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Bioinformatics (Oxford, England) Oct 2023The nuclear pore complex (NPC) is the only passageway for macromolecules between nucleus and cytoplasm, and an important reference standard in microscopy: it is massive...
MOTIVATION
The nuclear pore complex (NPC) is the only passageway for macromolecules between nucleus and cytoplasm, and an important reference standard in microscopy: it is massive and stereotypically arranged. The average architecture of NPC proteins has been resolved with pseudoatomic precision, however observed NPC heterogeneities evidence a high degree of divergence from this average. Single-molecule localization microscopy (SMLM) images NPCs at protein-level resolution, whereupon image analysis software studies NPC variability. However, the true picture of this variability is unknown. In quantitative image analysis experiments, it is thus difficult to distinguish intrinsically high SMLM noise from variability of the underlying structure.
RESULTS
We introduce CIR4MICS ('ceramics', Configurable, Irregular Rings FOR MICroscopy Simulations), a pipeline that synthesizes ground truth datasets of structurally variable NPCs based on architectural models of the true NPC. Users can select one or more N- or C-terminally tagged NPC proteins, and simulate a wide range of geometric variations. We also represent the NPC as a spring-model such that arbitrary deforming forces, of user-defined magnitudes, simulate irregularly shaped variations. Further, we provide annotated reference datasets of simulated human NPCs, which facilitate a side-by-side comparison with real data. To demonstrate, we synthetically replicate a geometric analysis of real NPC radii and reveal that a range of simulated variability parameters can lead to observed results. Our simulator is therefore valuable to test the capabilities of image analysis methods, as well as to inform experimentalists about the requirements of hypothesis-driven imaging studies.
AVAILABILITY AND IMPLEMENTATION
Code: https://github.com/uhlmanngroup/cir4mics. Simulated data: BioStudies S-BSST1058.
Topics: Humans; Nuclear Pore; Microscopy; Nuclear Pore Complex Proteins; Single Molecule Imaging; Software
PubMed: 37756700
DOI: 10.1093/bioinformatics/btad587 -
Vaccine Sep 2023Vaccine surveillance for children in England focuses on coverage at ages 1, 2, and 5 years. Previous studies exploring vaccine timeliness have used different arbitrary...
INTRODUCTION
Vaccine surveillance for children in England focuses on coverage at ages 1, 2, and 5 years. Previous studies exploring vaccine timeliness have used different arbitrary categories to define whether vaccines were received 'late' or 'on time'. This paper aims to provide more detailed and holistic information on timing and patterns of vaccine uptake across the childhood immunisation schedule in England.
METHODS
We included all children born in England between 2006 and 2014 and registered in the Clinical Practice Research Datalink (CPRD) Aurum, a primary care electronic health record. We described vaccine uptake for representative antigens (pertussis, pneumococcus, measles) by age in days and stratified by ethnicity, region and birth cohort. Alluvial diagrams were used to illustrate common journeys through the vaccination schedule, and we applied survival analysis using accelerated failure time models (AFT) to predict age of vaccine receipt based on timing of previous doses.
RESULTS
573,015 children were followed up until their fifth birthday, when they had 90.16 % coverage for two doses of measles, mumps, rubella (MMR) vaccine and 88.78% coverage for four doses of diphtheria, tetanus, pertussis (DTP) vaccine. Overall, the later the age at which a vaccine was due, the more delay in vaccination. Children of Black Ethnicity or from London showed deviating uptake patterns. If a child received their third DTP dose more than a year later than recommended, they would receive the next dose 2.7 times later than a child who was vaccinated on time. A smaller delay was found for children who did not receive first MMR dose on time.
DISCUSSION
We showed that the risk of vaccination delay increased with the age of the child and significant delay of previous doses. Primary care data can help to promptly identify children at higher risk of delayed vaccination.
Topics: Child; Humans; Infant; Measles-Mumps-Rubella Vaccine; Cohort Studies; Whooping Cough; Vaccination; Immunization Schedule; Measles; Mumps; Diphtheria-Tetanus-Pertussis Vaccine
PubMed: 37574342
DOI: 10.1016/j.vaccine.2023.08.002 -
International Journal of Legal Medicine Nov 2023Computed tomography (CT) scans are a convenient means to study 3D reconstructions of bones. However, errors associated with the different nature of the observation, e.g....
BACKGROUND
Computed tomography (CT) scans are a convenient means to study 3D reconstructions of bones. However, errors associated with the different nature of the observation, e.g. visual and tactile (on dry bone) versus visual only (on a screen) have not been thoroughly investigated.
MATERIALS AND METHODS
We quantified the errors between modalities for sex estimation protocols of nonmetric (categorical and ordinal) and metric data, using 200 dry pelves of archaeological origin and the CT reconstructions of the same bones. In addition, we 3D surface scanned a subsample of 39 pelves to compare observations with dry bone and CT data. We did not focus on the sex estimation accuracy but solely on the consistency of the scoring, hence, the interchangeability of the modalities.
RESULTS
Metric data yielded the most consistent results. Among the nonmetric protocols, ordinal data performed better than categorical data. We applied a slightly modified description for the trait with the highest errors and grouped the traits according to consistency and availability in good, intermediate, and poor.
DISCUSSION
The investigated modalities were interchangeable as long as the trait definition was not arbitrary. Dry bone (gold standard) performed well, and CT and 3D surface scans performed better. We recommend researchers test their affinity for using virtual modalities. Future studies could use our consistency analysis and combine the best traits, validating their accuracy on various modalities.
Topics: Humans; Sex Determination by Skeleton; Imaging, Three-Dimensional; Male; Forensic Anthropology; Tomography, X-Ray Computed; Female; Pelvis; Pelvic Bones
PubMed: 37336820
DOI: 10.1007/s00414-023-03034-w -
Porcine Health Management Jun 2023Across the European Union (EU), efforts are being made to achieve modernisation and harmonisation of meat inspection (MI) code systems. Lung lesions were prioritised as...
BACKGROUND
Across the European Union (EU), efforts are being made to achieve modernisation and harmonisation of meat inspection (MI) code systems. Lung lesions were prioritised as important animal based measures at slaughter, but existing standardized protocols are difficult to implement for routine MI. This study aimed to compare the informative value and feasibility of simplified lung lesion scoring systems to inform future codes for routine post mortem MI.
RESULTS
Data on lung lesions in finisher pigs were collected at slaughter targeting 83 Irish pig farms, with 201 batches assessed, comprising 31,655 pairs of lungs. Lungs were scored for cranioventral pulmonary consolidations (CVPC) and pleurisy lesions using detailed scoring systems, which were considered the gold standard. Using the data collected, scenarios for possible simplified scoring systems to record CVPC (n = 4) and pleurisy (n = 4) lesions were defined. The measurable outcomes were the prevalence and (if possible) severity scoring at batch level for CVPC and pleurisy. An arbitrary threshold was set to the upper quartile (i.e., the top 25% of batches with high prevalence/severity of CVPC or pleurisy, n = 50). Each pair of measurable outcomes was compared by calculating Spearman rank correlations and assessing if batches above the threshold for one measurable outcome were also above it for their pairwise comparison. All scenarios showed perfect agreement (k = 1) when compared among themselves and the gold standard for the prevalence of CVPC. The agreement among severity outcomes and the gold standard showed moderate to perfect agreement (k = [0.66, 1]). The changes in ranking were negligible for all measurable outcomes of pleurisy for scenarios 1, 2 and 3 when compared with the gold standard (rs ≥ 0.98), but these changes amounted to 50% for scenario 4.
CONCLUSIONS
The best simplified CVPC scoring system is to simply count the number of lung lobes affected excluding the intermediate lobe, which provides the best trade-off between value of information and feasibility, by incorporating information on CVPC prevalence and severity. While for pleurisy evaluation, scenario 3 is recommended. This simplified scoring system provides information on the prevalence of cranial and moderate and severe dorsocaudal pleurisy. Further validation of the scoring systems at slaughter and by private veterinarians and farmers is needed.
PubMed: 37391833
DOI: 10.1186/s40813-023-00324-y -
Scientific Reports Sep 2023Shot is one of the fundamental unit in the content structure of a film, which can provide insights into the film-director's ideas. By analyzing the properties and types...
Shot is one of the fundamental unit in the content structure of a film, which can provide insights into the film-director's ideas. By analyzing the properties and types of shots, we can gain a better understanding of a film's visual language. In this paper, we delve deeply into the task of shot type classification, proposing that utilizing multimodal video inputs can effectively improve the accuracy of the task, and that shot type classification is closely related to low-level spatiotemporal semantic features. To this end, we propose a Lightweight Weak Semantic Relevance Framework (LWSRNet) for classifying cinematographic shot types. Our framework comprises two modules: a Linear Modalities Fusion module (LMF Module) capable of fusing an arbitrary number of video modalities, and a Weak Semantic 3D-CNN based Feature Extraction Backbone (WSFE Module) for classifying shot movement and scale, respectively. Moreover, to support practical cinematographic analysis, we collect FullShots, a large film shot dataset containing 27K shots from 19 movies with professionally annotations for movement and scale information. Following experimental results validate the correctness of our proposed hypotheses, while our framework also outperforms previous methods in terms of accuracy with fewer parameters and computations, on both FullShots and MovieShots datasets. Our code is available at ( https://github.com/litchiar/ShotClassification ).
PubMed: 37752203
DOI: 10.1038/s41598-023-43281-w -
European Journal of Sport Science Jul 2023The aims of this study were to test the change and retention of player's overall tackling technique and technical components following a player-specific video-based...
The aims of this study were to test the change and retention of player's overall tackling technique and technical components following a player-specific video-based technical feedback and instruction intervention on both their dominant and non-dominant shoulders. Twenty-four ( = 24) rugby union players participated in a non-randomized control-intervention, which consisted of a video-based technical feedback and instruction group (video-based technical feedback) and a no video-based technical feedback and instruction group (control). During 3 sessions (baseline, intervention, retention) separated by one week, participants in each group performed six tackles (3 tackles on each shoulder) on a tackle simulator. In total, 432 tackles (video-based technical feedback = 216, control = 216) were analysed. Each tackle was analysed using a standardized list of technical criteria (arbitrary units, AU). For the dominant shoulder, tackling technique scores significantly improved from baseline to intervention for both groups. For the non-dominant shoulder, only the video-based technical feedback group improved their tackling technique from baseline to intervention (baseline 6.89 [6.33-7.45] AU vs. intervention 7.72 [7.35-8.10] AU = .001, ES = 0.60 ). For the retention session, the video-based technical feedback group scored significantly higher than the control group, for dominant (video-based technical feedback 8.00 [7.60-8.40] AU vs. control 7.22 [6.83-7.62] AU = .014, ES = 0.66 moderate) and non-dominant (video-based technical feedback 8.11 [7.81-8.41] AU vs. control 7.22 [6.90-7.55] = .004, ES = 0.96 moderate) tackles. This study demonstrates the efficacy of video-based technical feedback as a method to optimize tackle training for player safety and performance.Video-based technical feedback can improve tackling technique in both dominant and non-dominant shoulders.Video-based technical feedback group continued to improve following a retention interval of one week.The video-based technical feedback group showed a significant (with a effect size) improvement from baseline for two techniques - namely, "body position - upright to low" and "drive through contact with legs and shoulders".Video-based technical feedback can be used as a method to optimize tackle training for injury prevention and performance.
Topics: Humans; Football; Feedback; Rugby; Video Recording; Leg
PubMed: 36533306
DOI: 10.1080/17461391.2022.2160937 -
Medicine and Science in Sports and... Oct 2023Recent studies have questioned previous empirical evidence that mental fatigue negatively impacts physical performance. The purpose of this study was to investigate the... (Randomized Controlled Trial)
Randomized Controlled Trial
INTRODUCTION
Recent studies have questioned previous empirical evidence that mental fatigue negatively impacts physical performance. The purpose of this study was to investigate the critical role of individual differences in mental fatigue susceptibility by analyzing the neurophysiological and physical responses to an individualized mental fatigue task.
METHODS
In a preregistered ( https://osf.io/xc8nr/ ), randomized, within-participant design experiment, 22 recreational athletes completed a time to failure test at 80% of their peak power output under mental fatigue (individual mental effort) or control (low mental effort). Before and after the cognitive tasks, subjective feeling of mental fatigue, neuromuscular function of the knee extensors, and corticospinal excitability were measured. Sequential Bayesian analysis until it reached strong evidence in favor of the alternative hypothesis (BF 10 > 6) or the null hypothesis (BF 10 < 1/6) were conducted.
RESULTS
The individualized mental effort task resulted in a higher subjective feeling of mental fatigue in the mental fatigue condition (0.50 (95% confidence interval (CI), 0.39-0.62)) arbitrary units compared with control (0.19 (95% CI, 0.06-0.339)) arbitrary unit. However, exercise performance was similar in both conditions (control: 410 (95% CI, 357-463) s vs mental fatigue: 422 (95% CI, 367-477) s, BF 10 = 0.15). Likewise, mental fatigue did not impair knee extensor maximal force-generating capacity (BF 10 = 0.928) and did not change the extent of fatigability or its origin after the cycling exercise.
CONCLUSIONS
There is no evidence that mental fatigue adversely affects neuromuscular function or physical exercise; even if mental fatigue is individualized, computerized tasks seem not to affect physical performance.
Topics: Humans; Bayes Theorem; Exercise; Knee; Mental Fatigue; Muscle Fatigue
PubMed: 37227196
DOI: 10.1249/MSS.0000000000003221 -
Scientific Reports Nov 2023Our goal was to investigate the effects of head-thorax elevation (HUP) during chest compressions (CC) on lung ventilation. A prospective study was performed on seven...
Our goal was to investigate the effects of head-thorax elevation (HUP) during chest compressions (CC) on lung ventilation. A prospective study was performed on seven human cadavers. Chest was automatically compressed-decompressed in flat position and during progressive HUP from 18 to 35°. Lung ventilation was measured with electrical impedance tomography. In each cadaver, 5 sequences were randomly performed: one without CC at positive end-expiratory pressure (PEEP) 0cmHO, 3 s with CC at PEEP0, 5 or 10cmHO and 1 with CC and an impedance threshold device at PEEP0cmHO. The minimal-to-maximal change in impedance (VT in arbitrary unit a.u.) and the minimal impedance in every breathing cycle (EELI) the) were compared between flat, 18°, and 35° in each sequence by a mixed-effects model. Values are expressed as median (1st-3rd quartiles). With CC, between flat, 18° and 35° VT decreased at each level of PEEP. It was 12416a.u. (10,689; 14,442), 11,239 (7667; 13,292), and 6457 (4631; 9516), respectively, at PEEP0. The same was true with the impedance threshold device. EELI/VT significantly decreased from - 0.30 (- 0.40; - 0.15) before to - 1.13 (- 1.70; - 0.61) after the CC (P = 0.009). With HUP lung ventilation decreased with CC as compared to flat position. CC are associated with decreased in EELI.
Topics: Humans; Prospective Studies; Respiration, Artificial; Positive-Pressure Respiration; Thorax; Electric Impedance; Cadaver; Lung
PubMed: 37989865
DOI: 10.1038/s41598-023-47727-z -
International Journal of Infectious... Oct 2023SARS-CoV-2 remains a global health concern 3 years after its emergence. Safe and effective vaccines mitigate the pandemic impact, but the optimal schedule remains...
Vaccine-induced and hybrid immunity to SARS-CoV-2 after three or four doses of BNT162b2 - results from 22 months follow-up of a healthcare workers cohort, Israel, 2020-2022.
OBJECTIVES
SARS-CoV-2 remains a global health concern 3 years after its emergence. Safe and effective vaccines mitigate the pandemic impact, but the optimal schedule remains unclear, especially in a context where a high proportion of the population is infected.
METHODS
We periodically measured anti-spike SARS-CoV-2 immunoglobulin (Ig)G titers using a quantitative assay in an Israeli healthcare worker cohort who all received at least two BNT162b2 doses and either received further doses and/or were subsequently infected up to 22 months after dose two, and compared geometric mean concentrations according to number of doses received and infection status using analysis of variance.
RESULTS
Among the 993 included participants, infection after dose two led to higher geometric mean concentration IgG titers than a third dose (4285 vs 2845 arbitrary unit/ml 1-2 months after infection/vaccination, P = 0.03). In 16-18 months after dose two, those infected and those who received three or four vaccine doses all had IgG geometric mean concentration levels above 500 arbitrary unit/ml with no significant differences among groups (P = 0.6). IgG levels plateaued 16-22 months after dose two.
CONCLUSION
Three BNT162b2 doses provide long-term immunogenicity comparable to breakthrough infection after dose two. Dose four transiently increases IgG levels and may be especially important for providing additional protection to vulnerable individuals during periods of increased transmission risk.
Topics: Humans; Israel; SARS-CoV-2; BNT162 Vaccine; Follow-Up Studies; COVID-19; Vaccines; Health Personnel; Adaptive Immunity; Immunoglobulin G; Antibodies, Viral
PubMed: 37572957
DOI: 10.1016/j.ijid.2023.08.009 -
Optics Express Nov 2023Metasurfaces have enabled precise electromagnetic (EM) wave manipulation with strong potential to obtain unprecedented functionalities and multifunctional behavior in...
Metasurfaces have enabled precise electromagnetic (EM) wave manipulation with strong potential to obtain unprecedented functionalities and multifunctional behavior in flat optical devices. One promising aspect to achieve multifunction is polarization-dependent metadevices enabled by simultaneous phase control over orthogonally polarized waves. Among these, metasurfaces with geometric phase shows their natural and robust phase control ability over different circularly polarized waves. However, the phase responses under the circularly polarized incidence are locked to be opposite with each other, resulting in limited multifunctionality. In this study, we propose what we believe to be a novel transmission-type microwave metadevice constructed by linear-to-circular metasurface and spin-decoupled metasurface. By endowing independent phase adjustment capability to each unit structure in a spin-decoupled metasurface, the metadevice can reconfigure arbitrary phase wavefronts under orthogonal polarization state incidence, thereby achieving flexible multifunctionality. As a proof-of-concept, the feasibility and reliability of proposed metasurfaces were verified by simulating multifunctional directional deflection, off-axis focusing, and focused vortex beam generation. Finally, the multifunctional manipulation capability of the metadevice is successfully demonstrated by actually measuring the generation of orbital angular momentum modes. This work is expected to drive the application development of metasurface devices in wireless communication.
PubMed: 38041360
DOI: 10.1364/OE.505555