scholarly journals The risks of using the chi-square periodogram to estimate the period of biological rhythms

2020 ◽  
Author(s):  
Michael C. Tackenberg ◽  
Jacob J. Hughey
Keyword(s):  
Time Course ◽  
Wheel Running ◽  
Ex Vivo ◽  
Biological Rhythms ◽  
Chi Square ◽  
Time Courses ◽  
Short Time ◽  
Improved Accuracy ◽  
Over 40 Years ◽  
Simulated Time

AbstractThe chi-square periodogram (CSP), developed over 40 years ago, continues to be one of the most popular methods to estimate the period of circadian (circa 24-h) rhythms. Previous work has indicated the CSP is sometimes less accurate than other methods, but understanding of why and under what conditions remains incomplete. Using simulated rhythmic time-courses, we found that the CSP is prone to underestimating the period in a manner that depends on the true period and the length of the time-course. This underestimation bias is most severe in short time-courses (e.g., 3 days), but is also visible in longer simulated time-courses (e.g., 12 days) and in experimental time-courses of mouse wheel-running and ex vivo bioluminescence. We traced the source of the bias to discontinuities in the periodogram that are related to the number of time-points the CSP uses to calculate the observed variance for a given test period. By revising the calculation to avoid discontinuities, we developed a new version, the greedy CSP, that shows reduced bias and improved accuracy. Nonetheless, even the greedy CSP tended to be less accurate on our simulated time-courses than an alternative method, namely the Lomb-Scargle periodogram. Thus, although our study describes a major improvement to a classic method, it also suggests that users should generally avoid the CSP when estimating the period of biological rhythms.

scholarly journals The risks of using the chi-square periodogram to estimate the period of biological rhythms

2021 ◽  
Vol 17 (1) ◽  
pp. e1008567
Author(s):  
Michael C. Tackenberg ◽  
Jacob J. Hughey
Keyword(s):  
Time Course ◽  
Wheel Running ◽  
Ex Vivo ◽  
Biological Rhythms ◽  
Chi Square ◽  
Time Courses ◽  
Short Time ◽  
Improved Accuracy ◽  
Over 40 Years ◽  
Simulated Time

The chi-square periodogram (CSP), developed over 40 years ago, continues to be one of the most popular methods to estimate the period of circadian (circa 24-h) rhythms. Previous work has indicated the CSP is sometimes less accurate than other methods, but understanding of why and under what conditions remains incomplete. Using simulated rhythmic time-courses, we found that the CSP is prone to underestimating the period in a manner that depends on the true period and the length of the time-course. This underestimation bias is most severe in short time-courses (e.g., 3 days), but is also visible in longer simulated time-courses (e.g., 12 days) and in experimental time-courses of mouse wheel-running and ex vivo bioluminescence. We traced the source of the bias to discontinuities in the periodogram that are related to the number of time-points the CSP uses to calculate the observed variance for a given test period. By revising the calculation to avoid discontinuities, we developed a new version, the greedy CSP, that shows reduced bias and improved accuracy. Nonetheless, even the greedy CSP tended to be less accurate on our simulated time-courses than an alternative method, namely the Lomb-Scargle periodogram. Thus, although our study describes a major improvement to a classic method, it also suggests that users should generally avoid the CSP when estimating the period of biological rhythms.

The effect of language on recognition memory in first language and second language speakers: The case of placement events

2018 ◽  
Vol 23 (2) ◽  
pp. 651-669 ◽  
Author(s):  
Dietha Koster ◽  
Teresa Cadierno
Keyword(s):  
Second Language ◽  
Recognition Memory ◽  
Time Course ◽  
Memory Task ◽  
Object Position ◽  
Second Language Speakers ◽  
Recognition Phase ◽  
Time Courses ◽  
The One ◽  
Short Time

Aims and Objectives/Purpose/Research questions: German and Spanish differ in lexicalization of object position in placement events (e.g. They stand/lay-put the binoculars on the shelf). Do native (L1) speakers of these languages show different recognition memory for object position in placement scenes (“Thinking for Speaking” (TFS))? And if so, can learning German as a second language (L2) improve memory accuracy? Originality: There is very little research on the effect of language on memory in L2 speakers and no such studies have focused on placement events. By adopting a short time course (750 ms) between the prime and recognition phase this study makes a methodological advancement. Design/Methodology/Approach: We employed a design with L1 speakers ( N = 54) of German and Spanish, and a group of Spanish L2 learners ( N = 123) of German. Participants were presented with a two-phased memory task with minimum delay, with language and pictures showing placement events. Following the direction indicated by German placement verbs we changed position of objects in the picture recognition phase. L2 German speakers received a form-focused instruction on German placement verbs (stand/lay) before the memory task. Data and Analysis: We analysed recognition accuracy for object position changes. Findings/Conclusions: Results showed that L1 German speakers had more accurate recognition memory for object position changes than L1 Spanish speakers. When Spanish learners of L2 German performed the experiment in German, their accuracy exceeded L1 German speakers’ scores. Significance/Implications: The findings provide support for TFS effects on memory for object position in placement events for L1 speakers and show accuracy advantages for L2 speakers. Future studies should consider employing tasks with short time courses as the one used in this paper, in order to establish a base of controlled and reliable findings to unravel the linguistic relativity literature.

Destruction of Actin Filaments by Osmium Tetroxide

1977 ◽  
Vol 35 ◽  
pp. 466-467
Author(s):  
P. Maupin-Szamier ◽  
T. D. Pollard
Keyword(s):  
Actin Filaments ◽  
Time Course ◽  
Osmium Tetroxide ◽  
Rabbit Muscle ◽  
Muscle Actin ◽  
Sodium Phosphate Buffer ◽  
Transmission Electron ◽  
The Difference ◽  
Rates Of Decay ◽  
Short Time

We have studied the destruction of rabbit muscle actin filaments by osmium tetroxide (OSO4) to develop methods which will preserve the structure of actin filaments during preparation for transmission electron microscopy.Negatively stained F-actin, which appears as smooth, gently curved filaments in control samples (Fig. 1a), acquire an angular, distorted profile and break into progressively shorter pieces after exposure to OSO4 (Fig. 1b,c). We followed the time course of the reaction with viscometry since it is a simple, quantitative method to assess filament integrity. The difference in rates of decay in viscosity of polymerized actin solutions after the addition of four concentrations of OSO4 is illustrated in Fig. 2. Viscometry indicated that the rate of actin filament destruction is also dependent upon temperature, buffer type, buffer concentration, and pH, and requires the continued presence of OSO4. The conditions most favorable to filament preservation are fixation in a low concentration of OSO4 for a short time at 0°C in 100mM sodium phosphate buffer, pH 6.0.

scholarly journals Ex vivo accuracy of three electronic apex locators using different apical file sizes

2012 ◽  
Vol 23 (3) ◽  
pp. 199-204 ◽  
Author(s):  
Bruno Carvalho de Vasconcelos ◽  
Leonardo de Alencar Matos ◽  
Elilton Cavalcante Pinheiro-Júnior ◽  
Antônio Sérgio Teixeira de Menezes ◽  
Nilton Vivacqua-Gomes
Keyword(s):  
Root Canal ◽  
Ex Vivo ◽  
Chi Square ◽  
Apical Constriction ◽  
Visual Measurement ◽  
Chi Square Test ◽  
The Mean

This study evaluated the accuracy of three electronic apex locators (Root ZX, Novapex, and Justy II) in root canal length determinations using different apical file sizes, considering the apical constriction (AC) and the major foramen (MF) as anatomic references. The diameter of the apical foramina of 40 single-rooted teeth was determined by direct visual measurement and the master apical file was established. Electronic measurements were then performed using 3 instruments: the selected master apical file (adjusted file), one size smaller (intermediate file), and two sizes smaller (misfit file). The distances from the tip of files fixed in the canals to the MF and to the AC were measured digitally. Precision at AC and at MF for the misfit, intermediate and adjusted apical files was as follows: 80%/88%/83% and 78%/83%/95% (Root ZX); 80%/85%/80% and 68%/73%/73% (Novapex); and 78%/80%/78% and 65%/78%/70% (Justy II). Considering the mean discrepancies, statistically significant differences were found only for the adjusted file at MF, with Root ZX presenting the best results at MF. The chi-square test showed significant differences between the acceptable measurements at AC and at MF for the Justy II and Novapex (± 0.5 mm) regardless of file adjustment. Under the conditions of the present study, all devices provided acceptable electronic measurements regardless of file adjustment, except for Root ZX which had its performance improved significantly when the precisely fit apical file was used. Justy II and Novapex provided electronic measurements nearest to the AC.

scholarly journals Uptake and Distribution of Administered Bone Marrow Mesenchymal Stem Cell Extracellular Vesicles in Retina

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 730
Author(s):  
Biji Mathew ◽  
Leianne A. Torres ◽  
Lorea Gamboa Gamboa Acha ◽  
Sophie Tran ◽  
Alice Liu ◽  
...  
Keyword(s):  
Stem Cell ◽  
Mesenchymal Stem Cell ◽  
Extracellular Vesicles ◽  
Time Course ◽  
Ganglion Cells ◽  
Ex Vivo ◽  
Dependent Manner ◽  
Paracrine Effects

Cell replacement therapy using mesenchymal (MSC) and other stem cells has been evaluated for diabetic retinopathy and glaucoma. This approach has significant limitations, including few cells integrated, aberrant growth, and surgical complications. Mesenchymal Stem Cell Exosomes/Extracellular Vesicles (MSC EVs), which include exosomes and microvesicles, are an emerging alternative, promoting immunomodulation, repair, and regeneration by mediating MSC’s paracrine effects. For the clinical translation of EV therapy, it is important to determine the cellular destination and time course of EV uptake in the retina following administration. Here, we tested the cellular fate of EVs using in vivo rat retinas, ex vivo retinal explant, and primary retinal cells. Intravitreally administered fluorescent EVs were rapidly cleared from the vitreous. Retinal ganglion cells (RGCs) had maximal EV fluorescence at 14 days post administration, and microglia at 7 days. Both in vivo and in the explant model, most EVs were no deeper than the inner nuclear layer. Retinal astrocytes, microglia, and mixed neurons in vitro endocytosed EVs in a dose-dependent manner. Thus, our results indicate that intravitreal EVs are suited for the treatment of retinal diseases affecting the inner retina. Modification of the EV surface should be considered for maintaining EVs in the vitreous for prolonged delivery.

scholarly journals Pseudo-streaming potentials in Necturus gallbladder epithelium. II. The mechanism is a junctional diffusion potential.

1992 ◽  
Vol 99 (3) ◽  
pp. 317-338 ◽  
Author(s):  
L Reuss ◽  
B Simon ◽  
C U Cotton
Keyword(s):  
Time Course ◽  
Bathing Solution ◽  
Intercellular Spaces ◽  
Similar Time ◽  
Streaming Potentials ◽  
Osmotic Water ◽  
Lateral Intercellular Spaces ◽  
Transepithelial Voltage ◽  
Time Courses ◽  
Good Agreement

The mechanisms of apparent streaming potentials elicited across Necturus gallbladder epithelium by addition or removal of sucrose from the apical bathing solution were studied by assessing the time courses of: (a) the change in transepithelial voltage (Vms). (b) the change in osmolality at the cell surface (estimated with a tetrabutylammonium [TBA+]-selective microelectrode, using TBA+ as a tracer for sucrose), and (c) the change in cell impermeant solute concentration ([TMA+]i, measured with an intracellular double-barrel TMA(+)-selective microelectrode after loading the cells with TMA+ by transient permeabilization with nystatin). For both sucrose addition and removal, the time courses of Vms were the same as the time courses of the voltage signals produced by [TMA+]i, while the time courses of the voltage signals produced by [TBA+]o were much faster. These results suggest that the apparent streaming potentials are caused by changes of [NaCl] in the lateral intercellular spaces, whose time course reflects the changes in cell water volume (and osmolality) elicited by the alterations in apical solution osmolality. Changes in cell osmolality are slow relative to those of the apical solution osmolality, whereas lateral space osmolality follows cell osmolality rapidly, due to the large surface area of lateral membranes and the small volume of the spaces. Analysis of a simple mathematical model of the epithelium yields an apical membrane Lp in good agreement with previous measurements and suggests that elevations of the apical solution osmolality elicit rapid reductions in junctional ionic selectivity, also in good agreement with experimental determinations. Elevations in apical solution [NaCl] cause biphasic transepithelial voltage changes: a rapid negative Vms change of similar time course to that of a Na+/TBA+ bi-ionic potential and a slow positive Vms change of similar time course to that of the sucrose-induced apparent streaming potential. We conclude that the Vms changes elicited by addition of impermeant solute to the apical bathing solution are pseudo-streaming potentials, i.e., junctional diffusion potentials caused by salt concentration changes in the lateral intercellular spaces secondary to osmotic water flow from the cells to the apical bathing solution and from the lateral intercellular spaces to the cells. Our results do not support the notion of junctional solute-solvent coupling during transepithelial osmotic water flow.

scholarly journals Suitability of a Progenitor Cell-Enriching Device for In Vitro Applications

Coatings ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 146
Author(s):  
Antonio Celentano ◽  
Tami Yap ◽  
Giuseppe Pantaleo ◽  
Rita Paolini ◽  
Michael McCullough ◽  
...  
Keyword(s):  
Cell Viability ◽  
Time Course ◽  
Ex Vivo ◽  
Trypan Blue Exclusion ◽  
Trypan Blue Exclusion Test ◽  
Initial Reduction ◽  
Metal Wear ◽  
Class 1 ◽  
Electron Energy Loss

Rigenera® is a novel class-1 medical device that produces micro-grafts enriched of progenitors cells without ex vivo manipulation of donor tissues. The manufacturer’s protocol has been supported for a wide variety of clinical uses in the field of regenerative medicine. This study aimed to evaluate its potential use for in vitro cell models. Human primary oral fibroblasts were cultured under standard conditions and processed through Rigenera® over a time course of up to 5 min. Cell viability was assessed using a Trypan Blue exclusion test. It is possible to process fibroblasts through Rigenera® although an initial reduction of cell viability was observed. Additionally, debris was evident in the cell suspension of the processed samples. Scanning electron microscopy (SEM) microanalysis of the debris and electron energy-loss spectroscopy confirmed the presence of metal wear possibly due to the processing conditions used in this study. Interestingly, pore sizes within Rigeneracons® grids were found to range between 250–400 μm. This is the first report assessing the suitability of Rigenera® and Rigeneracons® for in vitro applications. Whilst Rigenera® workflow was found to be amenable to laboratory uses, our results strongly suggest that further research and development is necessary to support the utilization of this technology for enrichment of micro-graft derived cells and cell sorting in vitro.

scholarly journals Sodium and calcium currents in dispersed mammalian septal neurons.

1991 ◽  
Vol 97 (2) ◽  
pp. 303-320 ◽  
Author(s):  
A Castellano ◽  
J López-Barneo
Keyword(s):  
Time Constant ◽  
Time Course ◽  
Calcium Currents ◽  
Closing Time ◽  
Patch Clamp Technique ◽  
Average Value ◽  
Time To Peak ◽  
Time Courses ◽  
Fast Activation ◽  
Septal Neurons

Voltage-gated Na+ and Ca2+ conductances of freshly dissociated septal neurons were studied in the whole-cell configuration of the patch-clamp technique. All cells exhibited a large Na+ current with characteristic fast activation and inactivation time courses. Half-time to peak current at -20 mV was 0.44 +/- 0.18 ms and maximal activation of Na+ conductance occurred at 0 mV or more positive membrane potentials. The average value was 91 +/- 32 nS (approximately 11 mS cm-2). At all membrane voltages inactivation was well fitted by a single exponential that had a time constant of 0.44 +/- 0.09 ms at 0 mV. Recovery from inactivation was complete in approximately 900 ms at -80 mV but in only 50 ms at -120 mV. The decay of Na+ tail currents had a single time constant that at -80 mV was faster than 100 microseconds. Depolarization of septal neurons also elicited a Ca2+ current that peaked in approximately 6-8 ms. Maximal peak Ca2+ current was obtained at 20 mV, and with 10 mM external Ca2+ the amplitude was 0.35 +/- 0.22 nA. During a maintained depolarization this current partially inactivated in the course of 200-300 ms. The Ca2+ current was due to the activity of two types of conductances with different deactivation kinetics. At -80 mV the closing time constants of slow (SD) and fast (FD) deactivating channels were, respectively, 1.99 +/- 0.2 and 0.11 +/- 0.03 ms (25 degrees C). The two kinds of channels also differed in their activation voltage, inactivation time course, slope of the conductance-voltage curve, and resistance to intracellular dialysis. The proportion of SD and FD channels varied from cell to cell, which may explain the differential electrophysiological responses of intracellularly recorded septal neurons.

scholarly journals Mechanisms of autoantibody production in autoimmune MRL mice.

1980 ◽  
Vol 152 (5) ◽  
pp. 1302-1310 ◽  
Author(s):  
D S Pisetsky ◽  
G A McCarty ◽  
D V Peters
Keyword(s):  
Antibody Response ◽  
Time Course ◽  
Fundamental Difference ◽  
Autoantibody Production ◽  
Quantitative Expression ◽  
Autoantibody Response ◽  
Time Courses ◽  
Antibody Levels

The quantitative expression of anti-DNA and anti-Sm antibodies has been investigated in autoimmune MRL-lpr/lpr and MRL-+/+ mice. Anti-Sm antibodies were detected in sera from 21/23 lpr/lpr and 10/16 +/+ mice, with individual animals showing striking variation in the time-course and magnitude of this autoantibody response. The peak antibody levels of the responding animals of each substrain did not differ significantly. For anti-DNA antibody, a different pattern of responsiveness was observed. Individual animals of each substrain produced very similar responses in terms of the magnitude and time-course of serum anti-DNA antibody. The differences in the peak levels of the two substrains were highly significant, with lpr/lpr mice demonstrating a much greater anti-DNA antibody response than +/+ mice. In lpr/lpr mice tested for both autoantibody systems, serum anti-DNA and anti-Sm antibodies showed distinct time-courses. These studies indicate that anti-DNA and anti-Sm antibodies are expressed independently in MRL mice, with the expression of anti-DNA, but not anti-Sm antibody markedly influenced by the presence of the 1pr gene. A fundamental difference in the mechanisms involved in the generation of anti-DNA and anti-Sm antibodies is suggested by the quantitative pattern of the two responses.

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