Design, tuning, and blackbox optimization of laser systems.

Chirped pulse amplification (CPA) and subsequent nonlinear optical (NLO) systems constitute the backbone of myriad advancements in semiconductor manufacturing, communications, biology, defense, and beyond. Accurately and efficiently modeling CPA+NLO-based laser systems is challenging because of the complex coupled processes and diverse simulation frameworks. Our modular start-to-end model unlocks the potential for exciting new optimization and inverse design approaches reliant on data-driven machine learning methods, providing a means to create tailored CPA+NLO systems unattainable with current models.

Fusobacterium and Colorectal Cancer: Important Association or Random Coincidence?

The role of the microbiome in human cancer has become an area of intensive research and controversy. Many reports have highlighted the physical association of Fusobacterium with colorectal cancer. This association has provided diagnostic and therapeutic promise but has also given rise to several controversies regarding the influence of Fusobacterium species on human colorectal cancer.

COVID-19 response by the Hopi Tribe: impact of systems improvement during the first wave on the second wave of the pandemic.

The Hopi Tribe is a sovereign nation home to ~7500 Hopi persons living primarily in 12 remote villages. The Hopi Tribe, like many other American Indian nations, has been disproportionately affected by COVID-19. On 18 May 2020, a team from the US Centers for Disease Control and Prevention (CDC) was deployed on the request of the tribe in response to increases in COVID-19 cases.

Long-term hybrid stabilization of the carrier-envelope phase.

Controlling the carrier envelope phase (CEP) in mode-locked lasers over practically long timescales is crucial for real-world applications in ultrafast optics and precision metrology. We present a hybrid solution that combines a feed-forward technique to stabilize the phase offset in fast timescales and a feedback technique that addresses slowly varying sources of interference and locking bandwidth limitations associated with gain media with long upper-state lifetimes. We experimentally realize the hybrid stabilization system in an Er:Yb:glass mode-locked laser and demonstrate 75 hours of stabilization with integrated phase noise of 14 mrad (1 Hz to 3 MHz), corresponding to around 11 as of carrier to envelope jitter.

A SARS-CoV-2 Outbreak Illustrating the Challenges in Limiting the Spread of the Virus - Hopi Tribe, May-June 2020.

On June 3, 2020, a woman aged 73 years (patient A) with symptoms consistent with coronavirus disease 2019 (COVID-19) (1) was evaluated at the emergency department of the Hopi Health Care Center (HHCC, an Indian Health Services facility) and received a positive test result for SARS-CoV-2, the virus that causes COVID-19. The patient's symptoms commenced on May 27, and a sibling (patient B) of the patient experienced symptom onset the following day. On May 23, both patients had driven together and spent time in a retail store in Flagstaff, Arizona.

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs, and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high-throughput reduced representation expression profiling method that we term L1000. We show that L1000 is highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts.

An extended set of yeast-based functional assays accurately identifies human disease mutations.

We can now routinely identify coding variants within individual human genomes. A pressing challenge is to determine which variants disrupt the function of disease-associated genes. Both experimental and computational methods exist to predict pathogenicity of human genetic variation.

BioGRID: A Resource for Studying Biological Interactions in Yeast.

The Biological General Repository for Interaction Datasets (BioGRID) is a freely available public database that provides the biological and biomedical research communities with curated protein and genetic interaction data. Structured experimental evidence codes, an intuitive search interface, and visualization tools enable the discovery of individual gene, protein, or biological network function. BioGRID houses interaction data for the major model organism species--including yeast, nematode, fly, zebrafish, mouse, and human--with particular emphasis on the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe as pioneer eukaryotic models for network biology.

Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions.

The BioGRID database is an extensive repository of curated genetic and protein interactions for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and the yeast Candida albicans SC5314, as well as for several other model organisms and humans. This protocol describes how to use the BioGRID website to query genetic or protein interactions for any gene of interest, how to visualize the associated interactions using an embedded interactive network viewer, and how to download data files for either selected interactions or the entire BioGRID interaction data set.

The BioGRID interaction database: 2015 update.

The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of September 2014, the BioGRID contains 749,912 interactions as drawn from 43,149 publications that represent 30 model organisms.

Vital signs: sodium intake among U.S. school-aged children - 2009-2010.

Background: A national health objective is to reduce average U.S. sodium intake to 2,300 mg daily to help prevent high blood pressure, a major cause of heart disease and stroke.

WIC Infant and Toddler Feeding Practices Study: protocol design and implementation.

The federal Special Supplemental Nutrition Program for Women, Infants, and Children (WIC), which began in the 1970s, has undergone revisions in the past several years, including revision to contents of the supplemental food "packages" in 2009 based on recommendations provided by an Institute of Medicine (IOM) committee of The National Academies. In 2010, the IOM held a workshop to examine and recommend research priorities for the program. The overall purpose of the current (ie, second) WIC Infant and Toddler Feeding Practices Study (ITFPS-2) is to conduct a nationally representative, longitudinal study of contemporary WIC infant and toddler feeding practices.

School food and nutrition policy, monitoring and evaluation in the USA.

Objective: To provide an overview of school food and nutrition monitoring from 1980 to the Healthy Hunger-Free Kids Act of 2010 and data on school food availability in the USA.

Design: A review of the history of school food and nutrition policy, monitoring and evaluation efforts in the USA over the past three decades.

Setting: USA.

Exploring differences in self-rated health among Blacks, Whites, Mexicans, and Puerto Ricans.

Objectives: Self-rated health (SRH) is a robust predictor of subsequent health and mortality. Although age, gender, and race differences in SRH have been explored, less work has examined ethnic differences, particularly in the US.

Design: The current study uses representative data from six Chicago communities to compare levels and determinants of fair-poor health for Blacks, Whites, Mexicans, and Puerto Ricans (n=1311).

Saccharomyces Genome Database: the genomics resource of budding yeast.

The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for the budding yeast Saccharomyces cerevisiae.

Using the Saccharomyces Genome Database (SGD) for analysis of genomic information.

Analysis of genomic data requires access to software tools that place the sequence-derived information in the context of biology. The Saccharomyces Genome Database (SGD) integrates functional information about budding yeast genes and their products with a set of analysis tools that facilitate exploring their biological details. This unit describes how the various types of functional data available at SGD can be searched, retrieved, and analyzed.

A MOD(ern) perspective on literature curation.

Curation of biological data is a multi-faceted task whose goal is to create a structured, comprehensive, integrated, and accurate resource of current biological knowledge. These structured data facilitate the work of the scientific community by providing knowledge about genes or genomes and by generating validated connections between the data that yield new information and stimulate new research approaches. For the model organism databases (MODs), an important source of data is research publications.

Saccharomyces Genome Database provides mutant phenotype data.

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.

Microvesicles in haemoglobinopathies offer insights into mechanisms of hypercoagulability, haemolysis and the effects of therapy.

Levels of circulating red blood cell (RBC)-derived vesicles are increased in sickle cell anaemia (SCA) and thalassaemia intermedia (TI) but the mechanisms, effects and controlling factors may differ. This study found that levels of vesicles and intravascular haemolysis were linked as shown by the correlation between levels of vesicles and plasma Hb. Vesicle levels were 6-fold greater in SCA and 4-fold greater in TI than in controls.

Gene Ontology annotations at SGD: new data sources and annotation methods.

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae.

The black:white disparity in breast cancer mortality: the example of Chicago.

Objective: The black:white disparity in breast cancer mortality has been increasing in the U.S. In order to gain insight into this disparity in Chicago, we examined mortality data together with other important measures associated with breast cancer.

Expanded protein information at SGD: new pages and proteome browser.

The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available protein information and has prompted the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) to enhance the depth and accessibility of protein annotations.

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.

Sequencing and annotation of the entire Saccharomyces cerevisiae genome has made it possible to gain a genome-wide perspective on yeast genes and gene products. To make this information available on an ongoing basis, the Saccharomyces Genome Database (SGD) (http://www.yeastgenome.