Cognitive Information Processing

Contains reports on four research projects.Joint Services Electronics Programs (U. S. Army, U. S. Navy, and U. S. Air Force) under Contract DA 36-039-AMC-03200(E)National Science Foundation (Grant GK-835)National Institutes of Health (Grant 2 PO1 MH-04737-06)National Aeronautics and Space Administration (Grant NsG-496

Engaging stakeholders to inform national implementation of critical time intervention in a program serving homeless-experienced Veterans

The Veterans Affairs (VA) Grant and Per Diem Case Management “Aftercare” program provides 6 months of case management for homeless-experienced Veterans (HEVs) transitioning to permanent housing, with the aim of decreasing returns to homelessness. Implementing Critical Time Intervention (CTI)—an evidence-based case management practice—would standardize care across the 128 community-based agencies that provide Aftercare services. To prepare for national CTI implementation in Aftercare, guided by Replicating Effective Programs (REP), we conducted a four-site pilot in which we adapted a CTI implementation package (training, technical assistance, and external facilitation); characterized stakeholder perspectives regarding the acceptability and appropriateness of this package; and identified contextual factors that affected CTI implementation. We engaged a stakeholder workgroup to tailor existing CTI training and technical assistance materials for Aftercare. To provide tailored support for providers and leaders to adopt and incorporate evidence-based practices (EBPs) into routine care, we also developed external facilitation materials and processes. Over 9 months, we implemented this package at four sites. We conducted semi-structured interviews at pre-implementation, mid-implementation, and 6 months post-implementation, with HEVs (n = 37), case managers (n = 16), supervisors (n = 10), and VA leaders (n = 4); these data were integrated with templated reflection notes from the project facilitator. We used rapid qualitative analysis and targeted coding to assess the acceptability and appropriateness of CTI and our implementation package and identify factors influencing CTI implementation. Stakeholders generally found CTI acceptable and appropriate; there was consensus that components of CTI were useful and compatible for this setting. To adapt our implementation package for scale-up, this pilot highlighted the value of robust and tangible CTI training and technical assistance—grounded in real-world cases—that highlights the congruence of CTI with relevant performance metrics. Variations in agency-level contextual factors may necessitate more intense and tailored supports to implement and sustain complex EBPs like CTI. Processes used in this pilot are relevant for implementing other EBPs in organizations that serve vulnerable populations. EBP scale-up and sustainment can be enhanced by engaging stakeholders to tailor EBPs for specific contexts; pilot testing and refining implementation packages for scale-up; and using qualitative methods to characterize contextual factors that affect EBP implementation

Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections

Polyclonal infections occur when at least two unrelated strains of the same pathogen are detected in an individual. This has been linked to worse clinical outcomes in tuberculosis, as undetected strains with different antibiotic resistance profiles can lead to treatment failure. Here, we examine the amount of polyclonal infections in sputum and surgical resections from patients with tuberculosis in the country of Georgia. For this purpose, we sequence and analyse the genomes of Mycobacterium tuberculosis isolated from the samples, acquired through an observational clinical study (NCT02715271). Access to the lung enhanced the detection of multiple strains (40% of surgery cases) as opposed to just using a sputum sample (0-5% in the general population). We show that polyclonal infections often involve genetically distant strains and can be associated with reversion of the patient's drug susceptibility profile over time. In addition, we find different patterns of genetic diversity within lesions and across patients, including mutational signatures known to be associated with oxidative damage; this suggests that reactive oxygen species may be acting as a selective pressure in the granuloma environment. Our results support the idea that the magnitude of polyclonal infections in high-burden tuberculosis settings is underestimated when only testing sputum samples

Promoter prediction using physico-chemical properties of DNA

The ability to locate promoters within a section of DNA is known to be a very difficult and very important task in DNA analysis. We document an approach that incorporates the concept of DNA as a complex molecule using several models of its physico-chemical properties. A support vector machine is trained to recognise promoters by their distinctive physical and chemical properties. We demonstrate that by combining models, we can improve upon the classification accuracy obtained with a single model. We also show that by examining how the predictive accuracy of these properties varies over the promoter, we can reduce the number of attributes needed. Finally, we apply this method to a real-world problem. The results demonstrate that such an approach has significant merit in its own right. Furthermore, they suggest better results from a planned combined approach to promoter prediction using both physicochemical and sequence based techniques

АЛГОРИТМЫ ПОИСКА МУТАЦИЙ ЛЕКАРСТВЕННОЙ УСТОЙЧИВОСТИ В ГЕНОМАХ МИКОБАКТЕРИЙ ТУБЕРКУЛЕЗА

Analysis of whole-genome sequences often leads to problems of large dimensionality where the number of parameters exceeds the number of available observations. We offer methodology of genome-wide association study and investigate various approaches to assess contribution of mutations in the emergence and development of drug resistance in Mycobacterium tuberculosis. We present the results of our experiments aimed at identifying resistance mutations to the major anti- TB drugs based on data obtained from patients in Belarus.Предлагается методология полногеномного поиска ассоциаций на примере геномов возбудителей туберкулеза, а также исследуются различные алгоритмы и подходы к оценке вклада мутаций в возникновение и развитие лекарственной устойчивости. Приводятся результаты экспериментов по поиску мутаций лекарственной устойчивости к основным противотуберкулезным препаратам на основании данных о пациентах из Беларуси

Cerebral microcirculation and histological mapping after severe head injury: a contusion and acceleration experimental model

Background: Cerebral microcirculation after severe head injury is heterogeneous and temporally variable. Microcirculation is dependent upon the severity of injury, and it is unclear how histology relates to cerebral regional blood flow. Objective: This study assesses the changes of cerebral microcirculation blood flow over time after an experimental brain injury model in sheep and contrasts these findings with the histological analysis of the same regions with the aim of mapping cerebral flow and tissue changes after injury. Methods: Microcirculation was quantified using flow cytometry of color microspheres injected under intracardiac ultrasound to ensure systemic and homogeneous distribution. Histological analysis used amyloid precursor protein staining as a marker of axonal injury. A mapping of microcirculation and axonal staining was performed using adjacent layers of tissue from the same anatomical area, allowing flow and tissue data to be available from the same anatomical region. A mixed effect regression model assessed microcirculation during 4 h after injury, and those results were then contrasted to the amyloid staining qualitative score. results: Microcirculation values for each subject and tissue region over time, including baseline, ranged between 20 and 80 ml/100 g/min with means that did not differ statistically from baseline flows. However, microcirculation values for each subject and tissue region were reduced from baseline, although their confidence intervals crossing the horizontal ratio of 1 indicated that such reduction was not statistically significant. Histological analysis demonstrated the presence of moderate and severe score on the amyloid staining throughout both hemispheres. conclusion: Microcirculation at the ipsilateral and contralateral site of a contusion and the ipsilateral thalamus and medulla showed a consistent decline over time. Our data suggest that after severe head injury, microcirculation in predefined areas of the brain is reduced from baseline with amyloid staining in those areas reflecting the early establishment of axonal injuryJudith Bellapart, Kylie Cuthbertson, Kimble Dunster, Sara Diab, David G. Platts, Owen Christopher Raffel, Levon Gabrielian, Adrian Barnett, Jenifer Paratz, Rob Boots and John F. Frase

Mechanics of the IL2RA Gene Activation Revealed by Modeling and Atomic Force Microscopy

Transcription implies recruitment of RNA polymerase II and transcription factors (TFs) by DNA melting near transcription start site (TSS). Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites), located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studies, result in the progressive positioning of curvature apex towards the TSS, likely facilitating local DNA melting. In vitro assays confirm specific binding of the General Transcription Factors (GTFs) TBP and TFIIB over TATA-TSS position, where an inhibitory nucleosome prevented preinitiation complex (PIC) formation and uncontrolled DNA melting. These findings represent a substantial advance showing, first, that the structural properties of the IL2RA promoter are encoded in the DNA sequence and second, that during the initiation process DNA conformation is dynamic and not static

Neurogenic inflammation after traumatic brain injury and its potentiation of classical inflammation

Background: The neuroinflammatory response following traumatic brain injury (TBI) is known to be a key secondary injury factor that can drive ongoing neuronal injury. Despite this, treatments that have targeted aspects of the inflammatory pathway have not shown significant efficacy in clinical trials. Main body: We suggest that this may be because classical inflammation only represents part of the story, with activation of neurogenic inflammation potentially one of the key initiating inflammatory events following TBI. Indeed, evidence suggests that the transient receptor potential cation channels (TRP channels), TRPV1 and TRPA1, are polymodal receptors that are activated by a variety of stimuli associated with TBI, including mechanical shear stress, leading to the release of neuropeptides such as substance P (SP). SP augments many aspects of the classical inflammatory response via activation of microglia and astrocytes, degranulation of mast cells, and promoting leukocyte migration. Furthermore, SP may initiate the earliest changes seen in blood-brain barrier (BBB) permeability, namely the increased transcellular transport of plasma proteins via activation of caveolae. This is in line with reports that alterations in transcellular transport are seen first following TBI, prior to decreases in expression of tight-junction proteins such as claudin-5 and occludin. Indeed, the receptor for SP, the tachykinin NK1 receptor, is found in caveolae and its activation following TBI may allow influx of albumin and other plasma proteins which directly augment the inflammatory response by activating astrocytes and microglia. Conclusions: As such, the neurogenic inflammatory response can exacerbate classical inflammation via a positive feedback loop, with classical inflammatory mediators such as bradykinin and prostaglandins then further stimulating TRP receptors. Accordingly, complete inhibition of neuroinflammation following TBI may require the inhibition of both classical and neurogenic inflammatory pathways.Frances Corrigan, Kimberley A. Mander, Anna V. Leonard and Robert Vin

FASTPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis

This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a programme to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with GC or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyses sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and online version at http://primerdigital.com/tools/pcr.html.Peer reviewe