Writing Sample

Includes hole in the wall, a souvenir of hell, and rabin’s dead

Optimal Cox Regression Subsampling Procedure with Rare Events

Massive sized survival datasets are becoming increasingly prevalent with the development of the healthcare industry. Such datasets pose computational challenges unprecedented in traditional survival analysis use-cases. A popular way for coping with massive datasets is downsampling them to a more manageable size, such that the computational resources can be afforded by the researcher. Cox proportional hazards regression has remained one of the most popular statistical models for the analysis of survival data to-date. This work addresses the settings of right censored and possibly left truncated data with rare events, such that the observed failure times constitute only a small portion of the overall sample. We propose Cox regression subsampling-based estimators that approximate their full-data partial-likelihood-based counterparts, by assigning optimal sampling probabilities to censored observations, and including all observed failures in the analysis. Asymptotic properties of the proposed estimators are established under suitable regularity conditions, and simulation studies are carried out to evaluate the finite sample performance of the estimators. We further apply our procedure on UK-biobank colorectal cancer genetic and environmental risk factors

Unlocking Retrospective Prevalent Information in EHRs -- a Pairwise Pseudolikelihood Approach

Typically, electronic health record data are not collected towards a specific research question. Instead, they comprise numerous observations recruited at different ages, whose medical, environmental and oftentimes also genetic data are being collected. Some phenotypes, such as disease-onset ages, may be reported retrospectively if the event preceded recruitment, and such observations are termed ``prevalent". The standard method to accommodate this ``delayed entry" conditions on the entire history up to recruitment, hence the retrospective prevalent failure times are conditioned upon and cannot participate in estimating the disease-onset age distribution. An alternative approach conditions just on survival up to recruitment age, plus the recruitment age itself. This approach allows incorporating the prevalent information but brings about numerical and computational difficulties. In this work we develop consistent estimators of the coefficients in a regression model for the age-at-onset, while utilizing the prevalent data. Asymptotic results are provided, and simulations are conducted to showcase the substantial efficiency gain that may be obtained by the proposed approach. In particular, the method is highly useful in leveraging large-scale repositories for replicability analysis of genetic variants. Indeed, analysis of urinary bladder cancer data reveals that the proposed approach yields about twice as many replicated discoveries compared to the popular approach

Building Protein Domain Based Composite Biobricks for Mammalian Expression Systems

The purpose of this RFC is to describe a method that allows the design of protein domain based parts, starting with gene centered information and translate these informations into BBF RFC 25 compatible part. The method is designed to be used in mammalian expression systems

The impact of specialty settings on the perceived quality of medical ultrasound video

Health care professionals are increasingly viewing medical images and videos in a variety of environments. The perception of medical visual information across all specialties, career stages, and practice settings are critical to patient care and patient safety. Visual signal distortions, such as various types of noise and artifacts arising in medical imaging, affect the perceptual quality of visual content and potentially impact diagnoses. To optimize clinical practice, it is of fundamental importance to understand the way medical experts perceive visual quality. Psychophysical studies have been undertaken to evaluate the impact of visual distortions on the perceived quality of medical images and videos. However, very little research has been conducted on how speciality settings affect the perception of visual quality. In this paper, we investigate whether and how radiologists and sonographers differently perceive the quality of compressed ultrasound videos, via a dedicated subjective experiment. The findings can be used to develop useful solutions for improved visual experience and better image-based diagnoses

Prenatal diagnosis of proximal focal femoral deficiency: Literature review of prenatal sonographic findings

Proximal focal femoral deficiency (PFFD) is a rare musculoskeletal malformation that occurs in 0.11-0.2 per 10,000 live births. This congenital anomaly involves the pelvis and proximal femur with widely variable manifestations, from mild femoral shortening and hypoplasia to the absence of any functional femur and acetabular aplasia. Prenatal diagnosis of PFFD is still a challenge, but early recognition of this malformation could provide useful information to both parents and physicians concerning management and therapeutic planning. For this review, we analyzed all the cases of prenatally diagnosed PFFD that were reported in the literature from 1990 to 2014 and provide a description of the most common prenatal sonographic findings

“Atividades Investigativas Autênticas” para o Ensino de Razão e Proporção na Formação de Professores de Matemática para os Níveis Elementar e Médio

We present some elements related to the creation, implementation, and evaluation of the impact of “authentic investigative activities” that focus on the content as well as pedagogical knowledge and attitudes in pre-service education of elementary and high school mathematics teachers. A special learning model was developed, implemented, and tested as part of activities developed in institutions that provide pre-service teacher education in Israel. The model was developed following pilot studies investigating the change in mathematical and pedagogical knowledge of pre- and inservice mathematics teachers due to the application of “authentic investigative activities”. The conclusion of the study is that application of the model, incorporating theory and practice, leads to a dramatic positive change in the pre-service teachers’ content and pedagogical knowledge. In addition, an improvement occurred in their attitudes and beliefs towards learning and teaching mathematics in general, and ratio and proportion in particular. Keywords: Authentic Investigative Activities. Ratio and Proportion. Proportional Reasoning. Mathematics Teacher Education. Preservice Teacher Education.Neste artigo são apresentados elementos relacionados à criação, implementação e avaliação do impacto das chamadas “atividades investigativas autênticas” que focam tanto o conteúdo quanto o conhecimento pedagógico e as atitudes na formação inicial de professores de Matemática para os níveis de ensino elementar e médio. Um modelo especial de aprendizagem foi desenvolvido, implementado e testado como parte de atividades desenvolvidas em instituições israelenses voltadas à formação de professores. O modelo foi desenvolvido segundo estudos-piloto, investigando as alterações nos conhecimentos matemático e pedagógico de professores de Matemática – em formação e em atuação – ocorridas com a aplicação das “atividades investigativas autênticas”. As conclusões do estudo apontam que a aplicação do modelo – por meio do qual os professores ganham experiência e são expostos a atividades de raciocínio proporcional “autêntico”, incorporando teoria (pela leitura e análise de relevantes textos de pesquisa) e prática – produz uma alteração significativa quanto à abordagem ao conteúdo matemático e quanto ao conhecimento pedagógico. Além disso, alterações significativamente positivas ocorreram nas atitudes e crenças desses professores em relação ao ensino e à aprendizagem de Matemática, em geral e, em particular, em relação aos conceitos de razão e proporção. Palavras-chave: Atividades Investigativas Autênticas, Razão e Proporção, Raciocínio Proporcional, Formação de Professores de Matemática