Implementing Cancer Registry Data With the PCORnet Common Data Model: The Greater Plains Collaborative Experience.

Purpose: Electronic health records (EHRs) comprise a rich source of real-world data for cancer studies, but they often lack critical structured data elements such as diagnosis date and disease stage. Fortunately, such concepts are available from hospital cancer registries. We describe experiences from integrating cancer registry data with EHR and billing data in an interoperable data model across a multisite clinical research network.

Patient perceptions of surgical telehealth consultations during the COVID 19 pandemic in Australia: Lessons for future implementation.

Introduction: Prior studies of telehealth report high levels of patient satisfaction, but within carefully selected clinical scenarios. The COVID-19 pandemic led to telehealth replacing face-to-face care for many surgical consultations across a variety of situations. More evidence is needed regarding patient perceptions of telehealth in surgery, in particular, exploring barriers and facilitators associated with its sustained implementation beyond the pandemic.

Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network.

Clinical data networks that leverage large volumes of data in electronic health records (EHRs) are significant resources for research on coronavirus disease 2019 (COVID-19). Data harmonization is a key challenge in seamless use of multisite EHRs for COVID-19 research. We developed a COVID-19 application ontology in the national Accrual to Clinical Trials (ACT) network that enables harmonization of data elements that are critical to COVID-19 research.

Development of a COVID-19 Application Ontology for the ACT Network.

Clinical data networks that leverage large volumes of data in electronic health records (EHRs) are significant resources for research on coronavirus disease 2019 (COVID-19). Data harmonization is a key challenge in seamless use of multisite EHRs for COVID-19 research. We developed a COVID-19 application ontology in the national Accrual to Clinical Trials (ACT) network that enables harmonization of data elements that that are critical to COVID-19 research.

Utilization of telehealth by surgeons during the COVID 19 pandemic in Australia: lessons learnt.

Background: The COVID-19 pandemic has led to the rapid and widespread adoption of telehealth. There is a need for more evidence regarding the appropriateness of telehealth, as well as greater understanding of barriers to its sustained use within surgery in Australia.

Methods: A survey weblink was sent via email to 5558 Australian Fellows of the Royal Australasian College of Surgeons in August 2020.

Probability Learning in an Uncertain World: How Children Adjust to Changing Contingencies.

We regularly make predictions about future events, even in a world where events occur probabilistically rather than deterministically. Our environment may even be non-stationary such that the probability of an event may change suddenly or from one context to another. 4-6 year olds and adults viewed 3 boxes and guessed the location of a hidden toy.

Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria.

Phenylketonuria (PKU) is a genetic disease that is characterized by an inability to metabolize phenylalanine (Phe), which can result in neurotoxicity. To provide a potential alternative to a protein-restricted diet, we engineered Escherichia coli Nissle to express genes encoding Phe-metabolizing enzymes in response to anoxic conditions in the mammalian gut. Administration of our synthetic strain, SYNB1618, to the Pah PKU mouse model reduced blood Phe concentration by 38% compared with the control, independent of dietary protein intake.

Distributional learning of subcategories in an artificial grammar: Category generalization and subcategory restrictions.

There has been significant recent interest in clarifying how learners use distributional information during language acquisition. Many researchers have suggested that distributional learning mechanisms play a major role during grammatical category acquisition, since linguistic form-classes (like and ) and subclasses (like and grammatical gender) are primarily defined by the ways lexical items are distributed in syntactic contexts. Though recent experimental work has affirmed the importance of distributional information for category acquisition, there has been little evidence that learners can acquire linguistic based only on distributional cues.

The effect of Zipfian frequency variations on category formation in adult artificial language learning.

Successful language acquisition hinges on organizing individual words into grammatical categories and learning the relationships between them, but the method by which children accomplish this task has been debated in the literature. One proposal is that learners use the shared distributional contexts in which words appear as a cue to their underlying category structure. Indeed, recent research using artificial languages has demonstrated that learners can acquire grammatical categories from this type of distributional information.

Optimized dual threshold entity resolution for electronic health record databases--training set size and active learning.

Clinical databases may contain several records for a single patient. Multiple general entity-resolution algorithms have been developed to identify such duplicate records. To achieve optimal accuracy, algorithm parameters must be tuned to a particular dataset.

Genome-wide mapping of furfural tolerance genes in Escherichia coli.

Advances in genomics have improved the ability to map complex genotype-to-phenotype relationships, like those required for engineering chemical tolerance. Here, we have applied the multiSCale Analysis of Library Enrichments (SCALEs; Lynch et al. (2007) Nat.

A benchmark comparison of deterministic and probabilistic methods for defining manual review datasets in duplicate records reconciliation.

Introduction: Clinical databases require accurate entity resolution (ER). One approach is to use algorithms that assign questionable cases to manual review. Few studies have compared the performance of common algorithms for such a task.

From shared contexts to syntactic categories: the role of distributional information in learning linguistic form-classes.

A fundamental component of language acquisition involves organizing words into grammatical categories. Previous literature has suggested a number of ways in which this categorization task might be accomplished. Here we ask whether the patterning of the words in a corpus of linguistic input (distributional information) is sufficient, along with a small set of learning biases, to extract these underlying structural categories.

Strategy for directing combinatorial genome engineering in Escherichia coli.

We describe a directed genome-engineering approach that combines genome-wide methods for mapping genes to traits [Warner JR, Reeder PJ, Karimpour-Fard A, Woodruff LBA, Gill RT (2010) Nat Biotechnol 28:856-862] with strategies for rapidly creating combinatorial ribosomal binding site (RBS) mutation libraries containing billions of targeted modifications [Wang HH, et al. (2009) Nature 460:894-898]. This approach should prove broadly applicable to various efforts focused on improving production of fuels, chemicals, and pharmaceuticals, among other products.

Application of a cave inventory system to stimulate development of management strategies: the case of west-central Florida, USA.

The active management of air-filled cave systems is virtually non-existent within the karst landscape of west-central Florida. As in every karst landscape, caves are important because they contain a wide variety of resources (e.g.

A rewired green fluorescent protein: folding and function in a nonsequential, noncircular GFP permutant.

The sequential order of secondary structural elements in proteins affects the folding and activity to an unknown extent. To test the dependence on sequential connectivity, we reconnected secondary structural elements by their solvent-exposed ends, permuting their sequential order, called "rewiring". This new protein design strategy changes the topology of the backbone without changing the core side chain packing arrangement.

Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides.

A fundamental goal in biotechnology and biology is the development of approaches to better understand the genetic basis of traits. Here we report a versatile method, trackable multiplex recombineering (TRMR), whereby thousands of specific genetic modifications are created and evaluated simultaneously. To demonstrate TRMR, in a single day we modified the expression of >95% of the genes in Escherichia coli by inserting synthetic DNA cassettes and molecular barcodes upstream of each gene.

Bioinformatics-driven, rational engineering of protein thermostability.

A longstanding goal in protein engineering is to identify specific sequence changes that endow proteins with desired functional properties. As opposed to traditional rational and random protein engineering techniques, we have employed a bioinformatic approach to identify specific sequence changes that influence key functional properties of a protein within a defined superfamily. Specifically, we have used the Bayesian sequence-based algorithms PROBE and Classifier to identify a strand-turn-strand motif that contributes to thermophilicity among members of the serine protease subtilase superfamily.

Half-life of the doubly magic r-process nucleus 78Ni.

Nuclei with magic numbers serve as important benchmarks in nuclear theory. In addition, neutron-rich nuclei play an important role in the astrophysical rapid neutron-capture process (r process). 78Ni is the only doubly magic nucleus that is also an important waiting point in the r process, and serves as a major bottleneck in the synthesis of heavier elements.

Lead contamination of soils in Belize City, Belize, Central America.

In order to assess the amount and distribution of lead pollution in soils in Belize City, Belize, seventy-five samples were collected from three distinct areas around the city (roadsides, houses, and playgrounds and schools). This study has provided data to establish the first soil lead database for Belize City, Belize. The soil samples generally exhibited pH values above 7, less than 18% organic matter, and more than 50% sand was found in 92% of the samples.

Detection and analysis of xenon isotopes for the comprehensive nuclear-test-ban treaty international monitoring system.

The use of the xenon isotopes for detection of nuclear explosions is of great interest for monitoring compliance with the comprehensive nuclear-test-ban treaty (CTBT). Recently, the automated radioxenon sampler-analyzer (ARSA) was tested at the Institute for Atmospheric Radioactivity (IAR) in Freiburg, Germany to ascertain its use for the CTBT by comparing its results to laboratory-based analyses, determining its detection sensitivity and analyzing its results in light of historical xenon isotope levels and known reactor operations in the area. Xe-133 was detected nearly every day throughout the test at activity concentrations ranging between approximately 0.