The Cure: Making a game of gene selection for breast cancer survival prediction

Motivation: Molecular signatures for predicting breast cancer prognosis could greatly improve care through personalization of treatment. Computational analyses of genome-wide expression datasets have identified such signatures, but these signatures leave much to be desired in terms of accuracy, reproducibility and biological interpretability. Methods that take advantage of structured prior knowledge (e.g. protein interaction networks) show promise in helping to define better signatures but most knowledge remains unstructured. Crowdsourcing via scientific discovery games is an emerging methodology that has the potential to tap into human intelligence at scales and in modes previously unheard of. Here, we developed and evaluated a game called The Cure on the task of gene selection for breast cancer survival prediction. Our central hypothesis was that knowledge linking expression patterns of specific genes to breast cancer outcomes could be captured from game players. We envisioned capturing knowledge both from the players prior experience and from their ability to interpret text related to candidate genes presented to them in the context of the game. Results: Between its launch in Sept. 2012 and Sept. 2013, The Cure attracted more than 1,000 registered players who collectively played nearly 10,000 games. Gene sets assembled through aggregation of the collected data clearly demonstrated the accumulation of relevant expert knowledge. In terms of predictive accuracy, these gene sets provided comparable performance to gene sets generated using other methods including those used in commercial tests. The Cure is available at http://genegames.org/cure

Effect of Water Temperature on the Mechanical Properties of Water Quenched Medium Carbon Steel

The effect of water temperature on the hardness and impact strength of water quenched medium carbon steel was investigated. Two medium carbon steel, 0.33 wt % C and 0.42 wt % C, were heated to 900 oC and quenched in water at temperatures ranging from 35 oC (room temperature) to 95 oC. The results showed that hardness was reduced by over 18% and impact strength was improved by over 50%. The hard martensite structure which usually makes quenched steels highly brittle and of low toughness was replaced by tempered martensite structures thereby impacting better mechanical properties in the steel. Keywords: Water quenched temperature, Thermal Diffusivity, Hardness, Toughnes

Organizing knowledge to enable personalization of medicine in cancer

Interpretation of the clinical significance of genomic alterations remains the most severe bottleneck preventing the realization of personalized medicine in cancer. We propose a knowledge commons to facilitate collaborative contributions and open discussion of clinical decision-making based on genomic events in cancer

Oscillations of the superconducting critical current in Nb-Cu-Ni-Cu-Nb junctions

We report on experimental studies of superconductor-ferromagnet layered structures. Strong oscillations of the critical supercurrent were observed with the thickness variation of the ferromagnet. Using known microscopic parameters of Ni, we found reasonable agreement between the period of oscillations and the decay of the measured critical current, and theoretical calculations.Comment: 5 page

Thermodynamics and Phase Diagrams of layered superconductor/ferromagnet nanostructures

We study the thermodynamics of clean, layered superconductor/ferromagnet nanostructures using fully self consistent methods to solve the microscopic Bogoliubov-deGennes equations. From these self-consistent solutions the condensation free energies are obtained. The trilayer SFS junction is studied in particular detail: first order transitions between 0 and $\pi$ states as a function of the temperature $T$ are located by finding where the free energies of the two phases cross. The occurrence of these transitions is mapped as a function of the thickness $d_F$ of the F layer and of the Fermi wavevector mismatch parameter $\Lambda$. Similar first order transitions are found for systems with a larger number of layers: examples are given in the 7 layer (3 junction) case. The latent heats associated with these phase transitions are evaluated and found to be experimentally accessible. The transition temperature to the normal state is calculated from the linearized Bogoliubov-deGennes equations and found to be in good agreement with experiment. Thus, the whole three dimensional phase diagram in $T,d_F,\Lambda$ space can be found. The first order transitions are associated with dips in the transition temperature $T_c$ to the non-superconducting state, which should facilitate locating them. Results are given also for the magnetic moment and the local density of states (DOS) at the first order transition.Comment: 15 pages, 13 figure

A Systematic Review of Sellar and Parasellar Brown Tumors: An Analysis of Clinical, Diagnostic, and Management Profiles

Objective To systematically review and analyze clinical, diagnostic, and management trends in sellar and parasellar brown tumors reported in existing literature. Methods In this systematic review, PubMed, Ovid MEDLINE, Scopus, and Google Scholar databases were searched for reported cases of sellar/parasellar brown tumors. Relevant titles and abstracts were screened in accordance to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses protocol. Articles meeting inclusion criteria were subjected to data extraction, summarization, and analysis. A rare case of parasellar brown tumor was also presented. Results Eight reports (including the current report) were eligible for inclusion. Mean patient age was 42.75 years. Reported symptoms included visual disturbances (n = 6), headache (n = 5), fatigue (n = 3), nausea/vomiting (n = 2), chest pain (n = 1), neck pain (n = 1), and dysphagia (n = 1). In cases where computed tomography findings were provided (n = 6), lesions were noted to be expansile and lytic. Lesions were hyperintense on T2-weighted magnetic resonance imaging (66.7%) and demonstrated contrast enhancement (83.3%). Histology unanimously showed multinucleated giant cells in a fibrovascular connective tissue stroma. Dramatic symptom resolution was noted in all patients who underwent resection of the sellar/parasellar brown tumor (n = 4; 50%). Conclusions Sellar/parasellar brown tumors are a rare, tertiary manifestation of hyperparathyroidism and can be elusive to diagnose. Diagnosis requires a high index of clinical suspicion in addition to comprehensive biochemical testing, imaging, and histopathologic analysis. Surgical extirpation is favored in cases where the lesion is causing compressive symptoms, or if it is unresponsive to management of hyperparathyroidism

Body Mass Index, Blood Pressure and Serum Cortisol Level as Stress Index in Symptomatic HIV/AIDS Male Subjects on Antiretroviral Therapy Negative to Malaria Parasite in Nnewi, Anambra State, Nigeria

Background: HIV infection is a risk factor for a variety of endocrine problems. Objectives: This study investigated the body mass index (BMI), Systolic blood pressure (SBP), Diastolic blood pressure (DBP) and serum cortisol level as stress factor/index symptomatic HIV/AIDS male subjects on ART who are negative to malaria parasite in Nnewi, Anambra State, Nigeria. Methods: A total of 274 adult male participants aged between 18 and 60 (42 ±13) years were randomly recruited at the Voluntary Counseling and Testing (VCT) Centre in Nnamdi Azikiwe University Teaching Hospital and grouped based on WHO criteria for staging HIV into symptomatic HIV (stage 11) infected male participants on ART (A: n=69), Symptomatic HIV subjects not on ART (B: n= 69), Asymptomatic HIV positive subjects (C: n= 68) and HIV seronegative subjects (D: n= 68). Blood samples were collected from the participants for the determination of HIV status by immunochromatography and HIV confirmation by Western Blot. Enzyme-Linked Immunosorbent Assay (ELISA) was used to assay for cortisol level. Results: The results showed a significantly increased BMI and decreased mean serum cortisol level in HIV/AIDS seropositive participants on ART than in those, not on ART (p<0.05). Also, the BMI and mean serum cortisol level were significantly decreased and increased respectively in  HIV/AIDS seropositive participants not on ART than in Asymptomatic HIV positive subjects and control respectively (p<0.05). However, the mean SBP and DBP did not differ significantly between the groups studied (p>0.05). Conclusion: This study revealed a decreased stress index in HIV/AIDS subjects on ART with hypercortisolism and lower BMI in symptomatic HIV participants, not on ART. Keywords: HIV; AIDS; Malaria uninfected male subjects; Cortisol; Blood pressure; Antiretroviral therapy

Body Mass Index, Blood Pressure and Serum Cortisol Level as Stress Index in Symptomatic HIV/AIDS Male Subjects on Antiretroviral Therapy Negative to Malaria Parasite in Nnewi, Anambra State, Nigeria

Background: HIV infection is a risk factor for a variety of endocrine problems. Objectives: This study investigated the body mass index (BMI), Systolic blood pressure (SBP), Diastolic blood pressure (DBP) and serum cortisol level as stress factor/index symptomatic HIV/AIDS male subjects on ART who are negative to malaria parasite in Nnewi, Anambra State, Nigeria. Methods: A total of 274 adult male participants aged between 18 and 60 (42 ±13) years were randomly recruited at the Voluntary Counseling and Testing (VCT) Centre in Nnamdi Azikiwe University Teaching Hospital and grouped based on WHO criteria for staging HIV into symptomatic HIV (stage 11) infected male participants on ART (A: n=69), Symptomatic HIV subjects not on ART (B: n= 69), Asymptomatic HIV positive subjects (C: n= 68) and HIV seronegative subjects (D: n= 68). Blood samples were collected from the participants for the determination of HIV status by immunochromatography and HIV confirmation by Western Blot. Enzyme-Linked Immunosorbent Assay (ELISA) was used to assay for cortisol level. Results: The results showed a significantly increased BMI and decreased mean serum cortisol level in HIV/AIDS seropositive participants on ART than in those, not on ART (p<0.05). Also, the BMI and mean serum cortisol level were significantly decreased and increased respectively in  HIV/AIDS seropositive participants not on ART than in Asymptomatic HIV positive subjects and control respectively (p<0.05). However, the mean SBP and DBP did not differ significantly between the groups studied (p>0.05). Conclusion: This study revealed a decreased stress index in HIV/AIDS subjects on ART with hypercortisolism and lower BMI in symptomatic HIV participants, not on ART. Keywords: HIV; AIDS; Malaria uninfected male subjects; Cortisol; Blood pressure; Antiretroviral therapy