PULSE - Spring 2016, Issue One

PULSE is the bi-quarterly student-run lifestyle magazine of Central Washington University.https://digitalcommons.cwu.edu/pulse/1003/thumbnail.jp

Edge-Coupling of O-Band InP Etched-Facet Lasers to Polymer Waveguides on SOI by Micro-Transfer-Printing

O-band InP etched facets lasers were heterogeneously integrated by micro-transfer-printing into a 1.54~\mu \text{m} deep recess created in the 3~\mu \text{m} thick oxide layer of a 220 nm SOI wafer. A 7\times 1.5\,\,\mu \text{m}^{2} cross-section, 2 mm long multimode polymer waveguide was aligned to the ridge post-integration by e-beam lithography with \u3c 0.7~\mu \text{m} lateral misalignment and incorporated a tapered silicon waveguide. A 170 nm thick metal layer positioned at the bottom of the recess adjusts the vertical alignment of the laser and serves as a thermal via to sink the heat to the Si substrate. This strategy shows a roadmap for active polymer waveguide-based photonic integrated circuits

POTs: Protective Optimization Technologies

Algorithmic fairness aims to address the economic, moral, social, and political impact that digital systems have on populations through solutions that can be applied by service providers. Fairness frameworks do so, in part, by mapping these problems to a narrow definition and assuming the service providers can be trusted to deploy countermeasures. Not surprisingly, these decisions limit fairness frameworks' ability to capture a variety of harms caused by systems. We characterize fairness limitations using concepts from requirements engineering and from social sciences. We show that the focus on algorithms' inputs and outputs misses harms that arise from systems interacting with the world; that the focus on bias and discrimination omits broader harms on populations and their environments; and that relying on service providers excludes scenarios where they are not cooperative or intentionally adversarial. We propose Protective Optimization Technologies (POTs). POTs provide means for affected parties to address the negative impacts of systems in the environment, expanding avenues for political contestation. POTs intervene from outside the system, do not require service providers to cooperate, and can serve to correct, shift, or expose harms that systems impose on populations and their environments. We illustrate the potential and limitations of POTs in two case studies: countering road congestion caused by traffic-beating applications, and recalibrating credit scoring for loan applicants.Comment: Appears in Conference on Fairness, Accountability, and Transparency (FAT* 2020). Bogdan Kulynych and Rebekah Overdorf contributed equally to this work. Version v1/v2 by Seda G\"urses, Rebekah Overdorf, and Ero Balsa was presented at HotPETS 2018 and at PiMLAI 201

A Light Stop with Flavor in Natural SUSY

The discovery of a SM-like Higgs boson near 125 GeV and the flavor texture of the Standard Model motivate the investigation of supersymmetric quiver-like BSM extensions. We study the properties of such a minimal class of models which deals naturally with the SM parameters. Considering experimental bounds as well as constraints from flavor physics and Electro-Weak Precision Data, we find the following. In a self-contained minimal model - including the full dynamics of the Higgs sector - top squarks below a TeV are in tension with b->s{\gamma} constraints. Relaxing the assumption concerning the mass generation of the heavy Higgses, we find that a stop not far from half a TeV is allowed. The models have some unique properties, e.g. an enhancement of the h-> b\bar{b},\tau\bar{{\tau}} decays relative to the h->\gamma{\gamma} one, a gluino about 3 times heavier than the stop, an inverted hierarchy of about 3-20 between the squarks of the first two generations and the stop, relatively light Higgsino neutralino or stau NLSP, as well as heavy Higgses and a W' which may be within reach of the LHC.Comment: LaTeX, 22 pages, 4 figures; V2: references adde

Determinants of Disease Presentation and Outcome during Cryptococcosis: The CryptoA/D Study

BACKGROUND: Cryptococcosis is a life-threatening opportunistic fungal infection in both HIV-positive and -negative patients. Information on clinical presentation and therapeutic guidelines, derived mostly from clinical trials performed before introduction of highly active antiretroviral therapy in patients with cryptococcal meningoencephalitis, is missing data on extrameningeal involvement and infections by serotype D as opposed to serotype A of Cryptococcus neoformans. METHODS AND FINDINGS: The prospective multicenter study CryptoA/D was designed in France (1997–2001) to analyse the factors influencing clinical presentation and outcome without the bias of inclusion into therapeutic trials. Of the 230 patients enrolled, 177 (77%) were HIV-positive, 50 (22%) were female, and 161 (72.5%) were infected with serotype A. Based on culture results at baseline, cryptococcosis was more severe in men, in HIV-positive patients, and in patients infected with serotype A. Factors independently associated with mycological failure at week 2 independent of HIV status were initial dissemination (OR, 2.4 [95% confidence interval (CI), 1.2–4.9]), high (>1:512) serum antigen titre (OR, 2.6 [1.3–5.4]), and lack of flucytosine during induction therapy (OR, 3.8 [1.9–7.8]). The three-month survival was shorter in patients with abnormal neurology or brain imaging at baseline, and in those with haematological malignancy. CONCLUSIONS: Thus sex, HIV status, and infecting serotype are major determinants of presentation and outcome during cryptococcosis. We propose a modification of current guidelines for the initial management of cryptococcosis based on systematic fungal burden evaluation

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Background Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To overcome these shortcomings, the CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions, the first version of the Silver Standard Corpus (SSC-I). The four semantic groups are chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). This corpus has been used for the First CALBC Challenge asking the participants to annotate the corpus with their text processing solutions. Results All four PPs from the CALBC project and in addition, 12 challenge participants (CPs) contributed annotated data sets for an evaluation against the SSC-I. CPs could ignore the training data and deliver the annotations from their genuine annotation system, or could train a machine-learning approach on the provided pre-annotated data. In general, the performances of the annotation solutions were lower for entities from the categories CHED and PRGE in comparison to the identification of entities categorized as DISO and SPE. The best performance over all semantic groups were achieved from two annotation solutions that have been trained on the SSC-I. The data sets from participants were used to generate the harmonised Silver Standard Corpus II (SSC-II), if the participant did not make use of the annotated data set from the SSC-I for training purposes. The performances of the participants’ solutions were again measured against the SSC-II. The performances of the annotation solutions showed again better results for DISO and SPE in comparison to CHED and PRGE. Conclusions The SSC-I delivers a large set of annotations (1,121,705) for a large number of documents (100,000 Medline abstracts). The annotations cover four different semantic groups and are sufficiently homogeneous to be reproduced with a trained classifier leading to an average F-measure of 85%. Benchmarking the annotation solutions against the SSC-II leads to better performance for the CPs’ annotation solutions in comparison to the SSC-I

Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition)

The third edition of Flow Cytometry Guidelines provides the key aspects to consider when performing flow cytometry experiments and includes comprehensive sections describing phenotypes and functional assays of all major human and murine immune cell subsets. Notably, the Guidelines contain helpful tables highlighting phenotypes and key differences between human and murine cells. Another useful feature of this edition is the flow cytometry analysis of clinical samples with examples of flow cytometry applications in the context of autoimmune diseases, cancers as well as acute and chronic infectious diseases. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid. All sections are written and peer-reviewed by leading flow cytometry experts and immunologists, making this edition an essential and state-of-the-art handbook for basic and clinical researchers

Mycobacterium tuberculosis epitope-specific interferon-g production in healthy Brazilians reactive and non-reactive to tuberculin skin test

The interferon (IFN)-gamma response to peptides can be a useful diagnostic marker of Mycobacterium tuberculosis (MTB) latent infection. We identified promiscuous and potentially protective CD4(+) T-cell epitopes from the most conserved regions of MTB antigenic proteins by scanning the MTB antigenic proteins GroEL2, phosphate-binding protein 1 precursor and 19 kDa antigen with the TEPITOPE algorithm. Seven peptide sequences predicted to bind to multiple human leukocyte antigen (HLA)-DR molecules were synthesised and tested with IFN-gamma enzyme-linked immunospot (ELISPOT) assays using peripheral blood mononuclear cells (PBMCs) from 16 Mantoux tuberculin skin test (TST)-positive and 16 TST-negative healthy donors. Eighty-eight percent of TST-positive donors responded to at least one of the peptides, compared to 25% of TST-negative donors. Each individual peptide induced IFN-gamma production by PBMCs from at least 31% of the TST-positive donors. the magnitude of the response against all peptides was 182 +/- 230 x 10(6) IFN-gamma spot forming cells (SFC) among TST-positive donors and 36 +/- 62 x 10(6) SFC among TST-negative donors (p = 0.007). the response to GroEL2 (463-477) was only observed in the TST-positive group. This combination of novel MTB CD4 T-cell epitopes should be tested in a larger cohort of individuals with latent tuberculosis (TB) to evaluate its potential to diagnose latent TB and it may be included in ELISPOT-based IFN-gamma assays to identify individuals with this condition.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de São Paulo, Fac Med, Inst Coracao, Immunol Lab, São Paulo, BrazilUniversidade Federal de São Paulo, Fac Med, Dept Med, Div Imunol Clin & Alergia, São Paulo, BrazilFundacao Oswaldo Cruz, Lab Avancado Saude Publ, Salvador, BA, BrazilEscola Bahiana Med & Saude Publ, Salvador, BA, BrazilInst Invest Immunol, São Paulo, BrazilUniversidade Federal de São Paulo, Fac Med, Inst Coracao, Immunol Lab, São Paulo, BrazilUniversidade Federal de São Paulo, Fac Med, Dept Med, Div Imunol Clin & Alergia, São Paulo, BrazilWeb of Scienc