"The devil's in the detail": Release of an expanded, enhanced and dynamically revised forensic STR Sequence Guide.

The STR sequence template file published in 2016 as part of the considerations from the DNA Commission of the International Society for Forensic Genetics on minimal STR sequence nomenclature requirements, has been comprehensively revised and audited using the latest GRCh38 genome assembly. The list of forensic STRs characterized was expanded by including supplementary autosomal, X- and Y-chromosome microsatellites in less common use for routine DNA profiling, but some likely to be adopted in future massively parallel sequencing (MPS) STR panels. We outline several aspects of sequence alignment and annotation that required care and attention to detail when comparing sequences to GRCh37 and GRCh38 assemblies, as well as the necessary matching of MPS-based allele descriptions to previously established repeat region structures described in initial sequencing studies of the less well known forensic STRs. The revised sequence guide is now available in a dynamically updated FTP format from the STRidER website with a date-stamped change log to allow users to explore their own MPS data with the most up-to-date forensic STR sequence information compiled in a simple guide.

Variability in neuronal activity in primate cortex during working memory tasks.

Persistent elevated neuronal activity has been identified as the neuronal correlate of working memory. It is generally assumed in the literature and in computational and theoretical models of working memory that memory-cell activity is stable and replicable; however, this assumption may be an artifact of the averaging of data collected across trials, and needs experimental verification. In this study, we introduce a classification scheme to characterize the firing frequency trends of cells recorded from the cortex of monkeys during performance of working memory tasks. We examine the frequency statistics and variability of firing during baseline and memory periods. We also study the behavior of cells on individual trials and across trials, and explore the stability of cellular firing during the memory period. We find that cells from different firing-trend classes possess markedly different statistics. We also find that individual cells show substantial variability in their firing behavior across trials, and that firing frequency also varies markedly over the course of a single trial. Finally, the average frequency distribution is wider, the magnitude of the frequency increases from baseline to memory smaller, and the magnitude of frequency decreases larger than is generally assumed. These results may serve as a guide in the evaluation of current theories of the cortical mechanisms of working memory.

Patterned firing of parietal cells in a haptic working memory task.

Abstract Cells in the somatosensory cortex of the monkey are known to exhibit sustained elevations of firing frequency during the short-term mnemonic retention of tactile information in a haptic delay task. In this study, we examine the possibility that those firing elevations are accompanied by changes in firing pattern. Patterns are identified by the application of a pattern-searching algorithm to the interspike intervals of spike trains. By sequential use of sets of pattern templates with a range of temporal resolutions, we find patterned activity in the majority of the cells investigated. In general, the degree of patterning significantly increases during active memory. Surrogate analysis suggests that the observed patterns may not be simple linear stochastic functions of instantaneous or average firing frequency. Therefore, during the active retention of a memorandum, the activity of a 'memory cell' may be characterized not only by changes in frequency but also by changes in pattern.

FMRI study relevant to the Mozart effect: brain areas involved in spatial-temporal reasoning.

Behavioral studies, motivated by columnar cortical model predictions, have given evidence for music causally enhancing spatial-temporal reasoning. A wide range of behavioral experiments showed that listening to a Mozart Sonata (K.448) gave subsequent enhancements. An EEG coherence study gave evidence for a carryover from that Mozart Sonata listening condition to the subsequent spatial-temporal task in specific cortical regions. Here we present fMRI studies comparing cortical blood flow activation by the Mozart Sonata vs. other music. In addition to expected temporal cortex activation, we report dramatic statistically significant differences in activation by the Mozart Sonata (in comparison to Beethoven's Fur Elise and 1930s piano music) in dorsolateral pre-frontal cortex, occipital cortex and cerebellum, all expected to be important for spatial-temporal reasoning. It would be of great interest to explicitly test this expectation. We propose an fMRI study comparing (subject by subject) brain areas activated in music listening conditions and in spatial-temporal tasks.

Reliable short-term memory in the trion model: toward a cortical language and grammar.

It has previously been shown that Hebb learning in a single column in the trion model of cortical organization occurs by selection. Motivated by von Neumann's solution for obtaining reliability and by models of circulating cortical activity, we introduce Hebb intercolumnar couplings to achieve dramatic enhancements in reliability in the firing of connected columns. In order for these enhancements to occur, specific temporal phase differences must exist between the same inherent spatial-temporal memory patterns in connected columns. We then generalize the criteria of large enhancements in the global firing of the entire connected columnar network to investigate the case when different inherent memory patterns are in the columns. The spatial rotations as well as the temporal phases now are crucial. Only certain combinations of inherent memory patterns meet these criteria with the symmetry properties playing a major role. The columnar order of these memory patterns not in the same symmetry family can be extremely important. This yields the first higher-level architecture of a cortical language and grammar within the trion model. The implications of this result with regard to an innate human language and grammar are discussed.

Generation of retroviral packaging and producer cell lines for large-scale vector production and clinical application: improved safety and high titer.

For many applications, human clinical therapies using retroviral vectors still require many technological improvements in key areas of vector design and production. These improvements include higher unprocessed manufacturing titers, complement-resistant vectors, and minimized potential to generate replication-competent retrovirus (RCR). To address these issues, we have developed a panel of human packaging cell lines (PCLs) with reduced homology between retroviral vector and packaging components. These reduced-homology PCLs allowed for the use of a novel high multiplicity of transduction ("high m.o. t.") method to introduce multiple copies of provector within vector-producing cell lines (VPCLs), resulting in high-titer vector without the generation of RCR. In a distinct approach to increase vector yields, we integrated manufacturing parameters into screening strategies and clone selection for large-scale vector production. Collectively, these improvements have resulted in the development of diverse VPCLs with unprocessed titers exceeding 2 x 10(7) CFU/ml. Using this technology, human Factor VIII VPCLs yielding titers as high as 2 x 10(8) CFU/ml unprocessed supernatant were generated. These cell lines produce complement-resistant vector particles (N. J. DePolo et al., J. Virol. 73: 6708-6714, 1999) and provide the basis for an ongoing Factor VIII gene therapy clinical trial.

A review of the concept of the heart rate deflection point.

The heart rate deflection point (HRDP) is a downward or upward change from the linear HR-work relationship evinced during progressive incremental exercise testing. The HRDP is reported to be coincident with the anaerobic threshold. In 1982, Conconi and colleagues suggested that this phenomenon could be used as a noninvasive method to assess the anaerobic threshold. These researchers developed a field test to assess the HRDP, which has become popularised as the 'Conconi test'. Concepts used to define and assess the anaerobic threshold as well as methodological procedures used to determine the HRDP are diverse in the literature and have contributed to controversy surrounding the HRDP concept. Although the HRDP may be assessed in either field or laboratory settings, the degree of HR deflection is highly dependent upon the type of protocol used. The validity of HRDP to assess the anaerobic threshold is uncertain, although a high degree of relationship exists between HRDP and the second lactate turnpoint. The HRDP appears to be reliable when a positive identification is made; however, not all studies report 100% reproducibility. Although the physiological mechanisms explaining the HRDP are unresolved, a relationship exists between the degree and direction of HRDP and left ventricular function. The HRDP has potential to be used for training regulation purposes. Clinically, it may be incorporated to set exercise intensity parameters for cardiac rehabilitation.

Cross-modal and cross-temporal association in neurons of frontal cortex.

The prefrontal cortex is essential for the temporal integration of sensory information in behavioural and linguistic sequences. Such information is commonly encoded in more than one sense modality, notably sight and sound. Connections from sensory cortices to the prefrontal cortex support its integrative function. Here we present the first evidence that prefrontal cortex cells associate visual and auditory stimuli across time. We gave monkeys the task of remembering a tone of a certain pitch for 10 s and then choosing the colour associated with it. In this task, prefrontal cortex cells responded selectively to tones, and most of them also responded to colours according to the task rule. Thus, their reaction to a tone was correlated with their subsequent reaction to the associated colour. This correlation faltered in trials ending in behavioural error. We conclude that prefrontal cortex neurons are part of integrative networks that represent behaviourally meaningful cross-modal associations. The orderly and timely activation of neurons in such networks is crucial for the temporal transfer of information in the structuring of behaviour, reasoning and language.

Increasing epithelial junction permeability enhances gene transfer to airway epithelia In vivo.

Gene transfer to airway epithelia is the most direct approach for treating the progressive lung disease associated with cystic fibrosis. However, the transduction efficiency is poor when viral vectors are applied to the mucosal surface. We reported previously that gene transfer via the apical surface of human airway epithelia in vitro was improved by formulating vectors with ethyleneglycol-bis-(2-aminoethyl ether)- N,N,N',N'-tetraacetic acid (EGTA) in a hypotonic buffer. First, we investigated the mechanism for this enhancement. When 100-nm fluorescent beads were applied to the apical surface in the presence of EGTA, paracellular deposition of the particles was noted. Transmission electron microscopy verified that the epithelial junction complex was disrupted under these conditions. The Ca(2+) chelators EGTA, 1,2-bis (2-aminophenoxy)-ethane-N,N,N',N'-tetraacetic acid (BAPTA), and ethylenediaminetetraacetic acid all caused a rapid, reversible drop in transepithelial resistance and facilitated gene transfer with retrovirus or adenovirus in vitro. When Ca(2+) chelators were applied to rabbit tracheal epithelia or human nasal epithelia in vivo, the transepithelial voltage decreased, and amiloride sensitivity was lost, suggesting that epithelial junctions opened. Importantly, this novel formulation enhanced both retroviral- and adenoviral-mediated gene transfer to rabbit tracheal epithelia in vivo. This technique may have applications for vector or drug delivery to airway epithelia and other polarized cells.

Detecting symmetric patterns in EEG data: a new method of analysis.

Theoretical models of higher cognitive function predict that cortical activity will exhibit families of spatial-temporal patterns of activity whose individual members are related to each other by specific symmetry transformations. In the trion model, it is suggested that these inherent symmetries play a vital role in how we think and reason. We have developed a method of analysis (SYMMETRIC analysis), which detects families of patterns in EEG data, and characterizes the symmetry relationships between members of those pattern families. Using this analysis, significant symmetry families have been found in EEG and single unit spike train data. If symmetry is a crucial aspect of brain function, it is possible that different pathologies are associated with specific types of symmetry relationships in brain activity that could be detected in EEG data by a SYMMETRIC analysis.

Music enhances spatial-temporal reasoning: towards a neurophysiological basis using EEG.

Motivated by predictions from the structured trion model of the cortex, based on Mountcastle's columnar organizational principle, behavioral experiments have demonstrated a causal short-term enhancement of spatial-temporal reasoning in college students following listening to a Mozart Sonata (K.448) but not in control conditions. An EEG coherence study reported presence of right frontal and left temporoparietal activity induced by listening to the Mozart Sonata, which carried over into the spatial-temporal tasks in three of the seven subjects. In this paper, we present further predictions from the trion model and discuss how the new SYMMETRIC analysis method can be used in EEG recordings to help determine the neurophysiological basis of specific music enhancing spatial-temporal reasoning. We conclude with potential clinical applications of major significance.

The resistance of retroviral vectors produced from human cells to serum inactivation in vivo and in vitro is primate species dependent.

The ability to deliver genes as therapeutics requires an understanding of the vector pharmacokinetics similar to that required for conventional drugs. A first question is the half-life of the vector in the bloodstream. Retroviral vectors produced in certain human cell lines differ from vectors produced in nonhuman cell lines in being substantially resistant to inactivation in vitro by human serum complement (F. L. Cosset, Y. Takeuchi, J. L. Battini, R. A. Weiss, and M. K. Collins, J. Virol. 69:7430-7436, 1995). Thus, use of human packaging cell lines (PCL) may produce vectors with longer half-lives, resulting in more-efficacious in vivo gene therapy. However, survival of human PCL-produced vectors in vivo following systemic administration has not been explored. In this investigation, the half-lives of retroviral vectors packaged by either canine D17 or human HT1080 PCL were measured in the bloodstreams of macaques and chimpanzees. Human PCL-produced vectors exhibited significantly higher concentrations of circulating biologically active vector at the earliest time points measured (>1, 000-fold in chimpanzees), as well as substantially extended half-lives, compared to canine PCL-produced vectors. In addition, the circulation half-life of human PCL-produced vector was longer in chimpanzees than in macaques. This was consistent with in vitro findings which demonstrated that primate serum inactivation of vector produced from human PCL increased with increasing phylogenetic distance from humans. These results establish that in vivo retroviral vector half-life correlates with in vitro resistance to complement. Furthermore, these findings should influence the choice of animal models used to evaluate retroviral-vector-based therapies.

Keratinocyte growth factor induced epithelial proliferation facilitates retroviral-mediated gene transfer to distal lung epithelia in vivo.

BACKGROUND: Cell proliferation, vector titer and accessibility of target cells represent hurdles for efficient gene transfer to lung epithelia in vivo using recombinant murine leukemia (MuLV)-based retroviruses. We tested the hypothesis that the pulmonary epithelium is susceptible to retroviral-mediated gene transfer when stimulated to proliferate by a mitogen, keratinocyte growth factor (KGF). METHODS: Rats received keratinocyte growth factor (KGF, 2.5 micrograms/g x 4 doses, two consecutive days) intratracheally followed by high titer amphotropic retrovirus expressing beta-galactosidase. Gene transfer was assessed five days later. RESULTS: KGF stimulated transient proliferation in the bronchiolar and alveolar epithelia (30-40% PCNA positive cells at peak) which decreased to background levels seven days after administration. Gene transfer to epithelia (X-Gal positive cells) occurred more frequently in KGF treated rats, but proliferation exceeded the level of gene transfer. X-gal positive cells were noted in the alveolar epithelium and occasionally in the bronchiolar epithelium. In order to understand the discrepancy between the number of proliferating and transduced cells, primary rat tracheal epithelium cultured at the air-liquid interface was infected from either the apical or basolateral side. Gene transfer was achieved only through basolateral application of vector, suggesting that epithelial polarity represents a barrier to MuLV-based lung gene transfer in vivo. CONCLUSIONS: KGF transiently stimulates epithelial proliferation in vivo, facilitating MuLV-based gene transfer. Retroviral vectors may encounter multiple barriers which have evolved to defend the lung from infections.

Influence of cell polarity on retrovirus-mediated gene transfer to differentiated human airway epithelia.

Gene transfer with recombinant murine leukemia viruses (MuLV) provides the potential to permanently correct inherited lung diseases, such as cystic fibrosis (CF). Several problems prevent the application of MuLV-based recombinant retroviruses to lung gene therapy: (i) the lack of cell proliferation in mature pulmonary epithelia, (ii) inefficient gene transfer with a vector applied to the apical surface, and (iii) low titers of many retroviral preparations. We found that keratinocyte growth factor (KGF) stimulated proliferation of differentiated human tracheal and bronchial epithelia. Approximately 50% of epithelia divided in response to KGF as assessed by bromodeoxyuridine histochemistry. In airway epithelia stimulated to divide with KGF, high-titer ampho- and xenotropic enveloped vectors preferentially infected cells from the basal side. However, treatment with hypotonic shock or EGTA transiently increased transepithelial permeability, enhancing gene transfer with the vector applied to the mucosal surfaces of KGF-stimulated epithelia. Up to 35% of cells expressed the transgene after gene transfer. By using this approach, cells throughout the epithelial sheet, including basal cells, were targeted. Moreover, the Cl- transport defect in differentiated CF airway epithelia was corrected. These findings suggest that barriers to apical infection with MuLV can be overcome.

High-frequency transitions in cortical spike trains related to short-term memory.

Single-unit spike trains recorded from parietal cortex of monkeys performing a tactile short-term memory task show characteristic fluctuations (transitions) in their firing frequency that are related to memory. Spike trains recorded during the memory period, when the animal must retain information for the short term, show a higher rate of such transitions than spike trains recorded during intertrial baseline periods. In the present study, an analysis of multiple temporal resolutions over which these transitions are observed reveals that the memory-related transitions occur most prominently in the 25-50 Hz range. The results of this study suggest that, in the monkey, high frequency fluctuations of neuronal discharge in the parietal cortex are correlated with haptic short-term memory. The presence of such fluctuations are also consistent with theoretical models of short-term memory.

Effects of keratinocyte and hepatocyte growth factor in vivo: implications for retrovirus-mediated gene transfer to liver.

We have previously shown that intravenous administration of keratinocyte growth factor (KGF) induces hepatocyte proliferation, allowing for efficient and noninvasive in vivo gene transfer with high-titer retroviral vectors in mice. The distinctive periportal distribution of transduced cells led us to investigate the ability of virus-sized particles to perfuse the liver adequately after growth factor treatment. We found that perfusion was adequate, and that transduction was limited to the periportal region because only those cells were stimulated to divide. Cells in this region also showed increased expression of Ram-1, the receptor for the murine Moloney leukemia virus (MoMLV) amphotropic envelope, after KGF treatment. In further studies we found that recombinant hepatocyte growth factor (HGF) induces a different population of hepatocytes to divide and upregulate Ram-1. The differential pattern of induction suggested that combining KGF and HGF would improve gene transfer efficiency further. Indeed, simultaneous delivery of both growth factors leads to an overall increase in the number of proliferating cells. Importantly, when coupled with MoMLV delivery, efficiency of gene transfer increased. These results confirm the utility of growth factors for noninvasive hepatic gene transfer in mice, and demonstrate how experiments to define the mechanism of transduction can be taken advantage of to develop improved gene transfer protocols.

Symmetric temporal patterns in cortical spike trains during performance of a short-term memory task.

The trion model is a highly structured representation of cortical organization, which predicts families of symmetric spatial-temporal firing patterns inherent in cortical activity. The symmetries of these inherent firing patterns are used by the brain in short-term memory to perform higher level computations. In the present study, symmetric temporal patterns were searched for in spike trains recorded from cells in parietal cortex of a monkey performing a short-term memory task. A new method of analysis was used to map neuronal firing into sequences of integers representing relative levels of firing rate about the mean (i.e. -1, 0 and 1). The results of this analysis show families of patterns related by symmetry operations. These operations are: i. the interchanging of all the +1's and -1's in a given pattern sequence (C symmetry), ii. the inverting of the temporal sequence of the mapping (T symmetry), and iii. the combination of the two previous operations (CT symmetry). Patterns of a given family are found across cells, especially in the memory periods of the task; in most cases they reoccur within a given spike train. The pattern families predicted by the model and reported here should be further investigated in multiple microelectrode and EEG recordings.

Binary mapping of cortical spike trains in short-term memory.

Microelectrode studies in monkeys performing short-term memory tasks show the sustained elevated discharge of cortical neurons during the retention of recalled sensory information. Cortical cells that are part of memory networks are assumed to receive numerous inputs of excitatory as well as inhibitory nature and local as well as remote. Thus it is reasonable to postulate that the temporal and spatial summation of diverse inputs on any cell in an activated network will result in temporally discrete groups of spikes in its firing. The activation of a network in active memory supposedly increases the magnitude and diversity of those inputs and thus increases the discontinuities and frequency fluctuations in the firing of cells in the network. In this study we use a new method of analysis that allows the quantification of firing discontinuities in a spike train. We apply it to parietal cells recorded from monkeys during the performance of a tactile short-term memory task. In our method, time is divided into bins of equal duration and the measure of discontinuities is the total count of the number of transitions between consecutive time bins with and without spikes. The results of the analysis show that in many of the cells studied, discontinuities (transitions between spiking and nonspiking) reflect memory-related activity obscured in the measures of raw spike frequency over a wide range of frequencies. These cells show more firing transitions in active short-term memory than in baseline (intertrial) conditions.

Auditory memory cells in dorsolateral prefrontal cortex.

The activity of single neurons was recorded extracellularly from dorsolateral prefrontal cortex (DPC) of monkeys during the performance of a cross-modal audio-visual short-term memory task. Cells in DPC show sustained elevated firing levels (higher than spontaneous discharge) during the retention of the auditory stimulus. In some cells this elevated firing was significantly different depending on the particular auditory memorandum of each trial. These results support the notion that DPC participates in auditory short-term memory and the integration of auditory and visual information for prospective action.

Blood transfusion and blood conservation: cost and utilization issues.

Approximately 12 million red blood cell units are transfused to nearly 4 million patients annually in the United States (1). The conservation of blood has historically arisen from awareness that the inventory of this resource is limited (2), as well as the knowledge that blood transfusion carries a risk (3). Estimates of current blood transfusion risks (4-12), and the costs of transfusion complications (13-17), are summarized in Table 1. In addition, emphasis on the costs of health care has raised issues related to the costs of blood transfusion (18, 19). Finally, recent guidelines have emphasized that in the elective transfusion setting, no blood transfusion is a desirable outcome (20, 21). Furthermore, these guidelines along with consensus conference recommendations (22) have emphasized that if blood is to be transfused, autologous (the patient's own) blood is preferable to allogeneic (from an anonymous, volunteer donor) blood. Thus, the costs of blood conservation, for which an increasing array of technologic procedures and products have become available (Table 2), have also become an issue (23). The purpose of this review is to provide an overview of emerging data on the cost-effectiveness of blood and blood conservation interventions in order to help identify areas important for future investigation.