Longer Gaps Research Articles

End-bridging is required for pol μ to efficiently promote repair of noncomplementary ends by nonhomologous end joining

DNA polymerase μ is a member of the mammalian pol X family and reduces deletion during chromosome break repair by nonhomologous end joining (NHEJ). This biological role is linked to pol μ's ability to promote NHEJ of ends with noncomplementary 3′ overhangs, but questions remain regarding how it performs this role. We show here that synthesis by pol μ in this context is often rapid and, despite the absence of primer/template base-pairing, instructed by template. However, pol μ is both much less active and more prone to possible template independence in some contexts, including ends with overhangs longer than two nucleotides. Reduced activity on longer overhangs implies pol μ is less able to synthesize across longer gaps, arguing pol μ must bridge both sides of gaps between noncomplementary ends to be effective in NHEJ. Consistent with this argument, a pol μ mutant defective specifically on gapped substrates is also less active during NHEJ of noncomplementary ends both in vitro and in cells. Taken together, pol μ activity during NHEJ of noncomplementary ends can thus be primarily linked to pol μ's ability to work together with core NHEJ factors to bridge DNA ends and perform a template-dependent gap fill-in reaction.

The temporal resolution of goldfish hearing: An auditory evoked potential study of gap detection

Temporal processing in goldfish (Carassius auratus) was studied by measuring auditory evoked potentials (AEP) using gaps in continuous band-limited Gaussian noise. Long (>100 ms) silent gaps in high amplitude noise (30 dB SL) evoked distinct offset and onset responses, lasting 6090 ms. Offset and onset responses overlapped with shorter gaps and became difficult to distinguish for gaps <10 ms. The gap-response waveform was modeled as the sum of offset and temporally-shifted onset responses from the same animals (using 120-ms gaps). This model predicted the waveform of gap responses nearly perfectly for gaps longer than 6 ms. Waveforms evoked by shorter gaps (<6 ms) did not accurately fit this model, suggesting that one or both components of the gap response were inhibited or altered. Nonetheless, clear responses were evoked by gaps shorter than 1 ms at this intensity, while longer gaps (up to 10 ms) were required for detection in a low-intensity noise background. This study extends and confirms prior reports that the temporal resolution for goldfish is on the order of 1 ms, but there is also evidence for longer integration processes, over a period of several ms. [Work supported by Grants S06GM60654, R03MH067808, RR03037 (NIH).]

Is Regular Visiting Associated with Lower Costs? Analyzing Service Utilization Patterns in the First Nations Population in Canada

Using an administrative database of dental service records from the Non-Insured Health Benefits (NIHB) program of Health Canada for 1994-2001, the authors set out to test whether regular visitors had lower program expenditures. The age-specific mean expenditures per client were compared among those with regular examinations in 8, 7 and fewer years. The study further examined the effect of regular visiting over the first 6 years on expenditures in the last 2 years. "Continuity of care" was measured by the numbers of consecutive years prior to 2000 in which clients had a regular examination. In a "gap analysis" individuals were classified according to the number of years prior to 2000 since they last had an initial or recall examination. Mean expenditures per client were analyzed by age group and type of service. Over the 8-year period, clients with regular visits had the highest expenditures. In both the continuity of care and gap analyses, the findings were generally consistent; the more that clients visited over the first 6 years, the higher the expenditures in the final 2 years. Clients with more "regular" (initial and recall) examinations received a relatively standard, age-specific, pattern of service but incurred greater expenditures compared to clients with fewer regular, or longer gaps in, examinations. The observations of the authors in this client group do not support the thesis that regular visiting is associated with lower expenditures on dental care.

Temporal resolution in young and elderly subjects as measured by mismatch negativity and a psychoacoustic gap detection task

Objectives: The speech understanding difficulties of elderly persons with age-related hearing loss may be related in part to reduced auditory temporal resolution. To investigate the effects of aging on temporal resolution, the electrophysiological and psychoacoustic detection thresholds for a very short silent gap within a pure tone were determined, and the relation between the two test results was examined. Methods: Behavioral gap detection thresholds were determined in 10 young and 10 elderly normally hearing subjects using an adaptive test procedure. To elicit mismatch negativity (MMN), deviant stimuli with gap durations varying from 6 to 24 ms in 3 ms steps were presented in separate test blocks. Results: There were no significant differences in the psychoacoustic gap detection thresholds between young and elderly subjects. In contrast, longer gaps were needed to elicit MMN in elderly subjects. They also had significantly reduced MMN peak amplitudes, increased MMN peak latencies, a significantly smaller P2 amplitude and longer P2 latency in their responses to the standard stimulus when compared to the same measures in young subjects. Conclusions: Processing of basic temporal stimulus features in elderly subjects is considerably more reduced at the preattentive level (as indicated by MMN), than when attention is directed to the task (as indicated by the psychoacoustic results).

Sampling Errors in Wind Fields Constructed from Single and Tandem Scatterometer Datasets

Abstract Sampling patterns and sampling errors from various scatterometer datasets are examined. Four single and two tandem scatterometer mission scenarios are considered. The single scatterometer missions are ERS (with a single, narrow swath), NSCAT and ASCAT (dual swaths), and QuikSCAT (a single, broad swath obtained from the SeaWinds instrument). The two tandem scenarios are combinations of the broad-swath SeaWinds scatterometer with ASCAT and QuikSCAT. The dense, nearly uniform distribution of measurements within swaths, combined with the relatively sparse, nonuniform placement of the swaths themselves create complicated space–time sampling patterns. The temporal sampling of all of the missions is characterized by bursts of closely spaced samples separated by longer gaps and is highly variable in both latitude and longitude. Sampling errors are quantified by the expected squared bias of particular linear estimates of component winds. Modifications to a previous method that allow more efficient expecte...

Incorporation, Relative Homoplasy, and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses

Phylogenetic analysis of nucleotide and amino acid sequences requires the alignment of homologous sequences. The alignment procedure often requires the insertion of gaps, putatively corresponding to insertion or deletion events, which can be coded as phylogenetic characters. As a general class of phylogenetic characters, gaps have variously been suggested to be reliable (e.g., Lloyd and Calder, 1991; Van Dijk et al., 1999) or unreliable (e.g., Golenberg et al., 1993; Ford et al., 1995). This difference in opinion, coupled with the lack of a well-supported method for the coding of gaps, has led to a diversity of approaches by which gaps have been treated in, or excluded from, tree searches (Gonzalez, 1996). In an earlier paper we presented two methods, termed simple and complex indel coding, in which all gaps (excluding leading and trailing gaps, which are generally artifacts) can be coded from aligned sequence-based matrices (Simmons and Ochoterena, 2000). Simple indel coding, which is used in this study, is implemented by coding all gaps that have different 5' or 3' termini as separate presence/absence characters. Whenever a gap is being coded and the region it spans is completely included within the span of another gap, those sequences having the longer gap (i.e., one that extends to or beyond both the 5' and 3' termini of the gap being coded) are scored as inapplicable for the gap character being coded. Some have suggested on theoretical and empirical grounds that longer gaps are better phylogenetic characters than shorter gaps. Lloyd and Calder (1991) argued that multiresidue gaps are reliable phylogenetic characters because indels are unlikely to be repeated in the exact same position with the same length and sequence (for insertions); indels of different lengths at the same position are recognized as separate events. Similarly, van Ham et al. (1994) suggested that, based on the relative levels of homoplasy in the intergenic spacer between trnL and trnF, gaps longer than two positions are reliable phylogenetic characters. In this paper we assess the relative levels of homoplasy of gap and base characters from a selection of 38 published sequence-based matrices. We determine the potential phylogenetic information included in gap characters and the extent to which inclusion of gap characters alters the gene tree topology and branch support values. We also test the assertion that longer gaps are better phylogenetic characters than shorter gaps.

Over recovery in low pressure sparkgaps

The recovery characteristics of the low pressure sparkgaps in the time interval of 300 /spl mu/s to 50 ms by the influence of 1) gap spacings of 2.5 and 10 mm, 2) pulse voltages of 45 kV rising in 2.5 /spl mu/s for positive and negative polarities, and 3) the pressure range of 1.3-34.7 Pa, have been determined for hydrogen, argon, and deuterium gases. A two-pulse system, capable of generating two pulses rising to 45 kV each in 2.5 /spl mu/s and separated by a variable delay of 100 /spl mu/s to 50 ms, has been used to study the recovery characteristics. It has been observed that the breakdown voltage under the second pulse is higher than the breakdown voltage under the first pulse along the left-hand side of Paschen's characteristics [1] and this has been defined as over recovery (>100% recovery) in these studies. The over recovery was found to be up to 120% and is dependent on the gas pressure { 1 kA), and its reversal. This over recovery in low pressure sparkgaps is due to pressure reduction in the gap after the first pulse discharge. This finding seems to have been reported for the first time. The recovery times are independent of gas pressure for negative polarity. It increases with pressure for positive polarity. It increases with increase in molecular weight of the gas in the gap. Shorter gaps recover faster than longer gaps. The experimental setups, principal of over recovery, measurement of breakdown voltages, and currents, results and discussions are presented here.

Cat peripheral nerve regeneration across 50 mm gap repaired with a novel nerve guide composed of freeze-dried alginate gel

We have developed a novel artificial nerve guide composed of biodegradable freeze-dried alginate gel covered by polyglycolic acid mesh, and evaluated its effect on peripheral nerve regeneration, using a 50-mm gap cat sciatic nerve model. Functional reinnervation of motor and sensory nerves occurred 13 weeks after implantation, as demonstrated by recovery of compound muscle action potential (CMAP) and somatosensory evoked potential (SEP). For histologic evaluation, samples of tissue were harvested from the grafted material segment 7 months after operation. Many newly developed nerve fasciculi were found, and the implanted nerve guidance material had completely disappeared with little inflammation. These results indicate that freeze-dried alginate gel allows the nerve to regenerate across longer gaps than described in previous literature.

Influence of Physical Parameters of Nerve Chambers on Peripheral Nerve Regeneration and Reinnervation

We compared reinnervation of target organs after sciatic nerve section leaving gaps of 2, 4, 6, or 8 mm or gaps repaired with silicone tubes in different groups of mice. Functional reinnervation was assessed by noninvasive methods to determine recovery of sweating, nociceptive, and muscular functions in the hindpaw repeatedly during 3 months postoperation. The increase of gap length between nerve stumps delayed the beginning and reduced the degree of functional recovery achieved either with or without repair. When lesions were left unrepaired, functional reinnervation was only noticeable with a 2-mm gap and practically absent with longer gaps. With tube repair, reinnervation started earlier and achieved higher values than in the corresponding unrepaired groups. Tubulization was most effective with 4-mm gaps and comparatively less with shorter and longer gaps. With 4-mm gaps, recovery was higher when the silicone tube had a cross-sectional area 2.5 times that of the sciatic nerve than with narrower or wider tubes and when the wall was the thinnest available. In all cases muscle reinnervation showed a lower progression than sweating and nociceptive recovery.

Radiotherapy for T2 and T3 carcinoma of the bladder: the influence of overall treatment time

The influence of overall treatment time on local control rate was studied on a group of 147 patients with muscle invasive T2 or T3 transitional cell carcinoma of the urinary bladder. All patients received external radiotherapy at the Catharina Hospital, Eindhoven, The Netherlands between January 1974 and December 1984. Patients treated with overall treatment times shorter than 75 days ( n = 92) were irradiated during a continuous course; all but one patient, with overall treatment times of 75 days or more ( n = 55), received split-course radiotherapy. Actuarial local relapse-free probability at 3 years (LRFP 3) was computed from the onset of radiotherapy. LRFP 3 proved to be dependent on overall treatment time. For T2 stage, LRFP 3 was 80 ± 18% ( n = 5) and 54 ± 13% ( n = 13) for overall times between 15–44 and 45–74 days, respectively, 36 ± 14% ( n = 11) for overall times between 75 and 104 days and 64 ± 15% ( n = 11) for overall times longer than 105 days. For T3 stage, LRFP 3 was 33 ± 19% ( n = 6) and 48 ± 10% ( n = 25) for overall times between 15–44 and 45–74 days, respectively, 25 ± 14% ( n = 12) for overall times between 75 and 104 days and 22 ± 14% ( n = 9) for overall times longer than 105 days. The figures between brackets are numbers of patients relapsing within 3 years or at risk of relapse during at least 3 years. Patients who died without local relapse before 3 years were censored. We have reasons to believe that patient selection bias leads to overestimation of LRFP 3 for the split-course radiotherapy in retrospective studies where the ‘intention to treat’ cannot be recalled. This retrospective study suggests that prolonging overall time of radiotherapy has an effect on local control in T2 and T3 transitional cell carcinoma of the urinary bladder. Local control was the worst for patients treated by split-course radiotherapy with a gap of approximately one month. Local control was not further decreased (and seemed even improved) by longer gaps, but this observation is possibly biased as explained in the discussion section. For patients treated by continuous course radiotherapy we could not find a difference in local control rates between patients treated with overall times of 44 days or less and those treated with overall times of 45–74 days.

The three-loop model: a neural network for the generation of saccadic reaction times.

This paper presents a computer simulation of the three-loop model for the temporal aspects of the generation of visually guided saccadic eye movements. The intention is to reproduce complex experimental reaction time distributions by a simple neural network. The operating elements are artificial but realistic neurones. Four modules are constructed, each consisting of 16 neural elements. Within each module, the elements are connected in an all-to-all manner. The modules are working parallel and serial according to the anatomically and physiologically identified visuomotor pathways including the superior colliculus, the frontal eye fields, and the parietal cortex. Two transient-sustained input lines drive the network: one represents the visual activity produced by the onset of the saccade target, the other represents a central activity controlling the preparation of saccades, e.g. the end of active fixation. The model works completely deterministically; its stochastic output is a consequence of the stochastic properties of the input only. Simulations show how multimodal distributions of saccadic reaction times are produced as a natural consequence of the model structure. The gap effect on saccadic reaction times is correctly produced by the model: depending only on the gap duration (all model parameters unchanged) express, fast-regular, and slow-regular saccades are obtained in different numbers. In agreement with the experiments, bi- or trimodal distributions are produced only for medium gap durations (around 200 ms), while for shorter or longer gaps the express mode disappears and the distributions turn bi- or even unimodal. The effect of varying the strength of the transient-sustained components and the ongoing activity driving the hierarchically highest module are considered to account for the interindividual variability of the latency distributions obtained from different subjects, effects of different instructions to the same subject, and the observation of express makers (subjects who produce exclusively express saccades). How the model can be extended to describe the spatial aspects of the saccade system will be discussed as well as the effects of training and/or rapid adaptation to experimental conditions.

Glutamate activation of a single NMDA receptorchannel produces a cluster of channel openings

Activations of the N-methyl-D-aspartate (NMDA) receptor by glutamate were studied in outside-out patches from CA1 cells in rat hippocampal slices. Very low glutamate concentrations (20-100 nM) were used so that individual receptor activations would be well separated. The shut-time distribution contained at least five components, only the longest component being obviously concentration dependent. The three briefest shut-time components had time constants of 56 microseconds, 0.68 ms and 10.1 ms; all of these were independent of glutamate concentration. An individual activation of the receptor therefore produces a long cluster of channel openings that contains longer gaps than have been reported for receptor activations by other fast neurotransmitters. In addition, (i) some activations may contain still longer (mean 78 ms) shut periods generating 'super clusters', and (ii) a significant amount of NMDA current may be carried by prolonged ('high P(open)') periods during which the channel is open for most of the time. Such periods occur intermittently even at these very low glutamate concentrations. It is suggested that the slow time course of the NMDA receptor-mediated synaptic currents may be determined mainly by the channel activation kinetics.

The effect of age and experience on inhibition of the acoustic startle response by gaps in background noise

The acoustic startle response (ASR) is inhibited when the eliciting stimulus is preceded by a brief gap in background noise. The present study examined the ontogeny of ASR gap inhibition in the rat and the role of experience on its development. Independent groups of Long-Evans rats were tested for 3 consecutive days, at one of eight ages ranging from Postnatal Day (PND) 14–16 to PND 98–100. Gaps (0, 2,4, 8,16, 32, or 64 msec) in broad-band background noise (80 dB on/35 dB off) were presented 190 msec prior to the eliciting stimulus (a 13-kHz, 120-dB, 40–msec tone with 2.5-msec rise/decay). The results show that longer gaps (16–64 msec) inhibited the ASR at all ages; however, the magnitude of inhibition increased with age and repeated testing. The efficacy of shorter gaps (4–8 msec) in the inhibition of the ASR improved until PND 35–37, when the adult pattern was achieved. These findings indicate that both the magnitude of ASR gap inhibition and the efficacy of gaps of less than 16 msec are dependent on the age and experience of the animal.

Experimental study of the voltage recovery characteristics of small air gaps

The electrical recovery characteristics of relatively small air gaps between 0.3 and 9 mm were determined using a two-pulse method. The first pulse was used to over-volt the gap and initiate the arc current. The second pulse was used to determine the recovery voltage of the gap. A plot of the recovery voltage with time was obtained by varying the time delay of the second pulse relative to the arc extinction time of the first arc, in the time range form 50 mu s to 100 ms. It is found that the recovery characteristics are independent of the electrode materials (Cu, Al , St) and the arc current in the range from 40 to 200 A. It is also found that the shorter gaps and the rod plane gaps recover their dielectric strength faster than the longer gaps and the sphere gaps, respectively. >

Discharges due to separation of a corona-charged insulating sheet from a grounded metal cylinder

An experimental study shows that when a corona-charged PMMA (polymethyl methacrylate) sheet, 0.5 mm thick, is separated from a grounded metal cylinder, discharges occur in the wedge-shaped air gap. These discharges serve as a model for discharges that occur between dielectric films and transferring rollers. Two modes of discharges are found: weak microdischarges and stronger major discharges. The microdischarges are very weak, consisting of small light spots, but it is possible to observe them through two cascaded image intensifiers. Charges are deposited on the PMMA sheet by the discharges; these charges are visualized by means of bipolar electrographic powder. The microdischarges occur at the position where the air gap length is approximately=100 mu m, and yield striped powder figures. The occurrence can be explained by means of the partial capacitance model and Paschen's law. At high electrification levels, both microdischarges and major discharges occur; the major discharges appear at longer gaps, since some part of the initial charge cannot be neutralized by the microdischarges. Powder figures of major discharges are tree-like with negative electrification, and round-moon-like with positive electrification. The major discharges with negative electrification are hazardous, since they yield large and clear tracks. >

Permeable tubes increase the length of the gap that regenerating axons can span

After placement of stumps of transected rat sciatic nerve in an impermeable tube, the maximum gap the axons can span is 10 mm. The present study shows that the regenerating axons cross much longer gaps if the tube is made permeable. This improvement does not require another nerve as a transplant nor the preplacement of extracellular materials in the tube. Possible mechanisms for this improvement are discussed.

Formative Time Lags in Nitrogen, Oxygen and Dry Air in Crossed Electric and Magnetic Fields

Formative time lags in nitrogen, oxygen, and dry air are measured with and without a magnetic field over a range of gas pressures (0.05 ≤ p ≤ 20.2 torr, 5 kPa to 2 MPa, electric field strengths (1.8×104 ≤ E ≤ 60×104 V m-1) and magnetic field strengths (85×10-4 ≤ B ≤ 16×10-2 Tesla). For experiments below the Paschen minimum, the electrodes are designed to ensure that breakdown occurs over longer gaps and for experiments above the Paschen minimum, a coaxial cylindrical system is employed. The experimental technique consists of applying pulse voltages to the gap at various constant values of E/p and B/p and measuring the time lags from which the formative time lags are separated. In the gases studed, formative time lags decrease on application of a magnetic field at a given pressure for conditions below the Paschen minimum. The voltages at which the formative time lags remain the same without and with magnetic fields are determined, and electron molecule collision frequencies (v/p) are determined using the Effective Reduced Electric Field [EREF] concept. With increasing ratio of E/p in crossed fields, v/p decreases in all the three gases. Measurements above the Paschen minimum yield formative time lags which increase on application of a magnetic field. Formative time lags in nitrogen in E×B fields are calculated assuming an average collision frequency of 8.5×109 sec-1 torr-1. It is concluded that the EREF concept can be applied to explain formative time lags in E×B fields.

Two Classes of Single-Stranded Regions in DNA from Sea Urchin Embryos

Native DNA from sea urchin embryos contains single-stranded regions (gaps) of up to 3000 nucleotides. The longer gaps (more than 1400 nucleotides) are nonrandomly distributed and are rich in histone gene sequences, other moderately repetitive sequences, and polypyrimidines. The shorter gaps are associated with DNA replication. A method for isolation of the two classes of single-stranded DNA pieces is reported.

Corona and breakdown-voltage characteristics in sphere—plane and rod—rod gaps under impulse voltages of various wavefront durations

Studies were made of the electrical characteristics of the corona and the leader stroke preceding the impulse breakdown of sphere—plane and rod—rod gaps up to 40cm long, in atmospheric air. The studies were made with both positive- and negative-polarity voltages of front durations between 2 and 300 μs. The effect of wavefront duration on the breakdown voltage was also studied.The breakdown voltage of the sphere—plane gap with the sphere positive, and of the rod—rod gap under both polarities, increased with increasing wavefront duration from 2 to 17 μs, and thereafter it decreased for wavefronts up to 300 μs. With the sphere negative, the breakdown voltage of the gaps studied remained approximately constant for all durations of the wavefronts.With the sphere positive, the breakdown of all gap lengths studied was preceded by the propagation of a positive leader. When the sphere was negative, however, a change in the development of the leader from a negative leader to a positive leader was observed at a certain gap length. The leader development remained independent of the wavefront duration of the voltage wave.The breakdown of the rod—rod gap with the high-voltage rod positive was initiated by a positive leader for all gap lengths and voltage wavefronts. With the high-voltage rod negative, two different mechanisms of the leader development were found under the 7 μs and 17 μs-wavefront voltages. In gaps between 10 and 20cm long, a positive leader was observed, whereas in the longer gaps the breakdown was initiated by a negative leader. Under the 2μs-wavefront voltage, the breakdown in all gaps was preceded by a positive leader.

Insulating properties of high vacuum

Recent experimental work on the insulating properties of high vacuum is systematically reviewed. A resume of the prebreakdown conduction phenomena is given; in small gaps, the steady prebreakdown currents appear to be due to a modified type of field emission, while in longer gaps the contamination on the electrode surfaces gives rise to an ion-exchange mechanism, which is responsible for the microdischarges associated with these gaps. The parameters affecting the breakdown strength of a vacuum gap, and the different hypotheses postulated to explain the mechanism of breakdown, are considered in detail. No single hypothesis is able to account for all the experimental results reported, but it appears that a transition from one type of mechanism to another takes place as the interelectrode gap is increased. The paper also considers the important practical aspects of breakdown across solid insulating surfaces in vacuum.