Neuronally expressed PDL1, not PD1, suppresses acute nociception

PDL1 is a protein that induces immunosuppression by binding to PD1 expressed on immune cells. In line with historical studies, we found that membrane-bound PD1 expression was largely restricted to immune cells; PD1 was not detectable at either the mRNA or protein level in peripheral neurons using single neuron qPCR, immunolabeling and flow cytometry. However, we observed widespread expression of PDL1 in both sensory and sympathetic neurons that could have important implications for patients receiving immunotherapies targeting this pathway that include unexpected autonomic and sensory related effects. While signaling pathways downstream of PD1 are well established, little to no information is available regarding the intracellular signaling downstream of membrane-bound PDL1 (also known as reverse signaling). Here, we administered soluble PD1 to engage neuronally expressed PDL1 and found that PD1 significantly reduced nocifensive behaviors evoked by algogenic capsaicin. We used calcium imaging to examine the underlying neural mechanism of this reduction and found that exogenous PD1 diminished TRPV1-dependent calcium transients in dissociated sensory neurons. Furthermore, we observed a reduction in membrane expression of TRPV1 following administration of PD1. Exogenous PD1 had no effect on pain-related behaviors in sensory neuron specific PDL1 knockout mice. These data indicate that neuronal PDL1 activation is sufficient to modulate sensitivity to noxious stimuli and as such, may be an important homeostatic mechanism for regulating acute nociception.

Clinical Trial Considerations in Developing Treatments for Early Stages of Common, Chronic Kidney Diseases: A Scientific Workshop Cosponsored by the National Kidney Foundation and the US Food and Drug Administration

In the past decade, advances in the validation of surrogate end points for chronic kidney disease (CKD) progression have heightened interest in evaluating therapies in early CKD. In December 2020, the National Kidney Foundation sponsored a scientific workshop in collaboration with the US Food and Drug Administration (FDA) to explore patient, provider, and payor perceptions of the value of treating early CKD. The workshop reviewed challenges for trials in early CKD, including trial designs, identification of high-risk populations, and cost-benefit and safety considerations. Over 90 people representing a range of stakeholders including experts in clinical trials, nephrology, cardiology and endocrinology, patient advocacy organizations, patients, payors, health economists, regulators and policy makers attended a virtual meeting. There was consensus among the attendees that there is value to preventing the development and treating the progression of early CKD in people who are at high risk for progression, and that surrogate end points should be used to establish efficacy. Attendees also concluded that cost analyses should be holistic and include aspects beyond direct savings for treatment of kidney failure; and that safety data should be collected outside/beyond the duration of a clinical trial. Successful drug development and implementation of effective therapies will require collaboration across sponsors, patients, patient advocacy organizations, medical community, regulators, and payors.

Test of robustness of pharyngeal neural networks in Caenorhabditis elegans

The nematode worm Caenorhabditis elegans is a model for deciphering the neural circuitry that transmits information from sensory organ to muscle tissue. It is also studied for disentangling the characteristics of the network, the efficiency of its design, and for testing theoretical models on how information is encoded. For this study, the efficiency of the synaptic connections was studied by testing the robustness of the neural network. A randomization test of robustness was applied to previously computed neural modules of the pharynx of C. elegans. The results support robustness as a reason for the observed over connectiveness across the pharyngeal system. In addition, rare events of single-neuron loss may expectedly lead to loss of function in a neural system.

Themes of advanced information processing in the primate brain

Here is a review of several empirical examples of information processing that occur in the primate cerebral cortex. These include visual processing, object identification and perception, information encoding, and memory. Also, there is a discussion of the higher scale neural organization, mainly theoretical, which suggests hypotheses on how the brain internally represents objects. Altogether they support the general attributes of the mechanisms of brain computation, such as efficiency, resiliency, data compression, and a modularization of neural function and their pathways. Moreover, the specific neural encoding schemes are expectedly stochastic, abstract and not easily decoded by theoretical or empirical approaches.

Chronic rhinitis in South Africa - more than just allergy!

Chronic rhinitis is a troublesome condition for sufferers. It is tempting to label all patients with chronic nasal symptoms as having allergic rhinitis (AR), but many such patients have other causes of chronic rhinitis that need a specific diagnosis and management strategy. Even when the patient fully fits the definition of AR, their condition will be best served by combining medication with ongoing patient education.

Single-cell q-PCR derived expression profiles of identified sensory neurons

Sensory neurons are chemically and functionally heterogeneous, and this heterogeneity has been examined extensively over the last several decades. These studies have employed a variety of different methodologies, including anatomical, electrophysiological, and molecular approaches. Recent studies using next-generation sequencing techniques have examined the transcriptome of single sensory neurons. Although these reports have provided a wealth of exciting new information on the heterogeneity of sensory neurons, correlation with functional types is lacking. Here, we employed retrograde tracing of cutaneous and muscle afferents to examine the variety of mRNA expression profiles of individual, target-specific sensory neurons. In addition, we used an ex vivo skin/nerve/dorsal root ganglion/spinal cord preparation to record and characterize the functional response properties of individual cutaneous sensory neurons that were then intracellularly labeled with fluorescent dyes, recovered from dissociated cultures, and analyzed for gene expression. We found that by using single-cell quantitative polymerase chain reaction techniques and a set of 28 genes, we can identify transcriptionally distinct groups. We have also used calcium imaging and single-cell quantitative polymerase chain reaction to determine the correlation between levels of mRNA expression and functional protein expression and how functional properties correlated with the different transcriptional groups. These studies show that although transcriptomics does map to functional types, within any one functional subgroup, there are highly variable patterns of gene expression. Thus, studies that rely on the expression pattern of one or a few genes as a stand in for physiological experiments, runs a high risk of data misinterpretation with respect to function.

Measurements of neuronal morphological variation across the rat neocortex

Neuron morphology is highly variable across the mammalian brain. It is thought that these attributes of neuronal cell shape, such as soma surface area and branching frequency, are determined by biological function and information processing. In this study, a large data set of neurons across the rat neocortex were clustered by their anatomical characters for evidence of distinctiveness among neocortical regions and the somatosensory layers. This data set of neuronal morphologies was compiled from 31 different lab sources with a validation procedure so that data records are potentially comparable across research studies. With this large set of heterogeneous data and by clustering analysis, this study shows that neuronal morphological traits overlap among neocortical and somatosensory regions. In the context of past neuroanatomical studies, this result is not congruent with tissue level analysis and strongly suggests further sampling of neuronal data to lessen the effect of confounding factors, such as the influence of different methodologies from use of heterogeneous samples of neuronal data.

Corrigendum to "Structural correlates of modular organization of activity propagation in the primate somatosensory cortex" [IBROR 6S (2019) S540]

[This corrects the article DOI: 10.1016/j.ibror.2019.07.1681.].

Neuronal Morphology and Synapse Count in the Nematode Worm

The somatic nervous system of the nematode worm Caenorhabditis elegans is a model for understanding the physical characteristics of the neurons and their interconnections. Its neurons show high variation in morphological attributes. This study investigates the relationship of neuronal morphology to the number of synapses per neuron. Morphology is also examined for any detectable association with neuron cell type or ganglion membership.

Abstract PD3-07: A phase II pre-surgical trial of lapatinib for the treatment of women with HER2 positive or EGFR positive ductal carcinoma in situ

Background: Estrogen receptor (ER)-negative tumors and human epidermal growth factor 2-Neu (HER2) positive breast cancers are known to be more clinically aggressive subtypes of breast cancer and account for 30% of all breast cancers. Women with HER2 + breast cancers, whether ER+ or ER -, require cytotoxic chemotherapy with a HER2-targeting agent, and often have adverse outcomes. Thus, preventive agents are needed to reduce the incidence of these subtypes of aggressive breast cancer. Lapatinib, a dual tyrosine kinase inhibitor, inhibits epidermal growth factor receptors (EGFR) and HER2 kinases and has shown to decrease breast cell proliferation in invasive breast cancer and adjacent premalignant lesions. Therefore, we conducted a multi-institutional randomized Phase II clinical trial to study the effects of the signal transduction inhibitor lapatinib in women with HER2-positive or EGFR-positive ductal carcinoma in situ (DCIS).

Methods: Randomized participants received either lapatinib (750mg, 1000mg, or 1500mg) or placebo daily for 2-6 weeks prior to their surgery. After minimal accrual, the trial was later amended to lapatinib 1000mg or placebo. Pre-treatment breast tissue was obtained from initial diagnostic core biopsy and post-treatment breast tissue was obtained from surgical excision specimen. Blood was obtained prior to surgery to assess serum lapatinib level. Participants kept a daily symptom assessment log and had a cardiac assessment at baseline and prior to surgery. Patients were instructed to take drug up to and including the day before surgery. The dual primary endpoint for this study was change in proliferation in pre- versus post-treatment biopsies between the two treatment arms, as measured by Ki67 as well as toxicity assessment. Secondary endpoints included incidence of DCIS at surgery and modulation of tissue biomarker expression in growth factor receptors (EGFR, ErbB2); phosphorylated growth factor receptor (phospho-ErbB2); signal transduction markers (MAPK, phospho-MAPK); hormone receptors (ER, PR); and p27.

Results:Twenty-two women (mean age: 51; range: 32-66) with HER2+ or EGFR+ DCIS were treated with lapatinib (1,000 or 1,500 mg) or placebo for 2–6 weeks prior to surgical excision. Ki67 expression was significantly decreased in the lapatinib treatment arms compared to placebo (p=0.0122). Diarrhea, fatigue, and skin reactions were notable adverse events that occurred predominately in the lapatinib arm compared to placebo. No grade 3 or 4 events related to the study drug were noted during the study. No changes were noted in cardiac function. DCIS was present in all surgical specimens in both arms. Invasive breast cancer was noted in 1 patient on lapatinib 1000mg and 3 patients on placebo. No statistically significant changes were noted in signal transduction biomarkers

Conclusion:These results demonstrate the effectiveness of lapatinib in reducing proliferation in women with EGFR+ or HER2+ DCIS. Even low-grade toxicities can deter use of an agent in the prevention setting. This and the lack of a risk model for HER2+ and triple negative breast cancer make the development of larger scale clinical prevention trials of lapatinib for the prevention a challenge.

Citation Format: Thomas PS, Contreras A, Pruthi S, Krontiras H, Rimawi M, Garber J, Wang T, Hilsenbeck SG, Vornik LA, Gilmer T, Friedman R, Heckman-Stoddard BM, Dunn B, Kuerer H, Brown PH. A phase II pre-surgical trial of lapatinib for the treatment of women with HER2 positive or EGFR positive ductal carcinoma in situ [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD3-07.

The Theory and Art of Child Psychotherapy: A Corrective Developmental Approach

The history of child psychotherapy is sketched from the psychoanalytic pioneers Anna Freud and Melanie Klein to the popular "nondirective" approach of Virginia Axline. The author's approach to child psychotherapy, based on contemporary psychoanalytic theories, allows the therapist to play any parental role that helps to repair developmental deficiencies and conflicts. These include nurturing, supporting, mirroring, role modeling, challenging, and limit setting. Following Winnicott, psychotherapy is conceived as a play space in which therapist and child are both spontaneous. The value of interpretation and insight in child therapy is discussed. There follows a more detailed discussion of three major problem areas in child psychotherapy: handling anger and hostile aggression; handling issues related to sexuality; and handling narcissistic issues of inferiority and shame.

Evolutionary diversification of the vertebrate transferrin multi-gene family

In a phylogenetic analysis of vertebrate transferrins (TFs), six major clades (subfamilies) were identified: (a) S, the mammalian serotransferrins; (b) ICA, the mammalian inhibitor of carbonic anhydrase (ICA) homologs; (c) L, the mammalian lactoferrins; (d) O, the ovotransferrins of birds and reptiles; (e) M, the melanotransferrins of bony fishes, amphibians, reptiles, birds, and mammals; and (f) M-like, a newly identified TF subfamily found in bony fishes, amphibians, reptiles, and birds. A phylogenetic tree based on the joint alignment of N-lobes and C-lobes supported the hypothesis that three separate events of internal duplication occurred in vertebrate TFs: (a) in the common ancestor of the M subfamily, (b) in the common ancestor of the M-like subfamily, and (c) in the common ancestor of other vertebrate TFs. The S, ICA, and L subfamilies were found only in placental mammals, and the phylogenetic analysis supported the hypothesis that these three subfamilies arose by gene duplication after the divergence of placental mammals from marsupials. The M-like subfamily was unusual in several respects, including the presence of a uniquely high proportion of clade-specific conserved residues, including distinctive but conserved residues in the sites homologous to those functioning in carbonate binding of human serotransferrin. The M-like family also showed an unusually high proportion of cationic residues in the positively charged region corresponding to human lactoferrampin, suggesting a distinctive role of this region in the M-like subfamily, perhaps in antimicrobial defense.

Isolation and characterisation of the fungus Spiromastix asexualis sp. nov. from discospondylitis in a German Shepherd dog, and review of Spiromastix with the proposal of the new order Spiromastixales (Ascomycota)

The genus Spiromastix consists of several fungal species that have been isolated from soil and animal dung in various parts of the world. However, these species are considered to be of low pathogenic potential, as no cases of infections caused by these fungi have been reported. Here, we describe the clinical course of discospondylitis in a dog from which a fungus was cultured from a biopsy and identified as a Spiromastix species by morphologic characteristics and sequencing. Phylogenetic analysis determined this to be a new species, Spiromastix asexualis, which is described, and a new order, Spiromastixales, is proposed.

Functional tradeoffs underpin salinity-driven divergence in microbial community composition

Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

A metagenomic framework for the study of airborne microbial communities

Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.

Psychometric properties of an automated telephone-based PHQ-9

OBJECTIVE

This study aims to evaluate the psychometric properties of an automated version of the Patient Health Questionnaire-9 (PHQ-9) to further facilitate its use in primary care. We automated the PHQ-9 using a computer telephony modality (interactive voice response system) called telephone-linked communication (TLC).

SUBJECTS AND METHODS

Eighty subjects were divided into four depression categories: none, mild, moderate, and severe. The automated questionnaire, TLC-PHQ-9, was administered to all subjects five times over a 3-month period, at intervals of 0 (T1), 1, 3, 4, and 4 (T5) weeks, respectively. The Inventory of Depressive Symptomatology (IDS) was administered (paper-and-pencil) at T1 and T5. We examined (1) reliability, (2) validity, (3) sensitivity and specificity, and (4) sensitivity to change.

RESULTS

(1) Test-retest reliability showed substantial agreement between T1 and T2, with a weighted kappa of 0.76 (95% confidence interval [CI] 0.67-0.85). Cronbach's coefficient alpha values ranged from 0.913 to 0.918 for each TLC-PHQ-9 assessment. (2) The weighted kappa of 0.78 (95% CI 0.70-0.87) for T1 and 0.73 (95% CI 0.63-0.83) for T5 showed strong agreement between TLC-PHQ-9 and IDS in all depression categories. (3) TLC-PHQ-9 demonstrated good sensitivity (82.4%) and very good specificity (90.7%) for moderate-plus depression and poorer sensitivity (54.2%) but very good specificity (97.8%) for severe-plus depression. (4) The weighted kappa of 0.53 (95% CI 0.35-0.70) indicated moderate agreement between TLC-PHQ-9 and IDS.

CONCLUSIONS

An automated telephony administration of the PHQ-9 appears to be a valid and reliable tool for monitoring depression symptoms and has strong fidelity across patients.

Biometric identification of cardiosynchronous waveforms utilizing person specific continuous and discrete wavelet transform features

In this paper we explore how a Radio Frequency Impedance Interrogation (RFII) signal may be used as a biometric feature. This could allow the identification of subjects in operational and potentially hostile environments. Features extracted from the continuous and discrete wavelet decompositions of the signal are investigated for biometric identification. In the former case, the most discriminative features in the wavelet space were extracted using a Fisher ratio metric. Comparisons in the wavelet space were done using the Euclidean distance measure. In the latter case, the signal was decomposed at various levels using different wavelet bases, in order to extract both low frequency and high frequency components. Comparisons at each decomposition level were performed using the same distance measure as before. The data set used consists of four subjects, each with a 15 minute RFII recording. The various data samples for our experiments, corresponding to a single heart beat duration, were extracted from these recordings. We achieve identification rates of up to 99% using the CWT approach and rates of up to 100% using the DWT approach. While the small size of the dataset limits the interpretation of these results, further work with larger datasets is expected to develop better algorithms for subject identification.

Educating translational researchers in research informatics principles and methods: an evaluation of a model online course and plans for its dissemination

Translational research generates and/or uses very large amounts of diverse data. Informatics principles and methods address datasets that are large and complex, whereas few translational researchers know these principles and methods and many cannot design, carry out, or analyze the results of these studies optimally. With few exceptions, informatics education has not been directed to researchers, especially established researchers. To fill this gap, we carried out a formal needs assessment of research informatics education of translational researchers, focusing on established researchers. Using the results, we developed a model curriculum for educating researchers in research informatics and a first generation model online course in research informatics for researchers. We are completing a formal evaluation of this online course with a diverse group of translational researchers. From the results of this evaluation, we will create a second version of the online course, a dissemination plan to make it available to researchers nationally, and a plan to enhance the course over time. We will discuss the implications for the future of translational research and research informatics.

Phylogenetic analysis of genome rearrangements among five mammalian orders

Evolutionary relationships among placental mammalian orders have been controversial. Whole genome sequencing and new computational methods offer opportunities to resolve the relationships among 10 genomes belonging to the mammalian orders Primates, Rodentia, Carnivora, Perissodactyla and Artiodactyla. By application of the double cut and join distance metric, where gene order is the phylogenetic character, we computed genomic distances among the sampled mammalian genomes. With a marsupial outgroup, the gene order tree supported a topology in which Rodentia fell outside the cluster of Primates, Carnivora, Perissodactyla, and Artiodactyla. Results of breakpoint reuse rate and synteny block length analyses were consistent with the prediction of random breakage model, which provided a diagnostic test to support use of gene order as an appropriate phylogenetic character in this study. We discussed the influence of rate differences among lineages and other factors that may contribute to different resolutions of mammalian ordinal relationships by different methods of phylogenetic reconstruction.

Transcriptional switching model for the regulation of tumorigenesis and metastasis by the ha-ras oncogene - transcriptional changes in the ha-ras tumor-suppressor gene lysyl oxidase

A model system is described that allows an analysis of the molecular and biochemical changes associated with expression and suppression of the oncogenic and metastatic phenotype of cloned rat embryo fibroblast (CREF) cells. Ha-ras-transformed CREF cells are morphologically transformed, anchorage-independent and both tumorigenic and metastatic in athymic nude mice and syngeneic Fischer rats. Co-expression of the Ha-ras oncogene and Krev-1 tumor suppressor gene in CREF cells results in suppression of in vitro transformation. In contrast, Ha-ras/Krev-1 transformed CREF cells retain, with greatly extended latency periods, both tumorigenic and metastatic capabilities in athymic nude mice. The present study investigates changes in the Ha-ms suppressor gene, rrg (lysyl oxidase), during expression and suppression of the oncogenic phenotype in CREF cells. Nontumorigenic CREF cells and CREF cells transformed by the Ha-ras and Krev-1 gene that express a suppression in in vitro transformation contain elevated levels of lysyl oxidase mRNA and protein. In contrast, Ha-ms and Ha-ras/Krev-1 nude mouse tumor- and nude mouse lung metastasis-derived CREF cells contain reduced levels of lysyl oxidase mRNA and protein. Nuclear run-on assays indicate that suppression of lysyl oxidase expression in transformed subclones of CREF cells correlates with a reduction in transcription of the lysyl oxidase gene. Taken together, the current studies support a transcriptional switching model in which lysyl oxidase expression correlates directly with suppression of the Ka-ms-induced transformation phenotype and escape from oncogenic suppression correlates with a transcriptional silencing of the lysyl oxidase gene and decreased lysyl oxidase mRNA and protein.

Codon usage methods for horizontal gene transfer detection generate an abundance of false positive and false negative results

Bacteria acquire new DNA in a process known as horizontal gene transfer (HGT). To investigate the evolutionary impact of this transfer of DNA, various methods have been developed to detect past HGT events. For example, codon usage-based methods detect the presence of transferred genes by identifying atypical patterns of codon usage. However, some inherited genes exhibit atypical codon usage and some transferred genes have codon usage patterns similar to those of the inherited genes. In this study, we used a comparative phylogenetic approach with Methylobacterium and Caulobacter species to demonstrate that even well-designed codon usage methods fail to detect many HGT events and generate a high rate of false positives (60-75 %) and false negatives (23-61 %). Therefore, we recommend caution when employing codon usage methods to identify transferred genes and suggest that the rapidly increasing availability of bacterial genome sequences makes the phylogenetic approach the method of choice.

Randomised controlled trial of an automated, interactive telephone intervention (TLC Diabetes) to improve type 2 diabetes management: baseline findings and six-month outcomes

Background

Effective self-management of diabetes is essential for the reduction of diabetes-related complications, as global rates of diabetes escalate.

Methods

Randomised controlled trial. Adults with type 2 diabetes (n = 120), with HbA_1c greater than or equal to 7.5 %, were randomly allocated (4 × 4 block randomised block design) to receive an automated, interactive telephone-delivered management intervention or usual routine care. Baseline sociodemographic, behavioural and medical history data were collected by self-administered questionnaires and biological data were obtained during hospital appointments. Health-related quality of life (HRQL) was measured using the SF-36.

Results

The mean age of participants was 57.4 (SD 8.3), 63% of whom were male. There were no differences in demographic, socioeconomic and behavioural variables between the study arms at baseline. Over the six-month period from baseline, participants receiving the Australian TLC (Telephone-Linked Care) Diabetes program showed a 0.8% decrease in geometric mean HbA_1c from 8.7% to 7.9%, compared with a 0.2% HbA_1c reduction (8.9% to 8.7%) in the usual care arm (p = 0.002). There was also a significant improvement in mental HRQL, with a mean increase of 1.9 in the intervention arm, while the usual care arm decreased by 0.8 (p = 0.007). No significant improvements in physical HRQL were observed.

Conclusions

These analyses indicate the efficacy of the Australian TLC Diabetes program with clinically significant post-intervention improvements in both glycaemic control and mental HRQL. These observed improvements, if supported and maintained by an ongoing program such as this, could significantly reduce diabetes-related complications in the longer term. Given the accessibility and feasibility of this kind of program, it has strong potential for providing effective, ongoing support to many individuals with diabetes in the future.

Preliminary feasibility analysis of remote subject identification during hemodynamic monitoring by Radio Frequency Impedance

Non-contact, non-invasive monitoring of hemodynamic parameters would be ideal for medical monitoring in a variety of environments. Radio Frequency Impedance Interrogation (RFII) measures hemodynamic function via resonance frequency coupling to a hydrophilic protein molecule. While the application of this technology to hemodynamic monitoring has demonstrated initial success, this preliminary study examined the use of RFII for subject identification by waveform signal analysis, which would allow confirmation of the identity of a subject in an operational setting prior to rescue efforts. Preliminary results demonstrate an excellent recognition rate using the RFII signature and pattern classification. Each individual has a consistent pattern during the initial waveform identification period that is visually distinct from the other individuals in the data set. These results suggest that RFII may be of great utility in the pre-hospital triage setting for patient monitoring and for the rapid identification of subjects in the operational setting.

Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes

Factors affecting the reliability of Roche/454 pyrosequencing for analyzing sequence polymorphism in within-host viral populations were assessed by two experiments: 1) sequencing four clonal simian immunodeficiency virus (SIV) stocks and 2) sequencing mixtures in different proportions of two SIV strains with known fixed nucleotide differences. Observed nucleotide diversity and frequency of undetermined nucleotides were increased at sites in homopolymer runs of four or more identical nucleotides, particularly at AT sites. However, in the mixed-strain experiments, the effects on estimated nucleotide diversity of such errors were small in comparison to known strain differences. The results suggest that biologically meaningful variants present at a frequency of around 10% and possibly much lower are easily distinguished from artifacts of the sequencing process. Analysis of the clonal stocks revealed numerous rare variants that showed the signature of purifying selection and that elimination of variants at frequencies of less than 1% reduced estimates of nucleotide diversity by about an order of magnitude. Thus, using a 1% frequency cutoff for accepting a variant as real represents a conservative standard, which may be useful in studies that are focused on the discovery of specific mutations (such as those conferring immune escape or drug resistance). On the other hand, if the goal is to estimate nucleotide diversity, an optimal strategy might be to include all observed variants (even those at less than 1% frequency), while masking out homopolymer runs of four or more nucleotides.

Classification of cardiosynchronous waveforms by projection to a Legendre Polynomial sub-space

The use of Radio Frequency Impedance Interrogation (RFII) is being investigated for use as a noninvasive hemodynamic monitoring system and in the capacity of a biometric identifier. Biometric identification of subjects by cardiosynchronous waveform generated through RFII technology could allow the identification of subjects in operational and potentially hostile environments. Here, the filtering methods for extracting a unique biometric signature from the RFII signal are examined, including the use of Cepstral analysis for dynamically estimating the filter parameters.

METHODS

The projection of that signature to a Legendre Polynomial sub-space is proposed for increased class separability in a low dimensional space. Support Vector Machine (SVM) and k-Nearest Neighbor (k=3) classification are performed in the Legendre Polynomial sub-space on a small dataset.

RESULTS

Both the k-Nearest Neighbor and linear SVM methods demonstrated highly successful classification accuracy, with 93-100% accuracy demonstrated by various classification methods.

CONCLUSIONS

The results are highly encouraging despite the small sample size. Further analysis with a larger dataset will help to refine this process for the eventual application of RFII as a robust biometric identifier.

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.

Distinctive amino acid composition profiles in salivary proteins of the tick Ixodes scapularis

Bioinformatic analysis of the amino acid composition of proteins of the tick Ixodes scapularis showed that, in comparison to other secreted proteins, salivary proteins in general have higher frequencies of polar residues and lower frequencies of the non-polar residues leucine and valine. Computer prediction of linear B-cell epitopes showed that polar residues were associated with the presence of high-quality epitopes and that tick salivary proteins included significantly more proteins with predicted high-quality epitopes than did other secreted proteins. The results provided no evidence that salivary proteins as a whole have evolved characteristics minimizing their antigenicity to the vertebrate host. Certain salivary proteins may indeed have evolved low antigenicity, but the I. scapularis sialome include at least some apparently antigenic proteins that might be tested experimentally to determine whether they would be suitable candidates for anti-tick vaccines.

Overlooked and underserved: "action signs" for identifying children with unmet mental health needs

OBJECTIVE

The US Surgeon General has called for new approaches to close the mental health services gap for the large proportion of US children with significant mental health needs who have not received evaluation or services within the previous 6 to 12 months. In response, investigators sought to develop brief, easily understood, scientifically derived "warning signs" to help parents, teachers, and the lay public to more easily recognize children with unmet mental health needs and bring these children to health care providers' attention for evaluation and possible services.

METHOD

Analyses of epidemiologic data sets from >6000 children and parents were conducted to (1) determine the frequency of common but severely impairing symptom profiles, (2) examine symptom profile frequencies according to age and gender, (3) evaluate positive predictive values of symptom profiles relative to Diagnostic and Statistical Manual of Mental Disorders diagnoses, and (4) examine whether children with 1 or more symptom profiles receive mental health services.

RESULTS

Symptom-profile frequencies ranged from 0.5% to 2.0%, and 8% of the children had 1 or more symptom profile. Profiles generated moderate-to-high positive predictive values (52.7%-75.4%) for impairing psychiatric diagnoses, but fewer than 25% of children with 1 or more profiles had received services in the previous 6 months.

CONCLUSIONS

Scientifically robust symptom profiles that reflect severe but largely untreated mental health problems were identified. Used as "action signs," these profiles might help increase public awareness about children's mental health needs, facilitate communication and referral for specific children in need of evaluation, and narrow the child mental health services gap.

Genomic organization of the glutathione S-transferase family in insects

Cytosolic glutathione S-transferases (GSTs) are a large and diverse gene family in insects. They are classified into six major subclasses. Sigma, Omega, Zeta, and Theta have representatives across Metazoa while Delta and Epsilon are specific to Insecta and Holometabola, respectively. In this study, GSTs are assigned to a subclass by a combination of literature, phylogenetic, and genomic evidence. Moreover, it is confirmed that GSTs frequently cluster by genomic position as a result of recent gene expansions. These expansions are largely explained by the number of protein-coding genes in the genome, although life history is another contributing factor.

Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus

Several isolates of the marine cyanobacterial genus Prochlorococcus have smaller genome sizes than those of the closely related genus Synechococcus. In order to test whether loss of protein-coding genes has contributed to genome size reduction in Prochlorococcus, we reconstructed events of gene family evolution over a strongly supported phylogeny of 12 Prochlorococcus genomes and 9 Synechococcus genomes. Significantly, more events both of loss of paralogs within gene families and of loss of entire gene families occurred in Prochlorococcus than in Synechococcus. The number of nonancestral gene families in genomes of both genera was positively correlated with the extent of genomic islands (GIs), consistent with the hypothesis that horizontal gene transfer (HGT) is associated with GIs. However, even when only isolates with comparable extents of GIs were compared, significantly more events of gene family loss and of paralog loss were seen in Prochlorococcus than in Synechococcus, implying that HGT is not the primary reason for the genome size difference between the two genera.

Imaging optically induced neural activity in the brain

Infrared neural stimulation (INS) is well characterized for the peripheral nervous system; however, translation to the central nervous system (CNS) presents a new set of challenges which require us to consider different anatomy, multiple cell types, and the physiology associated with structures in the CNS. This study presents our first attempt to translate INS to in vivo stimulation of the CNS and to image the related response. The results from this study show that INS generates intrinsic optical signals of similar magnitude and shape associated with well characterized mechanical stimuli. The implications of this work could lead to neural implants which allows for single cell stimulation making it possible to design closed loop neural prosthetics.

Ongoing purifying selection on intergenic spacers in group A streptococcus

Bacterial intergenic spacers are non-coding genomic regions enriched with cis-regulatory elements for gene expression. A population genetics approach was used to investigate the evolutionary force shaping the genetic diversity of intergenic spacers among 13 genomes of group A streptococcus (GAS). Analysis of 590 genes and their linked 5' intergenic spacers showed reduced nucleotide diversity in spacers compared to synonymous nucleotide diversity in protein-coding regions, suggestive of past purifying selection on spacers. Certain spacers showed elevated nucleotide diversity indicative of past homologous recombination with divergent genotypes. In addition, analysis of the difference between mean nucleotide difference and number of segregating sites showed evidence of an excess of rare variants both at nonsynonymous sites in genes and at sites in spacers, which is evidence that there are numerous slightly deleterious variants in GAS populations with potential effects on both protein sequences and gene expression.

A survey of schistosome protein domain types: insights into unique biological properties

Using the PROSITE database and search tools, we conducted a comprehensive bioinformatic analysis of the predicted protein sequences of the flatworm parasites Schistosoma mansoni and Schistosoma japonicum and seven other animal genomes in order to identify novel schistosome-specific features. Our analyses revealed a relative paucity of proline-rich domains in schistosomes in comparison with their human host and a corresponding enrichment in schistosomes of asparagine-rich, serine-rich, and threonine-rich domains. Domain types found in both schistosome species but not in human included the two-component system sensor histidine kinase/response regulator; C83 family peptidase; DyP-type peroxidase; and densovirus NS1-type domain. Unique features of the schistosome proteome may help guide development of new drugs, while the presence of a densovirus-derived protein in S. mansoni suggests that this species may be infected by a virus of this group, which might be useful as a biological control agent.

PolyAna: analyzing synonymous and nonsynonymous polymorphic sites

PolyAna (available at http://www.biol.sc.edu/~austin/) aids in the analysis of natural selection on protein-coding sequences by estimating sample gene diversity at individual polymorphic nucleotide sites, which are classified as synonymous, non-synonymous, or ambiguous.

The evolution of melanoma diagnosis: 25 years beyond the ABCDs

Early detection of malignant melanoma remains the key factor in lowering mortality from this cancer. Recognizing the importance of this issue 25 years ago, our group at New York University published in CA: A Cancer Journal for Clinicians the mnemonic "ABCD" to facilitate the early diagnosis of melanoma. Studies have demonstrated the usefulness of this paradigm in enhancing early melanoma diagnosis as a part of clinical examinations, mass screenings, and public education programs. Approaches to melanoma diagnosis have dynamically evolved during the ensuing quarter century. In the 1990s, dermoscopy enabled the recognition of new subsurface features to differentiate between malignant and benign pigmented lesions. During the last decade, new computer-based technologies have improved diagnostic sensitivity and specificity and may result in optimizing lesion selection for biopsy and pathology review. Despite all of the advances in melanoma diagnosis, timely recognition, detection, and rapid treatment of melanoma remain critical. Although pathologic examination remains the gold standard for diagnosis, this cancer has the potential to be diagnosed through noninvasive approaches because of its cutaneous location. From the development of the ABCDs through current attempts that use complex computer algorithms and genetic markers, a clinician's ability to detect melanoma in its earliest form has been augmented. However, a "good clinical eye" is still fundamental to selecting the lesions for evaluation among the sea of those that are prevalent. As current approaches are refined and new techniques are developed, the improved ability to diagnose this cancer will hopefully enhance reaching the goal of reducing melanoma mortality.