Capnographic analysis for disease classification

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 73-76).Existing methods for extracting diagnostic information from carbon dioxide in the exhaled breath are qualitative, through visual inspection, and therefore imprecise. In this thesis, we quantify the CO₂ waveform, or capnogram, in order to discriminate among various lung disorders. Quantitative analyses of the capnogram are conducted by extracting several physiological waveform features and performing classification by discriminant analysis with voting. Our classification methods are tested in distinguishing between records from subjects with normal lung function and patients with cardiorespiratory disease. In a second step, we discriminate between capnograms from patients with obstructive lung disease (chronic obstructive pulmonary disease) and those with restrictive lung disease (congestive heart failure). Our results demonstrate the diagnostic potential of capnography.by Rebecca J. Asher.S.M

Teenage dogs? Evidence for adolescent-phase conflict behaviour and an association between attachment to humans and pubertal timing in the domestic dog

The relationship between parent and child changes around adolescence, with children believed to have: (i) an earlier puberty if they have less secure attachments to their carer; (ii) a phase of increased conflict behaviour toward their carer; and (iii) heightened conflict behaviour when carer attachments are less secure. We find support for analogous associations in adolescent dogs based on behaviour and reproductive timing of potential guide dogs. Bitches with behaviour indicative of insecure attachments pre-adolescence became reproductively capable earlier. Providing the first empirical evidence to our knowledge in support of adolescent-phase behaviour in dogs, we found a passing phase of carer-specific conflict-like behaviour during adolescence (reduced trainability and responsiveness to commands), an effect that was more pronounced in dogs with behaviour indicative of less secure attachments. These results indicate a possibility for cross-species influence on reproductive development and highlight adolescence as a vulnerable time for dog–owner relationships

Attaining Doppler Precision of 10 cm s^(-1) with a Lock-in Amplified Spectrometer

We explore the radial velocity performance benefits of coupling starlight to a fast-scanning interferometer and a fast-readout spectrometer with zero readout noise. By rapidly scanning an interferometer, we can decouple wavelength calibration errors from precise radial velocity measurements, exploiting the advantages of lock-in amplification. In a Bayesian framework, we investigate the correlation between wavelength calibration errors and resulting radial velocity errors. We construct an end-to-end simulation of this approach to address the feasibility of achieving 10 cm s^(-1) radial velocity precision on a typical Sun-like star using existing, 5 m-class telescopes. We find that such a precision can be reached in a single night, opening up possibilities for ground-based detections of Earth-Sun analog systems

Neoadjuvant chemotherapy and trastuzumab versus neoadjuvant chemotherapy followed by post-operative trastuzumab for patients with HER2-positive breast cancer

Neoadjuvant chemotherapy plus trastuzumab (NCT) increases the rate of pathological complete response (pCR) and event-free survival (EFS) compared to neoadjuvant chemotherapy (NC) alone in women with HER2 positive breast cancer (BC). pCR in this setting is associated with improved EFS. Whether NCT preferentially improves EFS in comparison to NC followed by adjuvant trastuzumab initiated postoperatively (NCAT) has not been addressed. Using clinical data from women with HER2 positive BC treated at 7 European institutions between 2007 and 2010 we sought to investigate the impact on breast cancer outcomes of concomitant (NCT) versus sequential (NCAT) treatment in HER2 positive early BC. The unadjusted hazard ratio (HR) for event free survival with NCT compared with NCAT was 0.63 (95% CI 0.37–1.08; p = 0.091). Multivariable analysis revealed that treatment group, tumour size and ER status were significantly associated with EFS from diagnosis. In the whole group NCT was associated with a reduced risk of an event relative to NCAT, an effect that was confined to ER negative (HR: 0.25; 95% CI, 0.10–0.62; p = 0.003) as opposed to ER positive tumours (HR: 1.07; 95% CI, 0.46–2.52; p = 0.869). HER2 positive/ER negative BC treated with NC gain greatest survival benefit when trastuzumab is administered in both the neoadjuvant and adjuvant period rather than in the adjuvant period alone. These data support the early introduction of targeted combination therapy in HER2 positive/ER negative BC

PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net

Weathering the seasons of cancer survivorship: mind-body therapy use and reported reasons and outcomes by stages of cancer survivorship

Mind-body therapies (MBT), a subset of complementary and alternative medicine (CAM), are used by cancer survivors to manage symptoms related to their cancer experience. MBT use may differ by cancer survivorship stage (i.e., acute, short-term, long-term) because each stage presents varying intensities of medical activities, associated emotions, and treatment effects. We examined the relationship between MBT use and survivorship stage (acute: 5 years since diagnosis) using the CAM supplement of the 2012 National Health Interview Survey. We also examined reported reasons for and outcomes of MBT use and frequency of MBT types

Pelvic floor functional outcomes after total abdominal versus total laparoscopic hysterectomy for endometrial cancer

Pelvic floor functioning is an important concern for women requiring a hysterectomy for endometrial cancer. The incidence of pelvic floor symptoms has not been reported in women who have undergone a hysterectomy for early-stage endometrial cancer.To evaluate pelvic floor function in women who have had surgical treatment for early stage endometrial cancer as part of the multinational Laparoscopic Approach to Cancer of the Endometrium (LACE) trial and to compare patients' outcomes who had total abdominal total versus total laparoscopic hysterectomy.Multinational, phase 3, randomized non-inferiority trial comparing disease-free survival of patients who had total abdominal hysterectomy versus total laparoscopic hysterectomy. This substudy analyses the results from a self-administered validated questionnaire on pelvic floor symptoms (Pelvic Floor Distress Inventory (PFDI)) administered pre-operatively, and at follow-up visits 6, 18, 30, 42, and 54 months post-operatively.Overall, 381 patients with endometrial cancer were included in the analysis (total abdominal hysterectomy n=195; total laparoscopic hysterectomy n=186). At 6-months post-surgery both groups experienced an improvement in Pelvic Floor Distress Inventory scores compared to presurgical pelvic floor wellbeing (total abdominal hysterectomy: mean change -11.17, 95% CI: -17.11 to -5.24; total laparoscopic hysterectomy mean change -10.25, 95% CI: -16.31 to -4.19). The magnitude of change from baseline in pelvic floor symptoms did not differ between both treatment groups up to 54 months post-surgery.These findings suggest that pelvic floor function in terms of urinary, bowel and prolapse symptoms are unlikely to deteriorate following abdominal or laparoscopic hysterectomy and are reassuring for women undergoing hysterectomy for early stage endometrial cancer

Kamodo’s model-agnostic satellite flythrough: Lowering the utilization barrier for heliophysics model outputs

Heliophysics model outputs are increasingly accessible, but typically are not usable by the majority of the community unless directly collaborating with the relevant model developers. Prohibitive factors include complex file output formats, cryptic metadata, unspecified and often customized coordinate systems, and non-linear coordinate grids. Some pockets of progress exist, giving interfaces to various simulation outputs, but only for a small set of outputs and typically not with open-source, freely available packages. Additionally, the increasing array of tools built upon these sporadic interfaces are typically model-specific. We present Kamodo’s model-agnostic satellite flythrough capabilities as the solution to the utilization barrier for heliophysics model outputs. Developed at the Community Coordinated Modeling Center, these flythrough capabilities are built in Python upon a network of model-agnostic interfaces developed in collaboration with model developers, providing interpolation results the community can trust. Kamodo’s flythrough capabilities present the user with a growing variety of flythrough tools based upon a rapidly expanding library of heliophysics model outputs in several domains, currently including a variety of Ionosphere-Thermosphere-Mesosphere and global magnetosphere model outputs. Each capability is designed to be easily accessible via simplistic model-agnostic syntax, with the entire package freely available in the cloud on Github. Here, we describe the tools developed, include several sample applications for common science questions, demonstrate interoperability with selected packages, and summarize ongoing developments

Patient-delivered tDCS on chronic neuropathic pain in prior responders to TMS (a randomized controlled pilot study)

Background: Successful response to repetitive transcranial magnetic stimulation (rTMS) of the motor cortex requires continued maintenance treatments. Transcranial Direct Current Stimulation (tDCS) may provide a more convenient alternative. Methods: This pilot study aimed to examine the feasibility of a randomized, double-blind, double-crossover pilot study for patients to self-administer tDCS motor cortex stimulation for 20 minutes/day over five consecutive days. Primary outcomes were as follows: usability of patient-administered tDCS, compliance with device, recruitment, and retention rates. Secondary outcomes were as follows: effect on overall pain levels and quality of life via Short Form-36 anxiety and depression via Hospital Anxiety and Depression Scale, and Mini-Mental State scores. Results: A total of 24 subjects with neuropathic pain, who had previously experienced rTMS motor cortex stimulation (13 with reduction in pain scores, 11 nonresponders) were recruited at the Pain Research Institute, Fazakerley, UK. A total of 21 subjects completed the study. Recruitment rate was 100% but retention rate was only 87.5%. All patients reported satisfactory usability of the tDCS device. No significant difference was shown between Sham vs Anodal (-0.16, 95% CI: -0.43 to 0.11) P=0.43, Sham vs Cathodal (0.11, 95% CI: -0.16 to 0.37) P=0.94, or Cathodal vs Anodal (-0.27, 95% CI: -0.54 to 0.00) P=0.053 treatments. Furthermore, no significant changes were demonstrated in anxiety, depression, or quality of life measurements. The data collected to estimate sample size for a definitive study suggested that the study's sample size was already large enough to detect a change of 15% in pain levels at 90% power for the overall group of 21 patients. Conclusion: This study did not show a beneficial effect of tDCS in this group of patients and does not support the need for a larger definitive study using the same experimental paradigm

Designing a Regional System of Social Indicators to Evaluate Nonpoint Source Water Projects

A collaborative team has developed a system to measure the social outcomes of nonpoint source water projects as indicators of progress towards environmental goals. The system involves a set of core indicators, additional supplemental indicators, and a process for collecting and using the indicators. This process is supported by methodologies and instruments for data collection, analysis, and reporting that are coordinated and supported through detailed written guidance and an on-line data management tool. Its multi-state scope and application offer a unique opportunity to target, measure, and report interim resource management accomplishments consistently at multiple levels