Automating CIRI Ratings of Human Rights Reports Using Gate

This thesis involves parsing document-based reports from the United States Human Rights Reports and rating the human practices for various countries based on the CIRI (Cingranelli-Richards) Human Rights Data Project dataset. The United States Human Rights Reports are annual reports that cover internationally recognized human rights practices regarding individual, civil, political, and worker rights. Students, scholars, policymakers, and analysts used the CIRI data for practical and research purposes. CIRI analyzed the annual reports from 1981 to 2011 and then stopped releasing the dataset for any further years, but a possible reason is due to the manual process of scouring the Human Rights Reports and then rating each human rights practice for each country. This manual process provides a solid foundation for creating a new automated process. The automated process uses the rating values provided by CIRI in the 1981-2011 dataset as expected values to evaluate the accuracy of the rating process. To transition to an automated process, the General Architecture for Text Engineering (GATE) application is used. GATE is an open source project used for developing solutions for text processing. GATE is used in conjunction with the coding schemes provided within the CIRI Coding Manual to create an automated ratings process. The CIRI Coding Manual uses qualitative and quantitative criteria. The original and automated ratings are evaluated using GATE’s Annotation Diff Tool to get the F-measure for every country in the dataset. The evaluation cases range between 1999 and 2011 because those are the only years included in both the CIRI dataset and the Human Rights Reports. The F-measure results are more accurate when quantitative criteria is used to rate human rights practices. The primary contribution of this thesis is a method for automating each country’s human practice ratings so that the purpose of the CIRI project can be continued

Potential of the TROPOspheric Monitoring Instrument (TROPOMI) onboard the Sentinel-5 Precursor for the monitoring of terrestrial chlorophyll fluorescence

Global monitoring of sun-induced chlorophyll fluorescence (SIF) is improving our knowledge about the photosynthetic functioning of terrestrial ecosystems. The feasibility of SIF retrievals from spaceborne atmospheric spectrometers has been demonstrated by a number of studies in the last years. In this work, we investigate the potential of the upcoming TROPOspheric Monitoring Instrument (TROPOMI) onboard the Sentinel-5 Precursor satellite mission for SIF retrieval. TROPOMI will sample the 675–775 nm spectral window with a spectral resolution of 0.5 nm and a pixel size of 7 km × 7 km. We use an extensive set of simulated TROPOMI data in order to assess the uncertainty of single SIF retrievals and subsequent spatio-temporal composites. Our results illustrate the enormous improvement in SIF monitoring achievable with TROPOMI with respect to comparable spectrometers currently in-flight, such as the Global Ozone Monitoring Experiment-2 (GOME-2) instrument. We find that TROPOMI can reduce global uncertainties in SIF mapping by more than a factor of 2 with respect to GOME-2, which comes together with an approximately 5-fold improvement in spatial sampling. Finally, we discuss the potential of TROPOMI to map other important vegetation parameters at a global scale with moderate spatial resolution and short revisit time. Those include leaf photosynthetic pigments and proxies for canopy structure, which will complement SIF retrievals for a self-contained description of vegetation condition and functioning

Electron‐deficient p‐benzoyl‐l‐phenylalanine derivatives increase covalent chemical capture yields for protein–protein interactions

The photoactivatable amino acid p‐benzoyl‐l‐phenylalanine (pBpa) has been used for the covalent capture of protein–protein interactions (PPIs) in vitro and in living cells. However, this technique often suffers from poor photocrosslinking yields due to the low reactivity of the active species. Here we demonstrate that the incorporation of halogenated pBpa analogs into proteins leads to increased crosslinking yields for protein–protein interactions. The analogs can be incorporated into live yeast and upon irradiation capture endogenous PPIs. Halogenated pBpas will extend the scope of PPIs that can be captured and expand the toolbox for mapping PPIs in their native environment.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149350/1/pro3621.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149350/2/pro3621_am.pd

Response of two mouse tumours to hyperthermia with CCNU or melphalan.

The in vivo response of B16 melanoma and Lewis lung carcinoma to combinations of hyperthermia and graded doses of CCNU or Melphalan was studied. To obtain dose-response curves and quantitative comparisons of different treatments, an agar-colony assay was used to measure survival of cells from excised tumours. For heating experiments, the use of 2 tumours per animal, one heated and one not, allowed all other factors to be kept constant. When tumours were immersed in a water-bath at 43 degrees C for 1 h, Thermal Enhancement Ratios (TER) measured from the slopes of the dose-response curves were up to 1.6 for CCNU and 2.4 for Melphalan. Direct heat killing of about 1 decade was seen for 1 h at 43 degrees C. The anaesthetic Saffan also enhanced drug cell kill; the largest Dose Modifying Factor (2.7) was measured for Melphalan in the Lewis lung tumour. The duration of heating, and waterbath temperature, both influenced the enhancement of cell killing by CCNU, as did the time of excision of tumours between 0 and 3 1/2 h after treatment. There was no difference in effect between 3 1/2 and 24 h. The interaction between heat and CCNU varied if the interval between them was altered. The maximum effect was found if the heat and drug were given in close sequence

A Bifunctional Amino Acid Enables Both Covalent Chemical Capture and Isolation of in Vivo Protein–Protein Interactions

In vivo covalent chemical capture by using photoactivatable unnatural amino acids (UAAs) is a powerful tool for the identification of transient protein–protein interactions (PPIs) in their native environment. However, the isolation and characterization of the crosslinked complexes can be challenging. Here, we report the first in vivo incorporation of the bifunctional UAA BPKyne for the capture and direct labeling of crosslinked protein complexes through post‐crosslinking functionalization of a bioorthogonal alkyne handle. Using the prototypical yeast transcriptional activator Gal4, we demonstrate that BPKyne is incorporated at the same level as the commonly used photoactivatable UAA pBpa and effectively captures the Gal4–Gal80 transcriptional complex. Post‐crosslinking, the Gal4–Gal80 adduct was directly labeled by treatment of the alkyne handle with a biotin‐azide probe; this enabled facile isolation and visualization of the crosslinked adduct from whole‐cell lysate. This bifunctional amino acid extends the utility of the benzophenone crosslinker and expands our toolbox of chemical probes for mapping PPIs in their native cellular environment.Using the bifunctional unnatural amino acid, BPKyne, we have developed a strategy to capture and directly label transient protein–protein interactions (PPIs) in their native environment. Click chemical functionalization post‐crosslinking with a biotin–azide probe enabled the isolation of transcriptional protein complexes from yeast cells. This amino acid will expand the toolbox for the discovery of new PPIs in live cells.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135955/1/cbic201600578.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135955/2/cbic201600578_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135955/3/cbic201600578-sup-0001-misc_information.pd

Innate immune pathways associated with lung radioprotection by soy isoflavones

Introduction: Radiation therapy for lung cancer causes pneumonitis and fibrosis. Soy isoflavones protect against radiation-induced lung injury, but the mediators of radio- protection remain unclear. We investigated the effect of radiation on myeloid-derived suppressor cells (MDSCs) in the lung and their modulation by soy isoflavones for a potential role in protection from radiation-induced lung injury. Methods: BALB/c mice (5–6 weeks old) received a single 10 Gy dose of thoracic irra- diation and soy isoflavones were orally administrated daily before and after radiation at 1 mg/day. Arginase-1 (Arg-1) and nuclear factor κB (NF-κB) p65 were detected in lung tissue by western blot analysis and immunohistochemistry. Lung MDSC subsets and their Arg-1 expression were analyzed by flow cytometry. Cytokine levels in the lungs were measured by ELISA. Results: At 1 week after radiation, CD11b+ cells expressing Arg-1 were decreased by radiation in lung tissue yet maintained in the lungs treated with radiation and soy isoflavones. Arg-1 was predominantly expressed by CD11b+Ly6ClowLy6G+ granulocytic MDSCs (gr-MDSCs). Arg-1 expression in gr-MDSCs was reduced by radiation and preserved by supplementation with soy isoflavones. A persistent increase in Arg-1+ cells was observed in lung tissue treated with combined radiation and soy isoflavones at early and late time points, compared to radiation alone. The increase in Arg-1 expression mediated by soy isoflavones could be associated with the inhibition of radiation-induced activation of NF-κB and the control of pro-inflammatory cytokine production demon- strated in this study. Conclusion: A radioprotective mechanism of soy isoflavones may involve the promotion of Arg-1-expressing gr-MDSCs that could play a role in downregulation of inflammation and lung radioprotection