Using a logical model to predict the growth of yeast

<p>Abstract</p> <p>Background</p> <p>A logical model of the known metabolic processes in <it>S. cerevisiae </it>was constructed from iFF708, an existing Flux Balance Analysis (FBA) model, and augmented with information from the KEGG online pathway database. The use of predicate logic as the knowledge representation for modelling enables an explicit representation of the structure of the metabolic network, and enables logical inference techniques to be used for model identification/improvement.</p> <p>Results</p> <p>Compared to the FBA model, the logical model has information on an additional 263 putative genes and 247 additional reactions. The correctness of this model was evaluated by comparison with iND750 (an updated FBA model closely related to iFF708) by evaluating the performance of both models on predicting empirical minimal medium growth data/essential gene listings.</p> <p>Conclusion</p> <p>ROC analysis and other statistical studies revealed that use of the simpler logical form and larger coverage results in no significant degradation of performance compared to iND750.</p

pubmed2ensembl: A Resource for Mining the Biological Literature on Genes

The last two decades have witnessed a dramatic acceleration in the production of genomic sequence information and publication of biomedical articles. Despite the fact that genome sequence data and publications are two of the most heavily relied-upon sources of information for many biologists, very little effort has been made to systematically integrate data from genomic sequences directly with the biological literature. For a limited number of model organisms dedicated teams manually curate publications about genes; however for species with no such dedicated staff many thousands of articles are never mapped to genes or genomic regions.To overcome the lack of integration between genomic data and biological literature, we have developed pubmed2ensembl (http://www.pubmed2ensembl.org), an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species. We use several sources of curated (e.g., Entrez Gene) and automatically generated (e.g., gene names extracted through text-mining on MEDLINE records) sources of gene-publication links, allowing users to filter and combine different data sources to suit their individual needs for information extraction and biological discovery. In addition to extending the Ensembl BioMart database to include published information on genes, we also implemented a scripting language for automated BioMart construction and a novel BioMart interface that allows text-based queries to be performed against PubMed and PubMed Central documents in conjunction with constraints on genomic features. Finally, we illustrate the potential of pubmed2ensembl through typical use cases that involve integrated queries across the biomedical literature and genomic data.By allowing biologists to find the relevant literature on specific genomic regions or sets of functionally related genes more easily, pubmed2ensembl offers a much-needed genome informatics inspired solution to accessing the ever-increasing biomedical literature

Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping

Interactions of E. coli lac repressor (LacR) with a pair of operator sites on the same DNA molecule can lead to the formation of looped nucleoprotein complexes both in vitro and in vivo. As a major paradigm for loop-mediated gene regulation, parameters such as operator affinity and spacing, repressor concentration, and DNA bending induced by specific or non-specific DNA-binding proteins (e.g., HU), have been examined extensively. However, a complete and rigorous model that integrates all of these aspects in a systematic and quantitative treatment of experimental data has not been available. Applying our recent statistical-mechanical theory for DNA looping, we calculated repression as a function of operator spacing (58–156 bp) from first principles and obtained excellent agreement with independent sets of in-vivo data. The results suggest that a linear extended, as opposed to a closed v-shaped, LacR conformation is the dominant form of the tetramer in vivo. Moreover, loop-mediated repression in wild-type E. coli strains is facilitated by decreased DNA rigidity and high levels of flexibility in the LacR tetramer. In contrast, repression data for strains lacking HU gave a near-normal value of the DNA persistence length. These findings underscore the importance of both protein conformation and elasticity in the formation of small DNA loops widely observed in vivo, and demonstrate the utility of quantitatively analyzing gene regulation based on the mechanics of nucleoprotein complexes

Depression care management for late-life depression in China primary care: Protocol for a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>As a major public health issue in China and worldwide, late-life depression is associated with physical limitations, greater functional impairment, increased utilization and cost of health care, and suicide. Like other chronic diseases in elders such as hypertension and diabetes, depression is a chronic disease that the new National Health Policy of China indicates should be managed in primary care settings. Collaborative care, linking primary and mental health specialty care, has been shown to be effective for the treatment of late-life depression in primary care settings in Western countries. The primary aim of this project is to implement a depression care management (DCM) intervention, and examine its effectiveness on the depressive symptoms of older patients in Chinese primary care settings.</p> <p>Methods/Design</p> <p>The trial is a multi-site, primary clinic based randomized controlled trial design in Hangzhou, China. Sixteen primary care clinics will be enrolled in and randomly assigned to deliver either DCM or care as usual (CAU) (8 clinics each) to 320 patients (aged ≥ 60 years) with major depression (20/clinic; n = 160 in each treatment condition). In the DCM arm, primary care physicians (PCPs) will prescribe 16 weeks of antidepressant medication according to the treatment guideline protocol. Care managers monitor the progress of treatment and side effects, educate patients/family, and facilitate communication between providers; psychiatrists will provide weekly group psychiatric consultation and CM supervision. Patients in both DCM and CAU arms will be assessed by clinical research coordinators at baseline, 4, 8, 12, 18, and 24 months. Depressive symptoms, functional status, treatment stigma and clients' satisfaction will be used to assess patients' outcomes; and clinic practices, attitudes/knowledge, and satisfaction will be providers' outcomes.</p> <p>Discussion</p> <p>This will be the first trial of the effectiveness of a collaborative care intervention aiming to the management of late-life depression in China primary care. If effective, its finding will have relevance to policy makers who wish to scale up DCM treatments for late-life depression in national wide primary care across China.</p> <p>Study Registration</p> <p>The DCM project is registered through the National Institutes of Health sponsored by clinical trials registry and has been assigned the identifier: <a href="http://www.clinicaltrials.gov/ct2/show/NCT01287494">NCT01287494</a></p

A cluster randomized trial of standard quality improvement versus patient-centered interventions to enhance depression care for African Americans in the primary care setting: study protocol NCT00243425

<p>Abstract</p> <p>Background</p> <p>Several studies document disparities in access to care and quality of care for depression for African Americans. Research suggests that patient attitudes and clinician communication behaviors may contribute to these disparities. Evidence links patient-centered care to improvements in mental health outcomes; therefore, quality improvement interventions that enhance this dimension of care are promising strategies to improve treatment and outcomes of depression among African Americans. This paper describes the design of the BRIDGE (Blacks Receiving Interventions for Depression and Gaining Empowerment) Study. The goal of the study is to compare the effectiveness of two interventions for African-American patients with depression--a standard quality improvement program and a patient-centered quality improvement program. The main hypothesis is that patients in the patient-centered group will have a greater reduction in their depression symptoms, higher rates of depression remission, and greater improvements in mental health functioning at six, twelve, and eighteen months than patients in the standard group. The study also examines patient ratings of care and receipt of guideline-concordant treatment for depression.</p> <p>Methods/Design</p> <p>A total of 36 primary care clinicians and 132 of their African-American patients with major depressive disorder were recruited into a cluster randomized trial. The study uses intent-to-treat analyses to compare the effectiveness of standard quality improvement interventions (academic detailing about depression guidelines for clinicians and disease-oriented care management for their patients) and patient-centered quality improvement interventions (communication skills training to enhance participatory decision-making for clinicians and care management focused on explanatory models, socio-cultural barriers, and treatment preferences for their patients) for improving outcomes over 12 months of follow-up.</p> <p>Discussion</p> <p>The BRIDGE Study includes clinicians and African-American patients in under-resourced community-based practices who have not been well-represented in clinical trials to improve depression care. The patient-centered and culturally targeted approach to depression care is a relatively new one that has not been tested in most previous studies. The study will provide evidence about whether patient-centered accommodations improve quality of care and outcomes to a greater extent than standard quality improvement strategies for African Americans with depression.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov NCT00243425</p

The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists

Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic relationships among predicted orthologs (based on the OrthoMCL method) to a query gene from any of eight eukaryotic organisms, and to see the orthologs in a wider evolutionary context (based on the Jaccard clustering method). In addition to the phylogenetic information, the database contains experimental results manually collected from the literature that can be compared to the computational analyses, as well as links to relevant human disease and gene information via the OMIM, model organism, and sequence databases. Our aim is for the P-POD resource to be extremely useful to typical experimental biologists wanting to learn more about the evolutionary context of their favorite genes. P-POD is based on the commonly used Generic Model Organism Database (GMOD) schema and can be downloaded in its entirety for installation on one's own system. Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools

The one dimensional Kondo lattice model at partial band filling

The Kondo lattice model introduced in 1977 describes a lattice of localized magnetic moments interacting with a sea of conduction electrons. It is one of the most important canonical models in the study of a class of rare earth compounds, called heavy fermion systems, and as such has been studied intensively by a wide variety of techniques for more than a quarter of a century. This review focuses on the one dimensional case at partial band filling, in which the number of conduction electrons is less than the number of localized moments. The theoretical understanding, based on the bosonized solution, of the conventional Kondo lattice model is presented in great detail. This review divides naturally into two parts, the first relating to the description of the formalism, and the second to its application. After an all-inclusive description of the bosonization technique, the bosonized form of the Kondo lattice hamiltonian is constructed in detail. Next the double-exchange ordering, Kondo singlet formation, the RKKY interaction and spin polaron formation are described comprehensively. An in-depth analysis of the phase diagram follows, with special emphasis on the destruction of the ferromagnetic phase by spin-flip disorder scattering, and of recent numerical results. The results are shown to hold for both antiferromagnetic and ferromagnetic Kondo lattice. The general exposition is pedagogic in tone.Comment: Review, 258 pages, 19 figure

Examining Morbidity and Mortality in Racial and Ethnic Minorities during the COVID-19 Pandemic: An Historical Perspective

ABSTRACT Examining increased morbidity and mortality in racial and ethnic minorities during the COVID-19 pandemic is essential to understanding health inequity, inequality, and injustice in our current healthcare system. Asian, Black, Latinx, American Indian, Alaskan Native, Native Hawaiian, and Other Pacific Islanders were disproportionately affected by the COVID-19 pandemic resulting in an increased incidence of infection, hospitalization, and death. Social determinants of health, including socioeconomic status, profoundly affected racial and ethnic minorities, resulting in the inability to social distance due to multigenerational living and without the opportunity to work remotely. The service industry during the pandemic was disproportionately constructed of racial and ethnic minorities, resulting in a larger percentage of those populations losing employment when the hospitality industry temporarily closed (due to halted travel). A significant number of racial and ethnic minorities were employed as essential workers such as nurse’s aides, public transportation drivers, sanitation workers, retail sales, and in the meatpacking industry. Others were employed in an environment where unpaid sick leave was the norm and absenteeism could result in loss of employment. Long-standing systems such as structural racism continue to perpetuate discriminatory practices affecting, employment, education, housing, and access to health care resulting in poorer mental and physical health outcomes. Social determinants of health and structural racism are the legacy of United States (US) Settler Colonialism, established upon indigenous elimination, racism, and immigrant exploitation

Digital education review

This paper considers a hybrid maintenance policy for a simple system comprising a single component that arises from a heterogeneous population. This population of components consists of two sub-populations that possess different failure characteristics. There are a substantial number of papers that deal with appropriate mixture distributions for the lifetime of a component from such a population. However, the study of maintenance policies for a system with this type of component is limited. By supposing that a component may be in a defective but operating state, so that there exists a delay time between defect arrival and failure, we consider a novel maintenance policy that is a hybrid of inspection and replacement policies. There are similarities in this approach with the concept of “burn-in” maintenance. The policies are investigated in the context of traction motor bearing failures. Under certain circumstances, particularly when the mixture parameter is large and the distribution of lifetimes for the two component types are well separated, the hybrid policy has significant cost savings over the standard age-based replacement policy and over the pure inspection policy. In addition to the cost metric, the mean time between operational failures of the system under the hybrid policy can be used to guide decision-making. This maintenance policy metric is calculated using simulation, and using an approximation which assumes that operational failures occur according to a Poisson process with a rate that can be calculated in a straightforward way. The simulation and approximation results show good agreement