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This paper describes NeuroExtract, a pilot system which facilitates the integrated retrieval of Internet-based information relevant to the neurosciences. The approach involved extracting descriptive metadata from the sources using domain-specific queries; retrieving, processing, and organizing the data into structured text files; searching the data files using text-based queries; and, providing the results in a Web page along with descriptions to entries and URL links to the original sources. NeuroExtract has been implemented for three bioscience resources, SWISSPROT, GEO, and PDB, which provide neuroscience-related information as sub-topics. We discuss several issues that arose in the course of NeuroExtract's implementation. This project is a first step in exploring how this general approach might be used, in conjunction with other query mediation approaches, to facilitate the integration of many Internet-accessible resources relevant to the neurosciences. [ABSTRACT FROM AUTHOR]

Data sparsity and schema evolution issues affecting clinical informatics and bioinformatics communities have led to the adoption of vertical or object-attribute-value-based database schemas to overcome limitations posed when using conventional relational database technology. This paper explores these issues and discusses why biomedical data are difficult to model using conventional relational techniques. The authors propose a solution to these obstacles based on a relational database engine using a sparse, column-store architecture. The authors provide benchmarks comparing the performance of queries and schema-modification operations using three different strategies: (1) the standard conventional relational design; (2) past approaches used by biomedical informatics researchers; and (3) their sparse, column-store architecture. The performance results show that their architecture is a promising technique for storing and processing many types of data that are not handled well by the other two semantic data models. [ABSTRACT FROM AUTHOR]

The present study described an open source application, ResourceLog, that allows website administrators to record and analyze the usage of online resources. The application includes four components: logging, data mining, administrative interface, and back-end database. The logging component is embedded in the host website. It extracts and streamlines information about the Web visitors, the scripts, and dynamic parameters from each page request. The data mining component runs as a set of scheduled tasks that identify visitors of interest, such as those who have heavily used the resources. The identified visitors will be automatically subjected to a voluntary user survey. The usage of the website content can be monitored through the administrative interface and subjected to statistical analyses. As a pilot project, ResourceLog has been implemented in SenseLab, a Web-based neuroscience database system. ResourceLog provides a robust and useful tool to aid system evaluation of a resource-driven Web application, with a focus on determining the effectiveness of data sharing in the field and with the general public. [ABSTRACT FROM AUTHOR]

The rapid advances in high-throughput biotechnologies such as DNA microarrays and mass spectrometry have generated vast amounts of data ranging from gene expression to proteomics data. The large size and complexity involved in analyzing such data demand a significant amount of computing power. High-performance computation (HPC) is an attractive and increasingly affordable approach to help meet this challenge. There is a spectrum of techniques that can be used to achieve computational speedup with varying degrees of impact in terms of how drastic a change is required to allow the software to run on an HPC platform. This paper describes a high- productivity/low-maintenance (HP/LM) approach to HPC that is based on establishing a collaborative relationship between the bioinformaticist and HPC expert that respects the former's codes and minimizes the latter's efforts. The goal of this approach is to make it easy for bioinformatics researchers to continue to make iterative refinements to their programs, while still being able to take advantage of HPC. The paper describes our experience applying these HP/LM techniques in four bioinformatics case studies: (1) genome-wide sequence comparison using Blast, (2) identification of biomarkers based on statistical analysis of large mass spectrometry data sets, (3) complex genetic analysis involving ordinal phenotypes, (4) large-scale assessment of the effect of possible errors in analyzing microarray data. The case studies illustrate how the HP/LM approach can be applied to a range of representative bioinformatics applications and how the approach can lead to significant speedup of computationally intensive bioinformatics applications, while making only modest modifications to the programs themselves. [ABSTRACT FROM AUTHOR]

This report describes XDesc (eXperiment Description), a pilot project that serves as a case study exploring the degree to which an informatics capability developed in a clinical application can be ported for use in the biosciences. In particular, XDesc uses the Entity-Attribute-Value database implementation (including a great deal of metadata-based functionality) developed in TrialDB, a clinical research database, for use in describing the samples used in microarray experiments stored in the Yale Microarray Database (YMD). XDesc was linked successfully to both TrialDB and YMD, and was used to describe the data in three different microarray research projects involving Drosophila. In the process, a number of new desirable capabilities were identified in the bioscience domain. These were implemented on a pilot basis in XDesc, and subsequently "folded back" into TrialDB itself, enhancing its capabilities for dealing with clinical data. This case study provides a concrete example of how informatics research and development in clinical and bioscience domains has the potential for synergy and for cross-fertilization. [ABSTRACT FROM AUTHOR]

The article discusses issues that arise in implementing computer-based decision support using childhood immunization as a source of examples. The examples include (1) IMM/Serve, a program that provides patient-specific recommendations, (2) informatics tools developed to help validate IMM/Serve's knowledge and functionality, and (3) tools developed to explore how computers can help ensure immunization data quality. Issues discussed include the complexity of creating computer-based decision support, the need for a continuing process of revision and testing as the health field evolves over time, and the potential value of computer-based tools to assist in this process. [ABSTRACT FROM AUTHOR]

This case study explored 1) how much online clinical data is required to obtain patient-specific recommendations from a computer-based clinical practice guideline, 2) whether the availability of increasing amounts of online clinical data might allow a higher specificity of those recommendations, and 3) whether that increased specificity is necessarily desirable. The "quick reference guide" version of the guideline for acute postoperative pain management in adults, developed by the Agency for Health Care Policy and Research, was analyzed. Patient-specific data items that might be used to tailor the computer's output for a particular case were grouped into rough categories depending on how likely they were to be available online and how readily they might be determined from online clinical data. The patient-specific recommendations were analyzed to determine to what degree the amount of text produced depended on the online availability of different categories of data. An examination of example recommendations, however, illustrated that high specificity may not always be desirable. The study provides a concrete illustration of how the richness of online clinical data can affect patient-specific recommendations, and describes a number of related design trade-offs in converting a clinical guideline into an interactive, computer-based form. [ABSTRACT FROM AUTHOR]

Objective: Residing in communities characterized by socioeconomic disadvantage confers risk of cardiometabolic diseases. Residing in disadvantaged communities may also confer the risk of neurodegenerative brain changes via cardiometabolic pathways. This study tested whether features of communities-apart from conventional socioeconomic characteristics-relate not only to cardiometabolic risk but also to relative tissue reductions in the cerebral cortex and hippocampus., Methods: Participants were 699 adults aged 30 to 54 years (340 women; 22.5% non-White) whose addresses were geocoded to compute community indicators of socioeconomic disadvantage, as well as air and toxic chemical pollutant exposures, homicide rates, concentration of employment opportunities, land use (green space), and availability of supermarkets and local resources. Participants also underwent assessments of cortical and hippocampal volumes and cardiometabolic risk factors (adiposity, blood pressure, fasting glucose, and lipids)., Results: Multilevel structural equation modeling demonstrated that cardiometabolic risk was associated with community disadvantage ( β = 0.10, 95% confidence interval [CI] = 0.01 to 0.18), as well as chemical pollution ( β = 0.11, 95% CI = 0.02 to 0.19), homicide rates ( β = 0.10, 95% CI = 0.01 to 0.18), employment opportunities ( β = -0.16, 95% CI = -0.27 to -0.04), and green space ( β = -0.12, 95% CI = -0.20 to -0.04). Moreover, cardiometabolic risk indirectly mediated the associations of several of these community features and brain tissue volumes. Some associations were nonlinear, and none were explained by participants' individual-level socioeconomic characteristics., Conclusions: Features of communities other than conventional indicators of socioeconomic disadvantage may represent nonredundant correlates of cardiometabolic risk and brain tissue morphology in midlife., (Copyright © 2023 by the American Psychosomatic Society.)

Introduction: Inverted papillomas of the middle ear are extremely rare tumors that carry an increased risk of recurrence and malignant transformation. There are currently 59 cases of middle ear inverted papillomas reported in the literature. The objective in this study was to systematically evaluate outcomes regarding middle ear inverted papillomas with respect to demographics, anatomical tumor sites, malignant transformation status, recurrence rate and HPV status., Study Design: Retrospective case series and systematic review., Methods: A systematic review was completed on June 25, 2020 with a search strategy including PubMed, Embase, Scopus and Google Scholar. This revealed 181 articles. Full-text review was completed, and 66 articles were included. 115 articles were eliminated due to duplication of articles from databases, article titles not applicable to the aims of the systematic review and articles describing inverted papilloma of body sites other than middle ear., Discussion: Thirty-one cases of primary inverted papillomas of the middle ear were found in the literature with an additional 26 cases of secondary tumors. Four case reports did not specify primary versus secondary. The malignant transformation rate was 34.4% with a 53.6% recurrence rate. Treatment of middle ear inverted papillomas is primarily surgical with adjuvant radiation therapy considered for patients with recurrence or malignant transformation. Frequent clinical follow up of these patients is critical due to the increased rate of recurrence and malignant transformation., Conclusion: Inverted papillomas of the middle ear are rare tumors that carry a high risk of recurrence and malignant transformation necessitating complete resection and frequent clinical follow up., (© The Author(s) 2022.)

Objective: Frontal sinus osteomyelitis is a severe complication which can result from chronic rhinosinusitis, trauma, or as a complication of reconstruction or obliteration of the frontal sinus. The objective of the current study is to evaluate the contemporary management of frontal sinus osteomyelitis in light of recent advancements in endoscopic surgical techniques., Methods: Review of a prospectively collected database of patients with frontal sinus pathology was performed from 2008-2020. Data from individuals with frontal sinus osteomyelitis was collected including demographics, etiology, surgical technique, adjunctive medical treatments, complications, and clinical follow up., Results: Sixteen patients (average age 48.3, range 8-84) were included in the study. An open approach was utilized in 6 patients (2 osteoplastic flaps, 3 Reidel procedures, 1 cranialization). Seven patients underwent completely endoscopic approaches (3 Draf IIB, 4 Draf III), while 3 individuals had combined procedures (Lynch with Draf III, osteoplastic flap + Draf III, fistula excision + Draf IIb). All patients received 6 weeks of antibiotics. Average clinical follow up was 24.4 months with no patients requiring revision procedures., Conclusion: Endoscopic, endoscopic-assisted, and open approaches were utilized successfully in the current series of patients with osteomyelitis of the anterior table of the frontal sinus. While the progression of endoscopic techniques allows an additional surgical treatment option, it is important to select patients appropriately as open procedures continue to have an important role in the treatment algorithm.

Objective: Spontaneous cerebrospinal fluid (CSF) leaks represent a unique subset of skull base pathology and require distinctive management. Perioperative evaluation and management of intracranial hypertension are essential in preventing further erosion of the skull base and development of recurrent leak. The objective of this study is to evaluate the safety and utility of an expedited protocol for recording and managing intracranial hypertension following endoscopic repair of spontaneous CSF leaks., Methods: Prospectively collected data was reviewed in patients undergoing endoscopic repair of spontaneous CSF leaks between January 2017 and March 2020. A standard intracranial pressure monitoring protocol was compared to an expedited protocol (EP), and data regarding the two groups was compared for leak location, short-term success of skull base repair, complications, hospital length of stay, and cost-based analysis., Results: Fifty-five patients (standard protocol, n = 28 vs. EP, n = 27) were included in the study. Leak location was similar between cohorts, with the lateral recess being the most common locations in both groups (37.9% vs. 40.6%; P = .90). Postoperative complications (3.6% vs. 7.4%; P = .53) and ventriculoperitoneal shunt rate (32.1% vs. 22.2%; P = .41) were similar among cohorts. There was no difference in lumbar drain complications (0% vs. 7.4%; P = .14) or recurrent leak (7.1% vs. 0%; P = .16). Length of stay was shorter in the EP group [median(interquartile range): 3(1) vs. 2 (1); P < .01]. Total hospital charges were similar between groups (median (USD/$1,000): 83.57 ± 49.58 vs. 83.93 ± 46.11; P = .18)., Conclusion: An expedited monitoring protocol shortened hospital stay without increased risk of complications., Level of Evidence: III Laryngoscope, 131:E408-E412, 2021., (© 2020 The American Laryngological, Rhinological and Otological Society, Inc.)

Background: The relationship between gastrointestinal (GI) bacteria and the response to anti-CTLA-4 and anti-PD-1 immunotherapy in the treatment of cancer can potentially be enhanced to allow patients to maximally respond to these treatments. Insight into the complex interaction between gut microbiota and the human adaptive immune system will help guide future immunotherapeutic cancer treatments to allow a more robust clinical response and fewer adverse effects in patients requiring these drugs. This review highlights these interactions as well as the potential for the creation of "oncomicrobiotics" that would selectively tailor one's GI bacteria to maximally respond to anti-CTLA-4 and anti-PD-1 treatments will fewer adverse effects., Main Body: CTLA-4 is an antigen on the surface of T cells which, upon stimulation, leads to inhibition of activated T cells to terminate the immune response. However, many types of tumor cells can upregulate CTLA-4 in the tumor microenvironment, allowing these cells to evade targeting and destruction by the body's immune system by prematurely inhibiting T cells. Increased representation of Bacteroides fragilis , Burkholderia cepacia and the Faecalibacterium genus in the GI tract of patients receiving CTLA-4-based immunotherapy led to a stronger therapeutic effect while minimizing adverse side effects such as colitis. In addition, by introducing bacteria involved in vitamin B and polyamine transport to the GI tracts of patients treated with anti-CTLA-4 drugs led to increased resistance to colitis while maintaining therapeutic efficacy. PD-1 is another molecule upregulated in many tumor microenvironments which acts in a similar manner to CTLA-4 to tone down the anti-neoplastic actions of T cells. Antibodies to PD-1 have shown promise to help allow the body's natural immune response to appropriately target and destroy tumor cells. The presence of Bifidobacterium breve and longum , Akkermansia muciniphila and Faecalibacterium prausnitzii in the GI tracts of cancer patients has the potential to create a more robust immune response to anti-PD-1 drugs and prolonged survival. The development of "oncomicrobiotics" has the potential to help tailor one's gut microbiota to allow patients to maximally respond to immunotherapy without sacrificing increases in toxicity. These oncomicrobiotics may possibly include antibiotics, probiotics, postbiotics and/or prebiotics. However, many challenges lie ahead in the creation of oncomicrobiotics., Conclusion: The creation of oncomicrobiotics may allow many patients receiving anti-CTLA-4 and PD-1 immunotherapy to experience prolonged survival and a better quality of life., Competing Interests: Competing interestsThe authors declare they have no competing interests., (© The Author(s) 2020.)

Background: The COVID-19 pandemic has radically shifted healthcare operations within hospitals and universities across the globe. However, the effect of the COVID-19 pandemic on research endeavors and clinical trials is unclear., Objective: This study investigates the impact of the COVID-19 pandemic on basic science and clinical research within the rhinology community., Methods: A cross-sectional study was designed utilizing an 8-question survey to identify changes to rhinology research. Questions evaluated the impact of the COVID-19 pandemic on administrative research support and staffing, basic science research, clinical trials and resident research involvement., Results: Seventy-one participants responded to the survey (8.5% response rate). Most respondents noted changes in IACUC/IRB approval (faster, 33%; slower, 31%). Of those who employed laboratory personnel, 64% were able to continue staff employment with full salary. The majority of animal research and in vitro studies were halted (64% and 56%, respectively), but animal care and cell line maintenance were allowed to continue. Clinical trial enrollment was most commonly limited to COVID derived studies (51%). Forty-seven percent of respondents noted increased resident research participation., Conclusion: The rapid spread of the SARS-CoV-2 virus has markedly impacted rhinology-related research. Maintaining safe workplace practices as restrictions are lifted will hopefully mitigate the spread of the virus and allow research productivity to resume., Competing Interests: Declaration of competing interest The authors have no relevant conflicts of interest to disclose., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Objectives: Congenital encephaloceles provide unique diagnostic and reconstructive challenges for the pediatric rhinologist. The objectives of the current study were to evaluate contemporary treatment strategies for congenital encephaloceles focusing on presentation, surgical technique, and outcomes., Methods: Multi-institutional retrospective chart review of congenital encephaloceles (2003-2019). Data regarding demographics, presenting symptoms, associated abnormalities, surgical technique, size, location, and complications were collected., Results: Fourteen patients with 15 congenital encephaloceles were treated using endoscopic techniques (avg 6.0 years, range 2 months-22 years) with mean follow up of 23 months. The majority presented with nasal obstruction (n = 13); only one child had cerebrospinal fluid (CSF) rhinorrhea. Associated anomalies included nasal deformities, congenital hypopituitarism, and Morning Glory syndrome. Average encephalocele size was 2.44 cm (range 0.5-3.6 cm) with mean skull base defect size of 8.6 x 7.7 mm. Locations included the foramen cecum (n = 9), central sphenoid (n = 3), midline anterior cranial fossa (n = 1), orbital plate of frontal bone (n = 1), and ethmoid roof (n = 1). Because of favorable expansion from encephaloceles, it was unnecessary to postpone surgeries to allow nasal cavity growth. Three individuals had prior operations, including surgeries for "nasal polyp" or "adenoid cyst". Two patients had post-operative complications (meningitis and CSF leak) effectively treated with no further sequelae., Conclusions: In the current study, congenital encephaloceles in children as young as 2 months were successfully repaired using endoscopic techniques. Endoscopic approaches remain a safe and effective intervention for management of these lesions., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Glucocorticoids (GCs) are excellent anti-inflammatory drugs but are dose-limited by on-target toxicity. We sought to solve this problem by delivering GCs to immune cells with antibody-drug conjugates (ADCs) using antibodies containing site-specific incorporation of a non-natural amino acid, novel linker chemistry for in vitro and in vivo stability, and existing and novel glucocorticoid receptor (GR) agonists as payloads. We directed fluticasone propionate to human antigen-presenting immune cells to afford GR activation that was dependent on the targeted antigen. However, mechanism of action studies pointed to accumulation of free payload in the tissue culture supernatant as the dominant driver of activity and indeed administration of the ADC to human CD74 transgenic mice failed to activate GR target genes in splenic B cells. Suspecting dissipation of released payload, we designed an ADC bearing a novel GR agonist payload with reduced permeability which afforded cell-intrinsic activity in human B cells. Our work shows that antibody-targeting offers significant potential for rescuing existing and new dose-limited drugs outside the field of oncology.

Objectives: To examine the effect of the Tool to Reduce Inappropriate Medications (TRIM), a web tool linking an electronic health record (EHR) to a clinical decision support system, on medication communication and prescribing., Design: Randomized clinical trial., Setting: Primary care clinics at a Veterans Affairs Medical Center., Participants: Veterans aged 65 and older prescribed seven or more medications randomized to receipt of TRIM or usual care (N = 128)., Intervention: TRIM extracts information on medications and chronic conditions from the EHR and contains data entry screens for information obtained from brief chart review and telephonic patient assessment. These data serve as input for automated algorithms identifying medication reconciliation discrepancies, potentially inappropriate medications (PIMs), and potentially inappropriate regimens. Clinician feedback reports summarize discrepancies and provide recommendations for deprescribing. Patient feedback reports summarize discrepancies and self-reported medication problems., Measurements: Primary: subscales of the Patient Assessment of Care for Chronic Conditions (PACIC) related to shared decision-making; clinician and patient communication. Secondary: changes in medications., Results: 29.7% of TRIM participants and 15.6% of control participants provided the highest PACIC ratings; this difference was not significant. Adjusting for covariates and clustering of patients within clinicians, TRIM was associated with significantly more-active patient communication and facilitative clinician communication and with more medication-related communication among patients and clinicians. TRIM was significantly associated with correction of medication discrepancies but had no effect on number of medications or reduction in PIMs., Conclusion: TRIM improved communication about medications and accuracy of documentation. Although there was no association with prescribing, the small sample size provided limited power to examine medication-related outcomes., (© 2017, Copyright the Authors Journal compilation © 2017, The American Geriatrics Society.)

Background: The US Veterans Administration (VA) has developed a robust and mature computational infrastructure in support of its electronic health record (EHR). Web technology offers a powerful set of tools for structuring clinical decision support (CDS) around clinical care. This paper describes informatics challenges and design issues that were confronted in the process of building three Web-based CDS systems in the context of the VA EHR., Methods: Over the course of several years, we implemented three Web-based CDS systems that extract patient data from the VA EHR environment to provide patient-specific CDS. These were 1) the VACS (Veterans Aging Cohort Study) Index Calculator which estimates prognosis for HIV+ patients, 2) Neuropath/CDS which assists in the medical management of patients with neuropathic pain, and 3) TRIM (Tool to Reduce Inappropriate Medications) which identifies potentially inappropriate medications in older adults and provides recommendations for improving the medication regimen., Results: The paper provides an overview of the VA EHR environment and discusses specific informatics issues/challenges that arose in the context of each of the three Web-based CDS systems. We discuss specific informatics methods and provide details of approaches that may be useful within this setting., Conclusions: Informatics issues and challenges relating to data access and data availability arose because of the particular architecture of the national VA infrastructure and the need to link to that infrastructure from local Web-based CDS systems. Idiosyncrasies of VA patient data, especially the medication data, also posed challenges. Other issues related to specific functional needs of individual CDS systems. The goal of this paper is to describe these issues so that our experience may serve as a useful foundation to assist others who wish to build such systems in the future.

Neuron modeling may be said to have originated with the Hodgkin and Huxley action potential model in 1952 and Rall's models of integrative activity of dendrites in 1964. Over the ensuing decades, these approaches have led to a massive development of increasingly accurate and complex data-based models of neurons and neuronal circuits. ModelDB was founded in 1996 to support this new field and enhance the scientific credibility and utility of computational neuroscience models by providing a convenient venue for sharing them. It has grown to include over 1100 published models covering more than 130 research topics. It is actively curated and developed to help researchers discover and understand models of interest. ModelDB also provides mechanisms to assist running models both locally and remotely, and has a graphical tool that enables users to explore the anatomical and biophysical properties that are represented in a model. Each of its capabilities is undergoing continued refinement and improvement in response to user experience. Large research groups (Allen Brain Institute, EU Human Brain Project, etc.) are emerging that collect data across multiple scales and integrate that data into many complex models, presenting new challenges of scale. We end by predicting a future for neuroscience increasingly fueled by new technology and high performance computation, and increasingly in need of comprehensive user-friendly databases such as ModelDB to provide the means to integrate the data for deeper insights into brain function in health and disease., Competing Interests: The authors declare no competing financial interests.

Tissue regeneration requires not only the replacement of lost cells and tissues, but also the recreation of morphologies and patterns. Skin pigment pattern is a relatively simple system that can allow researchers to uncover the underlying mechanisms of pattern formation. To gain insight into how pigment patterns form, undergraduate students in the senior level course Developmental Biology designed an experiment that assayed pigment patterns in original and regenerated caudal fins of wild-type, striped, and mutant, spotted zebrafish. A majority of the WT fins regenerated with a similar striped pattern. In contrast, the pattern of spots even in the original fins of the mutants varied among individual fish. Similarly, the majority of the spots in the mutants did not regenerate with the same morphology, size, or spacing as the original fins. This was true even when only a small amount of fin was removed, leaving most of the fin to potentially reseed the pattern in the regenerating tissue. This suggests that the mechanism that creates the wild-type, striped pattern persists to recreate the pattern during regeneration. The mechanism that creates the spots in the mutants, however, must include an unknown element that introduces variability.

Study Objective: To create a clinical decision support system (CDSS) for evaluating problems with medications among older outpatients based on a broad set of criteria., Design: Web-based CDSS development., Setting: Primary care clinics at a Veterans Affairs medical center., Participants: Forty veterans 65 years and older who were prescribed seven or more medications that included those for treatment of diabetes mellitus and hypertension., Measurements and Main Results: The Tool to Reduce Inappropriate Medications (TRIM) uses a program to extract age, medications, and chronic conditions from the electronic health record to identify high-risk patients and as input for evaluating the medication regimen. Additional health variables obtained through chart review and direct patient assessment are entered into a Web-based program. Based on a series of algorithms, TRIM generates feedback reports for clinicians. TRIM identified medication reconciliation discrepancies in 98% (39/40) of veterans, potentially inappropriate medications in 58% (23/40), potential problems with feasibility (based on poor adherence and/or cognitive impairment) in 25% (10/40), potential overtreatment of hypertension in 50% (20/40), potential overtreatment of diabetes in 43% (17/40), inappropriate dosing of renally excreted medications in 5% (2/40), and patient-reported adverse reactions in 5% (2/40)., Conclusion: This evaluation of TRIM demonstrated that data elements can be extracted from the electronic health record to identify older primary care patients at risk for potentially problematic medication regimens. Supplemented with chart review and direct patient assessment, these data can be processed through clinical algorithms that identify potential problems and generate patient-specific feedback reports. Additional work is necessary to assess the effects of TRIM on medication deprescribing., (© 2016 Pharmacotherapy Publications, Inc.)

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results., (Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.)

A new class of high-performance n-type organic thermoelectric materials, self-doping perylene diimide derivatives with modified side chains, is reported. These materials achieve the highest n-type thermoelectric performance of solution-processed organic materials reported to date, with power factors as high as 1.4 μW/mK(2). These results demonstrate that molecular design is a promising strategy for enhancing organic thermoelectric performance., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Ecohydrodynamics investigates the hydrodynamic constraints on ecosystems across different temporal and spatial scales. Ecohydrodynamics play a pivotal role in the structure and functioning of marine ecosystems, however the lack of integrated complex flow models for deep-water ecosystems beyond the coastal zone prevents further synthesis in these settings. We present a hydrodynamic model for one of Earth's most biologically diverse deep-water ecosystems, cold-water coral reefs. The Mingulay Reef Complex (western Scotland) is an inshore seascape of cold-water coral reefs formed by the scleractinian coral Lophelia pertusa. We applied single-image edge detection and composite front maps using satellite remote sensing, to detect oceanographic fronts and peaks of chlorophyll a values that likely affect food supply to corals and other suspension-feeding fauna. We also present a high resolution 3D ocean model to incorporate salient aspects of the regional and local oceanography. Model validation using in situ current speed, direction and sea elevation data confirmed the model's realistic representation of spatial and temporal aspects of circulation at the reef complex including a tidally driven current regime, eddies, and downwelling phenomena. This novel combination of 3D hydrodynamic modelling and remote sensing in deep-water ecosystems improves our understanding of the temporal and spatial scales of ecological processes occurring in marine systems. The modelled information has been integrated into a 3D GIS, providing a user interface for visualization and interrogation of results that allows wider ecological application of the model and that can provide valuable input for marine biodiversity and conservation applications.

This paper describes how DISCO, the data aggregator that supports the Neuroscience Information Framework (NIF), has been extended to play a central role in automating the complex workflow required to support and coordinate the NIF's data integration capabilities. The NIF is an NIH Neuroscience Blueprint initiative designed to help researchers access the wealth of data related to the neurosciences available via the Internet. A central component is the NIF Federation, a searchable database that currently contains data from 231 data and information resources regularly harvested, updated, and warehoused in the DISCO system. In the past several years, DISCO has greatly extended its functionality and has evolved to play a central role in automating the complex, ongoing process of harvesting, validating, integrating, and displaying neuroscience data from a growing set of participating resources. This paper provides an overview of DISCO's current capabilities and discusses a number of the challenges and future directions related to the process of coordinating the integration of neuroscience data within the NIF Federation.

The thermoelectric properties of a highperformance electron-conducting polymer, (P(NDIOD-T2), extrinsically doped with dihydro-1H-benzoimidazol-2-yl (NDBI) derivatives, are reported. The highest thermoelectric power factor that has been reported for a solution-processed n-type polymer is achieved; and it is concluded that engineering polymerdopant miscibility is essential for the development of organic thermoelectrics., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Our ability to understand the pathogenesis of problems surrounding lipid accretion requires attention towards quantifying lipid kinetics. In addition, studies of metabolic flux should also help unravel mechanisms that lead to imbalances in inter-organ lipid trafficking which contribute to dyslipidemia and/or peripheral lipid accumulation (e.g. hepatic fat deposits). This review aims to outline the development and use of novel methods for studying lipid kinetics in vivo. Although our focus is directed towards some of the approaches that are currently reported in the literature, we include a discussion of the older literature in order to put "new" methods in better perspective and inform readers of valuable historical research. Presumably, future advances in understanding lipid dynamics will benefit from a careful consideration of the past efforts, where possible we have tried to identify seminal papers or those that provide clear data to emphasize essential points. This article is part of a Special Issue entitled: Modulation of Adipose Tissue in Health and Disease., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Prior research has unearthed a link between early education and care (EEC) experiences and worse behavioral functioning for children, yet the research has not clearly delineated whether this link is due to early entry into care (timing), extensive hours of care (extent), or use of center-based care (type). Using a nationally representative sample of children followed from infancy through kindergarten (N ≈ 6,000), we assessed links between EEC timing, extent, and type, and children's kindergarten functioning. Both center-based and full-time preschool predicted heightened behavior problems and more limited learning behaviors in kindergarten, with care type and extent functioning additively. EEC during infancy and toddlerhood showed limited independent links with children's later functioning, but it exacerbated negative associations between preschool and children's kindergarten behaviors.

We have previously reported on a liquid chromatography-mass spectrometry method to determine the disposition of [(13)C18]-oleic acid following intravenous and oral administration in vivo. This approach has enabled us to study a variety of aspects of lipid metabolism including a quantitative assessment of triglyceride synthesis. Here we present a more rigorous evaluation of the constraints imposed upon the analytical method in order to generate accurate data using this stable-isotope tracer approach along with more detail on relevant analytical figures of merit including limits of quantitation, precision, and accuracy. The use of mass isotopomer distribution analysis (MIDA) to quantify plasma triglyceride synthesis is specifically highlighted, and a re-evaluation of the underlying mathematics has enabled us to present a simplified series of equations. The derivation of this MIDA model and the significance of all underlying assumptions are explored in detail, and examples are given of how it can successfully be applied to detect differences in plasma triglyceride synthesis in lean and high-fat diet fed mouse models. More work is necessary to evaluate the applicability of this approach to triglyceride stores with slower rates of turnover such as in adipose or muscle tissue; however, the present report provides investigators with the tools necessary to conduct such studies.

We present here, the salient aspects of three databases: Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of ORs; OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory rectors; and OdorModelDB disseminates information related to computational models of olfactory receptors (ORs). The data stored among these databases is integrated. Presented in this chapter are descriptions of these resources, which are part of the SenseLab suite of databases, a discussion of the computational infrastructure that enhances the efficacy of information storage, retrieval, dissemination, and automated data population from external sources.

Isotopic tracers have been used to examine lipid trafficking for many years, and data from those studies have typically yielded novel insight regarding the pathophysiology of dyslipidemia. Previous experimental designs were suitable for studies in humans because relatively large volumes of plasma could be regularly sampled. We have expanded on the earlier logic by applying high-throughput analytical methods that require reduced sample volumes. Specifically, we have examined the possibility of coupling gel-based separations of lipoproteins (e.g., lipoprint) with LC-MS/MS analyses of complex lipid mixtures as a way to routinely measure the labeling profiles of distinct lipids in discrete lipoprotein subfractions. We demonstrate the ability to measure the incorporation of [U-(13)C]oleate into triglycerides (TG), PLs (PL), and cholesterol esters (CE) in VLDL, LDL, and HDL particles in mice. Although rodent models of dyslipidemia are inherently different from humans because of alterations in enzyme activities and underlying metabolism, rodent models can be used to screen novel compounds for efficacy in altering a given biochemical pathway and therein enable studies of target engagement in vivo. We expect that it is possible to translate our approach for application in other systems, including studies in humans.

We use molecular dynamics (MD) to simulate diffusion in molten aluminum-copper (AlCu) alloys. The self-diffusivities and Maxwell-Stefan diffusivities are calculated for AlCu mixtures using the Green-Kubo formulas at temperatures from 1000 to 4000 K and pressures from 0 to 25 GPa, along with additional points at higher temperatures and pressures. The diffusivities are corrected for finite-size effects. The Maxwell-Stefan diffusivity is compared to the diffusivity calculated from the self-diffusivities using a generalization of the Darken equation. We find that the effects of cross-correlation are small. Using the calculated self-diffusivities, we have assessed whether dilute hard-sphere and dilute Lennard-Jones models apply to the molten mixture. Neither of the two dilute gas diffusivities describes the diffusivity in molten Al and Cu. We report generalized analytic models for the self-diffusivities and interdiffusivity (mutual diffusivity) that fit the MD results well. The MD-derived transport coefficients are in good agreement with the available experimental data. We also report MD calculations of the viscosity and an analytic fit to those results. The ionic thermal conductivity is discussed briefly.

The liver is a crossroad for metabolism of lipid and carbohydrates, with acetyl-CoA serving as an important metabolic intermediate and a precursor for fatty acid and cholesterol biosynthesis pathways. A better understanding of the regulation of these pathways requires an experimental approach that provides both quantitative metabolic flux measurements and mechanistic insight. Under conditions of high carbohydrate availability, excess carbon is converted into free fatty acids and triglyceride for storage, but it is not clear how excessive carbohydrate availability affects cholesterol biosynthesis. To address this, C57BL/6J mice were fed either a low-fat, high-carbohydrate diet or a high-fat, carbohydrate-free diet. At the end of the dietary intervention, the two groups received (2)H(2)O to trace de novo fatty acid and cholesterol synthesis, and livers were collected for gene expression analysis. Expression of lipid and glucose metabolism genes was determined using a custom-designed pathway focused PCR-based gene expression array. The expression analysis showed downregulation of cholesterol biosynthesis genes and upregulation of fatty acid synthesis genes in mice receiving the high-carbohydrate diet compared with the carbohydrate-free diet. In support of these findings, (2)H(2)O tracer data showed that fatty acid synthesis was increased 10-fold and cholesterol synthesis was reduced by 1.6-fold in mice fed the respective diets. In conclusion, by applying gene expression analysis and tracer methodology, we show that fatty acid and cholesterol synthesis are differentially regulated when the carbohydrate intake in mice is altered.

Protein synthesis can be estimated by measuring the incorporation of a labeled amino acid into a proteolytic peptide. Although prelabeled amino acids are typically administered, recent studies have tested (2)H(2)O; the assumption is that there is rapid equilibration of (2)H (in body water) with the carbon-bound hydrogens of amino acids before those amino acids are incorporated into a protein(s). We have determined the temporal changes in (2)H labeling of body water and amino acids which should build confidence in (2)H(2)O-based studies of protein synthesis when one aims to measure the (2)H labeling of proteolytic peptides., (Copyright © 2011 Elsevier Inc. All rights reserved.)

An ultraperformance liquid chromatography method using normal-phase solvents, a silica column, and evaporative light-scattering detection is presented. The method is based on a quaternary gradient profile and is capable of resolving the major neutral and polar lipids present in plasma and animal tissue in under 5 min, with a total cycle time of 11 min. Limits of quantitation for 7 different lipid classes were on the order of 200 ng of material on column which enables an accurate analysis from as little as 20 μL of plasma or 50 mg of tissue for typical samples. Intraday and interday precision for the determination of the major lipid classes in human plasma ranged from 3.6 to 10.5% CV with a variability in retention time of less than 6%. The utility of the method is demonstrated through the separation and quantitation of lipids in mouse plasma, liver, and heart tissue., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The advantages of using (2)H(2)O to quantify cholesterol synthesis include i) homogeneous precursor labeling, ii) incorporation of (2)H via multiple pathways, and iii) the ability to perform long-term studies in free-living subjects. However, there are two concerns. First, the t(1/2) of tracer in body water presents a challenge when there is a need to acutely replicate measurements in the same subject. Second, assumptions are made regarding the number of hydrogens (n) that are incorporated during de novo synthesis. Our primary objective was to determine whether a step-based approach could be used to repeatedly study cholesterol synthesis a subject. We observed comparable changes in the (2)H-labeling of plasma water and total plasma cholesterol in African-Green monkeys that received five oral doses of (2)H(2)O, each dose separated by one week. Similar rates of cholesterol synthesis were estimated when comparing data in the group over the different weeks, but better reproducibility was observed when comparing replicate determinations of cholesterol synthesis in the same nonhuman primate during the respective dosing periods. Our secondary objective was to determine whether n depends on nutritional status in vivo; we observed n of ∼25 and ∼27 in mice fed a high-carbohydrate (HC) versus carbohydrate-free (CF) diet, respectively. We conclude that it is possible to acutely repeat studies of cholesterol synthesis using (2)H(2)O and that n is relatively constant.

A major impediment to understanding the biology of microorganisms inhabiting Antarctic environments is the logistical constraint of conducting field work primarily during the summer season. However, organisms that persist throughout the year encounter severe environmental changes between seasons. In an attempt to bridge this gap, we collected ice core samples from Pony Lake in early November 2004 when the lake was frozen solid to its base, providing an archive for the biological and chemical processes that occurred during winter freezeup. The ice contained bacteria and virus-like particles, while flagellated algae and ciliates over-wintered in the form of inactive cysts and spores. Both bacteria and algae were metabolically active in the ice core melt water. Bacterial production ranged from 1.8 to 37.9 μg CL(-1) day(-1). Upon encountering favorable growth conditions in the melt water, primary production ranged from 51 to 931 μg CL(-1) day(-1). Because of the strong H(2) S odor and the presence of closely related anaerobic organisms assigned to Pony Lake bacterial 16S rRNA gene clones, we hypothesize that the microbial assemblage was strongly affected by oxygen gradients, which ultimately restricted the majority of phylotypes to distinct strata within the ice column. This study provides evidence that the microbial community over-winters in the ice column of Pony Lake and returns to a highly active metabolic state when spring melt is initiated., (© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

The use of stable isotopically labeled substrates and analysis by mass spectrometry have provided substantial insight into rates of synthesis, disposition, and utilization of lipids in vivo. The information to be gained from such studies is of particular benefit to therapeutic research where the underlying causes of disease may be related to the production and utilization of lipids. When studying biology through the use of isotope tracers, care must be exercised in interpreting the data to ensure that any response observed can truly be interpreted as biological and not as an artifact of the experimental design or a dilutional effect on the isotope. We studied the effects of dosing route and tracer concentration on the mass isotopomer distribution profile as well as the action of selective inhibitors of microsomal tri-glyceride transfer protein (MTP) in mice and diacylglycerol acyltransferase 1 (DGAT1) in nonhuman primates, using a stable-isotopically labeled approach. Subjects were treated with inhibitor and subsequently given a dose of uniformly ¹³C-labeled oleic acid. Samples were analyzed using a rapid LC-MS technique, allowing the effects of the intervention on the assembly and disposition of triglycerides, cholesteryl esters, and phospholipids to be determined in a single 3 min run from just 10 μl of plasma.

We describe an assay and data evaluation technique for sorting a panel of murine monoclonal antibodies according to epitope specificities. The assay analyzes the simultaneous binding (pairing) of antibodies to an antigen and groups together antibodies with similar pairing profiles. Similar profiles indicate that the antibodies bind to the same or closely related epitopes. The assay works well with crude hybridoma supernatants and can be multiplexed. These features make the assay particularly suitable for the early phase of hybridoma/antibody screening when antibodies are available only as low volume culture harvest samples., (Copyright © 2011 Elsevier B.V. All rights reserved.)