Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics within human airway epithelium

Human airway epithelium (HAE) represents the primary site of viral infection for SARS-CoV-2. Comprising different cell populations, a lot of research has been aimed at deciphering the major cell types and infection dynamics that determine disease progression and severity. However, the cell type-specific replication kinetics, as well as the contribution of cellular composition of the respiratory epithelium to infection and pathology are still not fully understood. Although experimental advances, including Air-liquid interface (ALI) cultures of reconstituted pseudostratified HAE, as well as lung organoid systems, allow the observation of infection dynamics under physiological conditions in unprecedented level of detail, disentangling and quantifying the contribution of individual processes and cells to these dynamics remains challenging. Here, we present how a combination of experimental data and mathematical modelling can be used to infer and address the influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics. Using a stepwise approach that integrates various experimental data on HAE culture systems with regard to tissue differentiation and infection dynamics, we develop an individual cell-based model that enables investigation of infection and regeneration dynamics within pseudostratified HAE. In addition, we present a novel method to quantify tissue integrity based on image data related to the standard measures of transepithelial electrical resistance measurements. Our analysis provides a first aim of quantitatively assessing cell type specific infection kinetics and shows how tissue composition and changes in regeneration capacity, as e.g. in smokers, can influence disease progression and pathology. Furthermore, we identified key measurements that still need to be assessed in order to improve inference of cell type specific infection kinetics and disease progression. Our approach provides a method that, in combination with additional experimental data, can be used to disentangle the complex dynamics of viral infection and immunity within human airway epithelial culture systems.
Interpretation through emergence : reconstituting the lost complexity of the Late Neolithic/Early Bronze Age cosmovision by multi-disciplinary method

This PhD by publication and production represents some of the published outputs of a research project in interpreting some monuments of late Neolithic and Early Bronze Age (EBA) in NW Europe. In the course of this project it became clear that it is necessary to integrate a number of methodologies that presently are mainly conducted in isolation – behavioural ecology, social and cultural anthropology, archaeology and archaeoastronomy. This integrated methodology required not just a new way of conducting field work, but also a new interpretive method that requires analytically reconstructing the prehistoric monument building cultures. This interpretive method is based upon a return to ‘system theory’ through and taking with it many of the assumptions of post-constructionist thinking. I call this method - ‘re-emergence’, and its rationale and application are justified and explained in the Critical Review and in the published papers. Over the course of the past decade during which I have developed and applied these methods, I have simultaneously developed and tested a theory of ‘lunar-solar conflation’. This theory locates the monument building cultures of late Neolithic/EBA NW Europe as both a continuation and reversal of their Palaeolithic/Mesolithic forager forebears. At Stonehenge this is exhibited by cattle pastoralists confiscating Palaeolithic ritual entrainment upon monthly dark moons by substituting dark moon rituals which coincide with the solstices twice every nineteen years of the draconic cycle. The published papers of this PhD constitute the evidence and tests for this new theory. Early in this research programme, and quite coincidently, a film production company approached me to make a film on Stonehenge commissioned by National Geographic based upon my research. As I became the main participant, consultant and script writer for this film it is included as the ‘production’ part of my PhD.
The Role of Level of Play in Concussions in High School Athletes

Objectives: To examine level of play (LOP) as a risk factor for concussion severity and recovery-related outcomes among high school athletes, stratified by sex, and among boys, by sport (football, non-football male sports). Design/Setting: Secondary analysis of data collected through the High School Reporting Information Online surveillance system for academic years 2007-2008 through 2018-2019. Participants: A total of 9916 concussions were reported between the academic years 2007-2008 and 2018-2019 from 9 sports (5189 from football; 2096 from non-football male sports; 2631 from female sports). Main Outcome Measure: Examined the association between LOP (Freshman, Junior Varsity [JV], and Varsity teams) and concussion outcomes (number of concussion symptoms, symptom resolution time [SRT], and time to return to play [RTP]). Results: Compared with Varsity football athletes, concussed JV football athletes had on average 0.19 fewer concussion symptoms, longer SRT (>1 week vs <1 week: odds ratio [OR] = 1.3; 95% confidence interval [CI], 1.1-1.5), and longer RTP (1-3 weeks vs <1 week: OR = 1.5; 95% CI, 1.2-1.9; >3 weeks vs <1 week: OR = 1.6; 95% CI, 1.1-2.3). Compared with Varsity football athletes, Freshman football athletes had on average 0.48 fewer concussion symptoms, longer SRT (OR = 1.3; 95% CI, 1.1-1.5), and longer RTP (1-3 weeks vs <1 week: OR = 1.5; 95% CI, 1.1-2.0; >3 weeks vs <1 week: OR = 2.0; 95% CI, 1.3-3.0). Similarly, compared with female athletes on Varsity teams, concussed JV female athletes had longer RTP (1-3 weeks vs <1 week: OR = 1.8; 95% CI, 1.2-2.7). Trend analyses revealed an increase in the number of concussion symptoms between 2015-2016 and 2018-2019, a decrease between 2009-2010 and 2018-2019 for SRT of less than 1 week, and an increase between 2014-2015 and 2018-2019 for RTP of less than 1 week among Varsity football athletes. Among Varsity female athletes, there was a linear decrease during the study period for RTP of less than 1 week. Conclusions: Despite a higher number of symptoms overall and in recent years, Varsity football players had shorter RTP than Freshman and JV athletes.
A test of the interaction between central and peripheral respiratory chemoreflexes in humans

How central and peripheral chemoreceptor drives to breathe interact in humans remains contentious. We measured the peripheral chemoreflex sensitivity to hypoxia (PChS) at various isocapnic CO2 tensions ( PCO2${P_{{\mathrm{C}}{{\mathrm{O}}_{\mathrm{2}}}}}$ ) to determine the form of the relationship between PChS and central PCO2${P_{{\mathrm{C}}{{\mathrm{O}}_{\mathrm{2}}}}}$ . Twenty participants (10F) completed three repetitions of modified rebreathing tests with end‐tidal PO2${P_{{{\mathrm{O}}_{\mathrm{2}}}}}$ ( PETO2${P_{{\mathrm{ET}}{{\mathrm{O}}_{\mathrm{2}}}}}$ ) clamped at 150, 70, 60 and 45 mmHg. End‐tidal PCO2${P_{{\mathrm{C}}{{\mathrm{O}}_{\mathrm{2}}}}}$ ( PETCO2${P_{{\mathrm{ETC}}{{\mathrm{O}}_{\mathrm{2}}}}}$ ), PETO2${P_{{\mathrm{ET}}{{\mathrm{O}}_{\mathrm{2}}}}}$ , ventilation ( V̇$\dot{V}$E) and calculated oxygen saturation (SCO2) were measured breath‐by‐breath by gas‐analyser and pneumotach. The V̇$\dot{V}$E– PETCO2${P_{{\mathrm{ETC}}{{\mathrm{O}}_{\mathrm{2}}}}}$ relationship of repeat‐trials were linear‐interpolated, combined, averaged into 1 mmHg bins, and fitted with a double‐linear function ( V̇$\dot{V}$ES, L min−1mmHg−1). PChS was computed at intervals of 1 mmHg of PETCO2${P_{{\mathrm{ETC}}{{\mathrm{O}}_{\mathrm{2}}}}}$ as follows: the difference in V̇$\dot{V}$E between the three hypoxic profiles and the hyperoxic profile (∆ V̇$\dot{V}$E) was calculated; three ∆ V̇$\dot{V}$E values were plotted against corresponding SCO2; and linear regression determined PChS (Lmin−1mmHg−1%SCO2−1). These processing steps were repeated at each PETCO2${P_{{\mathrm{ETC}}{{\mathrm{O}}_{\mathrm{2}}}}}$ to produce the PChS vs. isocapnic PCO2${P_{{\mathrm{C}}{{\mathrm{O}}_{\mathrm{2}}}}}$ relationship. These were fitted with linear and polynomial functions, and Akaike information criterion identified the best‐fit model. One‐way repeated measures analysis of variance assessed between‐condition differences. V̇$\dot{V}$ES increased (P < 0.0001) with isoxic PETO2${P_{{\mathrm{ET}}{{\mathrm{O}}_{\mathrm{2}}}}}$ from 3.7 ± 1.5 L min−1mmHg−1 at 150 mmHg to 4.4 ± 1.8, 5.0 ± 1.6 and 6.0 ± 2.2 Lmin−1mmHg−1 at 70, 60 and 45 mmHg, respectively. Mean SCO2 fell progressively (99.3 ± 0%, 93.7 ± 0.1%, 90.4 ± 0.1% and 80.5 ± 0.1%; P < 0.0001). In all individuals, PChS increased with PETCO2${P_{{\mathrm{ETC}}{{\mathrm{O}}_{\mathrm{2}}}}}$ , and this relationship was best described by a linear model in 75%. Despite increasing central chemoreflex activation, PChS increased linearly with PETCO2${P_{{\mathrm{ETC}}{{\mathrm{O}}_{\mathrm{2}}}}}$ indicative of an additive central–peripheral chemoreflex response.
Modélisations micro-macro du comportement mécanique des matériaux poreux ductiles : application à l'argilite du Callovo-Oxfordien

Ce travail porte sur des modelisations, par techniques d’homogeneisation, de la plasticite des materiaux poreux ductiles. Differentes classes de milieux poreux (avec ou sans compressibilite plastique de la matrice) sont considerees. Pour une matrice de von Mises, nous avons obtenu une expression du critere macroscopique de plasticite des milieux contenant des cavites spheroidales aleatoirement orientees. Une extension du critere de Gurson est proposee pour des materiaux dont la matrice est plastiquement compressible et obeit a un critere elliptique. Les resultats obtenus sont appliques et illustres dans le cas des milieux a double porosite. Un accent particulier a ete ensuite mis sur les geomateriaux poreux. L’argilite du Callovo Oxfordien, geomateriau auquel on s’est interesse, est modelise comme un milieu heterogene, constitue a l’echelle mesoscopique d’une matrice elastoplastique poreuse et d’inclusions elastiques. La transition micro-meso aboutissant a la loi de la matrice argileuse est realisee pour une phase solide de type Drucker-Prager, a ecoulement associe ou non, et pour des cavites spheriques. Tandis que le passage meso-macro s’inscrit dans une demarche d'homogeneisation incrementale de Hill. Les capacites predictives du modele base sur une phase solide a loi d’ecoulement non associee ont ete demontrees a travers une large validation experimentale. Enfin, par souci de simplification du modele micro-macro propose pour l’argilite, une version simplifiee du modele est proposee en s’appuyant sur l’hypothese d'inclusions rigides. L'introduction d'une regle d'ecoulement macroscopique non associee a conduit a des predictions d’excellente qualite pour l’argilite.
Development and validation of an observational measure of symptoms of Reactive Attachment Disorder.

Background: Insecure attachment in infancy is associated with a range of later socioemotional problems; therefore, it is important to identify at ‐ risk children so that support can be provided. However, there are currently no well ‐ validated brief measures of infant attachment. The aim of this study is to create a brief version of the Attachment Q ‐ Sort (AQS), one of the gold ‐ standard measures of attachment. Method: Data was used from the National Institute of Child Health and Development Study of Child Care and Youth Development ( N = 1,364). The factor structure of the AQS was explored, and Item Response Theory was used to select a reduced number of items. Convergent validity of the shortened measure was assessed through associations with the Strange Situation Procedure. Correlations with sensitivity, externalising, and social competence were also examined. Results: The Brief Attachment Scale (BAS ‐ 16) was created consisting of two scales of eight items, relating to (a) harmonious interaction with the caregiver and (b) proximity ‐ seeking behaviours. The BAS ‐ 16 showed comparable convergent, discriminant, and concurrent validity to the full AQS. Conclusion: This brief version of the AQS shows potential as a screening measure for insecure attachment in infancy. Further development and validation is required in separate samples.
Adolescents running in conventional running shoes have lower vertical instantaneous loading rates but greater asymmetry than running barefoot or in partial-minimal shoes

ABSTRACT Footwear may moderate the transiently heightened asymmetry in lower limb loading associated with peak growth in adolescence during running. This repeated-measures study compared the magnitude and symmetry of peak vertical ground reaction force and instantaneous loading rates (VILRs) in adolescents during barefoot and shod running. Ten adolescents (age, 10.6 ± 1.7 years) ran at self-selected speed (1.7 ± 0.3 m/s) on an instrumented treadmill under three counter-balanced conditions; barefoot and shod with partial-minimal and conventional running shoes. All participants were within one year of their estimated peak height velocity based on sex-specific regression equations. Foot-strike patterns, peak vertical ground reaction force and VILRs were recorded during 20 seconds of steady-state running. Symmetry of ground reaction forces was assessed using the symmetry index. Repeated-measures ANOVAs were used to compare conditions (α=.05). Adolescents used a rearfoot foot-strike pattern during barefoot and shod running. Use of conventional shoes resulted in a lower VILR (P < .05, dz = 0.9), but higher VILR asymmetry (P < .05) than running barefoot (dz = 1.5) or in partial-minimal shoes (dz = 1.6). Conventional running shoes result in a lower VILR than running unshod or in partial-minimal shoes but may have the unintended consequence of increasing VILR asymmetry. The findings may have implications for performance, musculoskeletal development and injury in adolescents.
Speech understanding in noise for cochlear implant recipients using a spatial noise reduction setting in an off the ear sound processor with directional microphones

Purpose Cochlear implant (CI) recipients struggle to hear in competing background noise. ForwardFocus is a spatial noise reduction setting from Cochlear Ltd. (Sydney) that can simultaneously attenuate noise from multiple sources behind the listener. This study assessed hearing performance with ForwardFocus in an off-the-ear (OTE) sound processor. Method Twenty-two experienced adult CI recipients participated. Speech reception data was collected in fixed noise acutely in the clinic. After three to five weeks take home experience, subjective impressions were recorded, and evaluations were conducted for speech reception in quiet and roving noise. Results Group mean speech reception thresholds (SRT) were below 0 dB in two spatially-separated noise test conditions when using ForwardFocus in the OTE sound processor. SRT were −8.5 dB (SD 2.9) in 4-talker babble roving in a rear hemi-field (S0Nrearhemi) and −3.9 dB (SD 3.3) in 12-talker babble presented laterally and behind (S0N3). Results in S0N3 were significantly better with ForwardFocus On (p = 0.0018). Subjective ratings with the OTE were comparable to, or better than, with their walk-in BTE or OTE sound processor. Conclusions ForwardFocus provides significant benefits for speech recognition in competing background noise in an OTE sound processor. These results support clinicians in counselling CI recipients on potential sound processor options to consider.
Safety and Immunogenicity of V114 in Preterm Infants: A Pooled Analysis of Four Phase Three Studies

Background: Risk of invasive pneumococcal disease is 3-fold higher in preterm versus full-term infants. V114 is a 15-valent pneumococcal conjugate vaccine (PCV) containing the 13 serotypes in PCV13 plus 2 unique serotypes, 22F and 33F. A pooled subgroup analysis was performed in preterm infants (<37 weeks gestational age) enrolled in 4 pediatric phase 3 studies evaluating the safety and immunogenicity of different 4-dose regimens of V114 or PCV13. Methods: Healthy preterm infants were randomized 1:1 to receive V114/PCV13 in the 4 studies. Safety was evaluated as the proportion of participants with adverse events (AEs) following receipt of PCV. Serotype-specific antipneumococcal immunoglobulin G (IgG) geometric mean concentrations, IgG response rates and opsonophagocytic activity geometric mean titers were measured at 30 days postdose 3, pretoddler dose and 30 days postdose 4. Results: V114 and PCV13 were administered to 174 and 180 participants, respectively. Mean gestational age was 35.4 weeks (range: 27 – <37 weeks). Proportions of participants with AEs were comparable between vaccination groups; most AEs experienced were of short duration (≤3 days) and mild-to-moderate intensity. V114-elicited IgG geometric mean concentrations, IgG response rates and opsonophagocytic activity geometric mean titers were generally comparable to PCV13 for the 13 shared serotypes and higher for serotypes 22F and 33F at 30 days postdose 3 and postdose 4. Conclusions: In preterm infants, V114 was well tolerated and induced comparable immune responses to PCV13 for the 13 shared serotypes and higher immune responses to serotypes 22F and 33F. Results support the use of V114 in preterm infants.
Hyperpolarization-activated Cation Channels: from Genes to Function

pattern generation Invariant phase structure of olivo-cerebellar oscillations and its putative role in temporal conditioning Cerebellar theta oscillations are synchronized during hippocampal theta-contingent trace CaV3.1 is a tremor rhythm pacemaker in the inferior olive regulated by P/Q-and T-type calcium channels: a study in mutant mice Subthreshold membrane potential oscillations in inferior olive neurons are dynamically on the following topics: publishes original articles on the function of the nervous system. It is published 12 times a year (monthly)
Higher Summability and Discrete Weighted Muckenhoupt and Gehring Type Inequalities

Abstract In this paper, we prove some reverse discrete inequalities with weights of Muckenhoupt and Gehring types and use them to prove some higher summability theorems on a higher weighted space $l_{w}^{p}({\open N})$ form summability on the weighted space $l_{w}^{q}({\open N})$ when p>q. The proofs are obtained by employing new discrete weighted Hardy's type inequalities and their converses for non-increasing sequences, which, for completeness, we prove in our special setting. To the best of the authors' knowledge, these higher summability results have not been considered before. Some numerical results will be given for illustration.
Population genomics of harbour seal Phoca vitulina from northern British Columbia through California and comparison to the Atlantic subspecies

The harbour seal Phoca vitulina is a ubiquitous pinniped species found throughout coastal waters of the Northern Hemisphere. Harbour seal impacts on ecosystem dynamics may be significant due to their high abundance and food web position. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean, and P. v. vitulina in the Atlantic. Strong natal philopatry of harbour seals can result in fine-scale genetic structure and isolation-by-distance. Management of harbour seals is expected to benefit from improved resolution of seal population structure and dynamics. Here we use genotyping-by-sequencing to genotype 146 harbour seals from the eastern Pacific Ocean (i.e., British Columbia (BC), Oregon, and California) and the western Atlantic Ocean (i.e., Québec, Newfoundland, and Labrador). Using 12,742 identified variants, we confirm the recently identified elevated genetic diversity in the eastern Pacific relative to the western Atlantic and greatest differentiation between the subspecies. Further, we demonstrate that this is independent of reference genome bias or other potential technical artefacts. Coast-specific analyses with 8,933 and 3,828 variants in Pacific and Atlantic subspecies, respectively, identify divergence between BC and Oregon-California, and between Québec and Newfoundland-Labrador. Unexpected PCA outlier clusters were observed in two populations due to cryptic relatedness of individuals; subsequently, closely related samples were removed. Admixture analysis indicates an isolation-by-distance signature where Oregon seals contained some of the BC signature, whereas California did not. Additional sampling is needed in the central and north coast of BC to determine whether a discrete separation of populations exists within the region.
Alteration of the Chicken Upper Respiratory Microbiota, Following H9N2 Avian Influenza Virus Infection

Several studies have highlighted the importance of the gut microbiota in developing immunity against viral infections in chickens. We have previously shown that H9N2 avian influenza A virus (AIV) infection retards the diversity of the natural colon associated microbiota, which may further influence chicken health following recovery from infection. The effects of influenza infection on the upper respiratory tract (URT) microbiota are largely unknown. Here we showed that H9N2 AIV infection lowers alpha diversity indices in the acute phase of infection in URT, largely due to the family Lactobacillaceae being highly enriched during this time in the respiratory microbiota. Interestingly, microbiota diversity did not return to levels similar to control chickens in the recovery phase after viral shedding has ceased. Beta diversity followed similar trend following challenge. Lactobacillus associate statistically with the disturbed microbiota of infected chickens at acute and recovery phase of infection. Additionally, we study age-related changes in the respiratory microbiota during maturation in chickens. From 7 to 28 days of age, species richness and evenness were observed to advance over time as the microbial composition evolved. Maintaining microbiota homeostasis might be considered as a potential therapeutic target to prevent or aid recovery from H9N2 AIV infection.
Green algae CO2 capture is powered by alternative electron pathways of photosynthesis

On Earth, microalgae contribute to about half of global net photosynthesis. During photosynthesis, sunlight is converted into chemical energy (ATP and NADPH) used by metabolism to convert CO2 into biomass. Alternative electron pathways of photosynthesis have been proposed to generate additional ATP that is required for sustaining CO2 fixation, but the relative importance of each pathway remains elusive. Here, we dissect and quantify the contribution of cyclic, pseudo-cyclic and chloroplast to mitochondria electron flows for their ability to sustain net photosynthesis in the microalga Chlamydomonas reinhardtii. We show that each pathway has the potential to energize substantial CO2 fixation, can compensate each other, and that the additional energy requirement to fix CO2 is more than 3 times higher than previous estimations. We further show that all pathways have very different efficiencies at energizing CO2 fixation, with the chloroplast-mitochondria interaction being the most efficient, thus laying bioenergetic foundations for biotechnological improvement of CO2 capture.