imaging was subject to methodological errors, e.g., in the use of a transmission scan for attenuation correction. The use of Chang-AC was subject to variability from the definition of phantom contours. The project demonstrated the need for training and standardized protocols to achieve good levels of quantitative accuracy and precision in a multicentre setting. Absolute quantification of simple objects with no background was possible with the strictest protocol to about 6% with planar imaging and SPECT (with Chang-AC) and within 2% for SPECT-CT.
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