Free text phrase encoding and information extraction from medical notes

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (p. 87-90).The Laboratory for Computational Physiology is collecting a large database of patient signals and clinical data from critically ill patients in hospital intensive care units (ICUs). The data will be used as a research resource to support the development of an advanced patient monitoring system for ICUs. Important pathophysiologic events in the patient data streams must be recognized and annotated by expert clinicians in order to create a "gold standard" database for training and evaluating automated monitoring systems. Annotating the database requires, among other things, analyzing and extracting important clinical information from textual patient data such as nursing admission and progress notes, and using the data to define and document important clinical events during the patient's ICU stay. Two major text-related annotation issues are addressed in this research. First, the documented clinical events must be described in a standardized vocabulary suitable for machine analysis. Second, an advanced monitoring system would need an automated way to extract meaning from the nursing notes, as part of its decision-making process. The thesis presents and evaluates methods to code significant clinical events into standardized terminology and to automatically extract significant information from free-text medical notes.by Jennifer Shu.M.Eng

Steric Crowding Makes Challenging C sp3 –F Reductive Eliminations Feasible

A high-yielding fluorination of (triphos)Pt-R+ has been achieved using an array of F+ sources, with XeF2 yielding R–F in minutes. The C–F coupling proved to be a stereoretentive process that proceeds via a concerted reductive elimination from a putative dicationic Pt(IV) center. The larger the steric congestion of the (triphos)Pt–Csp3+ complexes, the more efficient the fluorination, seemingly a result of sterically accelerated C–F reductive elimination along with simultaneous deceleration of its competing processes (β-H elimination)

Electrophilic fluorination of cationic Pt-aryl complexes

The electrophilic fluorination of several (triphos)Pt-aryl+ establishes the first example of aryl–F coupling from a Pt center

Metrology Camera System of Prime Focus Spectrograph for Subaru Telescope

The Prime Focus Spectrograph (PFS) is a new optical/near-infrared multi-fiber spectrograph designed for the prime focus of the 8.2m Subaru telescope. PFS will cover a 1.3 degree diameter field with 2394 fibers to complement the imaging capabilities of Hyper SuprimeCam. To retain high throughput, the final positioning accuracy between the fibers and observing targets of PFS is required to be less than 10um. The metrology camera system (MCS) serves as the optical encoder of the fiber motors for the configuring of fibers. MCS provides the fiber positions within a 5um error over the 45 cm focal plane. The information from MCS will be fed into the fiber positioner control system for the closed loop control. MCS will be located at the Cassegrain focus of Subaru telescope in order to to cover the whole focal plane with one 50M pixel Canon CMOS camera. It is a 380mm Schmidt type telescope which generates a uniform spot size with a 10 micron FWHM across the field for reasonable sampling of PSF. Carbon fiber tubes are used to provide a stable structure over the operating conditions without focus adjustments. The CMOS sensor can be read in 0.8s to reduce the overhead for the fiber configuration. The positions of all fibers can be obtained within 0.5s after the readout of the frame. This enables the overall fiber configuration to be less than 2 minutes. MCS will be installed inside a standard Subaru Cassgrain Box. All components that generate heat are located inside a glycol cooled cabinet to reduce the possible image motion due to heat. The optics and camera for MCS have been delivered and tested. The mechanical parts and supporting structure are ready as of spring 2016. The integration of MCS will start in the summer of 2016.Comment: 11 pages, 15 figures. SPIE proceeding. arXiv admin note: text overlap with arXiv:1408.287

CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are overlapping, fatal neurodegenerative disorders in which the molecular and pathogenic basis remains poorly understood. Ubiquitinated protein aggregates, of which TDP-43 is a major component, are a characteristic pathological feature of most ALS and FTD patients. Here we use genome-wide linkage analysis in a large ALS/FTD kindred to identify a novel disease locus on chromosome 16p13.3. Whole-exome sequencing identified a CCNF missense mutation at this locus. Interrogation of international cohorts identified additional novel CCNF variants in familial and sporadic ALS and FTD. Enrichment of rare protein-altering CCNF variants was evident in a large sporadic ALS replication cohort. CCNF encodes cyclin F, a component of an E3 ubiquitin-protein ligase complex (SCFCyclin F). Expression of mutant CCNF in neuronal cells caused abnormal ubiquitination and accumulation of ubiquitinated proteins, including TDP-43 and a SCFCyclin F substrate. This implicates common mechanisms, linked to protein homeostasis, underlying neuronal degeneration

Prime Focus Spectrograph (PFS): the metrology camera system

The Prime Focus Spectrograph (PFS) is a new optical/near-infrared multi-fiber spectrograph designed for the prime focus of the 8.2m Subaru telescope. PFS will cover a 1.3 degree diameter field with 2394 fibers to complement the imaging capabilities of Hyper SuprimeCam. To retain high throughput, the final positioning accuracy between the fibers and observing targets of PFS is required to be less than 10 µ m. The metrology camera system (MCS) serves as the optical encoder of the fiber positioners for configuring of fibers. The MCS locates at the Cassegrain focus of the Subaru telescope to cover the whole focal plane with one 50M pixel CMOS sensor. The information from MCS will be fed into the fiber positioner control system for closed loop control. The MCS was delivered to Subaru Observatory in Apr. 2018 and it had two engineering runs in Oct. 2018 and Aug. 2019. The 1st engineering run concluded that the original mirror supports need to be improved to provide better image quality. The newly designed mirror supports were installed before the 2nd engineering run. The 2nd engineering run result shows that the MCS overall position accuracy is better than 4μm and the image processing time is less than 4 seconds. The MCS is ready for the system integration with other PFS components

Distribution of cervical intraepithelial neoplasia on the cervix in Chinese women: pooled analysis of 19 population based screening studies

Abstract Background Controversy remains whether a pattern of cervical intraepithelial neoplasia exists on the cervix. Our study aims at determining if the prevalence of histologically proven lesions differs by cervical four-quadrant location or by 12 o'clock surface locations of diagnosis. Methods We conducted a retrospective, histopathological study of 19 different population based cervical cancer screening studies from 1999 to 2010 by Cancer Hospital of Chinese Academy of Medical Sciences. The Institutional Review Board for human research subjects at CHCAMS approved all of the studies. During the colposcopy procedure, participant received either 4-quadrant biopsy or directed biopsy with/without endocervical curettage. Data of all samples were stratified by the methods of sampling. Kruskal-Wallis test was used to determine overall distribution of normal/CIN1, CIN2 and CIN3+ on the cervix. Results In total, 53,088 cervical samples were included in distribution analysis. 66.9 % samples were obtained by random biopsy, 16.1 % were by directed biopsy, and 17.0 % were by endocervical curettage. 95.9%of the biopsied samples were diagnosed as normal/CIN1, 2.0 % were CIN2, and 2.1 % were CIN3 + . CIN2 and CIN3+ were most often found in quadrants 2 and 3 (χKW2 = 46.6540, p < 0.0001) and at the 4- and 7-o'clock positions by directed biopsy (ORCIN2 = 2.572, 1.689, ORCIN3+ = 3.481, 1.678, respectively), and at the 5-, 6-, 7-, 9- and 12-o’clock positions by random biopsy. CIN3+ was least often found at the 11-o’clock position by directed biopsy (OR = 0.608). Conclusions Our results suggest a predisposition of specific locations on the cervix to CIN occurrence. Quadrants 2 and 3, especially the 4- and 7-o’clock positions should be preferentially targeted during biopsy. The decision for random biopsy should be reconsidered in future studies

The Sloan Digital Sky Survey Reverberation Mapping Project : how broad emission line widths change when luminosity changes

Funding: National Science Foundation of China (11721303, 11890693, 11991052) and the National Key R&D Program of China (2016YFA0400702, 2016YFA0400703). YS acknowledges support from an Alfred P. Sloan Research Fellowship and NSF grant AST-1715579. CJG, WNB, JRT, and DPS acknowledge support from NSF grants AST-1517113 and AST-1516784. KH acknowledges support from STFC grant ST/R000824/1. PBH acknowledges support from NSERC grant 2017-05983. YH acknowledges support from NASA grant HST-GO-15650.Quasar broad emission lines are largely powered by photoionization from the accretion continuum. Increased central luminosity will enhance line emissivity in more distant clouds, leading to increased average distance of the broad-line-emitting clouds and decreased averaged line width, known as the broad-line region (BLR) "breathing". However, different lines breathe differently, and some high-ionization lines, such as C IV, can even show "anti-breathing" where the line broadens when luminosity increases. Using multi-year photometric and spectroscopic monitoring data from the Sloan Digital Sky Survey Reverberation Mapping project, we quantify the breathing effect (Δlog W=αΔlog L) of broad Hα, Hβ, Mg II, C IV,and C III] for statistical quasar samples over z≈0.1−2.5. We found that Hβ displays the most consistent normal breathing expected from the virial relation (α∼−0.25), Mg II and Hα on average show no breathing (α∼0), and C IV (and similarly C III] and Si IV mostly shows anti-breathing (α>0). The anti-breathing of C IV can be well understood by the presence of a non-varying core component in addition to a reverberating broad-base component, consistent with earlier findings. The deviation from canonical breathing introduces extra scatter (aluminosity-dependent bias) in single-epoch virial BH mass estimates due to intrinsic quasar variability, which underlies the long argued caveats of C IV single-epoch masses. Using the line dispersion instead of FWHM leads to less, albeit still substantial, deviations from canonical breathing in most cases. Our results strengthen the need for reverberation mapping to provide reliable quasar BH masses, and quantify the level of variability-induced bias in single-epoch BH masses based on various lines.PostprintPeer reviewe