Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding the Right Biological: Eosinophil Subset Differences in Asthma and Chronic Obstructive Pulmonary Disease

1. The Global Asthma Report 2022. Int J Tuberc Lung Dis 2022;26: 1–104. 2. Serebrisky D, Wiznia A. Pediatric asthma: a global epidemic. Ann Glob Health 2019;85:6. 3. Sly PD, Bush A. From the cradle to the grave: the early-life origins of chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2016;193:1–2. 4. Arrieta MC, Stiemsma LT, Dimitriu PA, Thorson L, Russell S, Yurist-Doutsch S, et al.; CHILD Study Investigators. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med 2015;7:307ra152. 5. P erez-Losada M, Authelet KJ, Hoptay CE, Kwak C, Crandall KA, Freishtat RJ. Pediatric asthma comprises different phenotypic clusters with unique nasal microbiotas. Microbiome 2018;6:179. 6. Pijnenburg MW, Frey U, De Jongste JC, Saglani S. Childhood asthma: pathogenesis and phenotypes. Eur Respir J 2022;59:2100731. 7. Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, et al. Maturation of the gut microbiome and risk of asthma in childhood. Nat Commun 2018;9:141. 8. Teo SM, Tang HHF, Mok D, Judd LM, Watts SC, Pham K, et al. Airway microbiota dynamics uncover a critical window for interplay of pathogenic bacteria and allergy in childhood respiratory disease. Cell Host Microbe 2018;24:341–352.e5. 9. Abdel-Aziz MI, Thorsen J, Hashimoto S, Vijverberg SJH, Neerincx AH, Brinkman P, et al. Oropharyngeal microbiota clusters in children with asthma/wheeze associate with allergy, blood transcriptomic immune pathways and exacerbations risk. Am J Respir Crit Care Med 2023;208:142–154. 10. Thorsen J, Stokholm J, Rasmussen MA, Roggenbuck-Wedemeyer M, Vissing NH, Mortensen MS, et al. Asthma and wheeze severity and the oropharyngeal microbiota in children and adolescents. Ann Am Thorac Soc 2022;19:2031–2043. 11. Petersen C, Round JL. Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol 2014;16:1024–1033. 12. Torrego A, Hew M, Oates T, Sukkar M, Fan Chung K. Expression and activation of TGF-beta isoforms in acute allergen-induced remodelling in asthma. Thorax 2007;62:307–313. 13. Kwak HJ, Park DW, Seo JY, Moon JY, Kim TH, Sohn JW, et al. The Wnt/ b-catenin signaling pathway regulates the development of airway remodeling in patients with asthma. Exp Mol Med 2015;47:e198. 14. Jartti T, Gern JE. Role of viral infections in the development and exacerbation of asthma in children. J Allergy Clin Immunol 2017;140: 895–906.
The Hamiltonian Form of Field Dynamics

In classical dynamics one has usually supposed that when one has solved the equations of motion one has done everything worth doing. However, with the further insight into general dynamical theory which has been provided by the discovery of quantum mechanics, one is lead to believe that this is not the case. It seems that there is some further work to be done, namely to group the solutions into families (each family corresponding to one principal function satisfying the Hamilton-Jacobi equation). The family does not have any importance from the point of view of Newtonian mechanics; but it is a family which corresponds to one state of motion in the quantum theory, so presumably the family has some deep significance in nature, not yet properly understood.
Prolonging the therapeutic window for valproic acid treatment in a swine model of traumatic brain injury and hemorrhagic shock

In a swine model of hemorrhage and TBI, valproic acid administration (3- and 11-hours post-injury) improves neurological outcomes. BACKGROUND It has previously been shown that administration of valproic acid (VPA) can improve outcomes if given within an hour following traumatic brain injury (TBI). This short therapeutic window (TW) limits its use in real-life situations. Based upon its pharmacokinetic data, we hypothesized that TW can be extended to 3 hours if a second dose of VPA is given 8 hours after the initial dose. METHOD Yorkshire swine (40–45 kg; n = 10) were subjected to TBI (controlled cortical impact) and 40% blood volume hemorrhage. After 2 hours of shock, they were randomized to either (1) normal saline resuscitation (control) or (2) normal saline–VPA (150 mg/kg × two doses). First dose of VPA was started 3 hours after the TBI, with a second dose 8 hours after the first dose. Neurologic severity scores (range, 0–36) were assessed daily for 14 days, and brain lesion size was measured via magnetic resonance imaging on postinjury day 3. RESULTS Hemodynamic and laboratory parameters of shock were similar in both groups. Valproic acid–treated animals had significantly less neurologic impairment on days 2 (16.3 ± 2.0 vs. 7.3 ± 2.8) and 3 (10.9 ± 3.6 vs. 2.8 ± 1.1) postinjury and returned to baseline levels 54% faster. Magnetic resonance imaging showed no differences in brain lesion size on day 3. Pharmacokinetic data confirmed neuroprotective levels of VPA in the circulation. CONCLUSION This is the first study to demonstrate that VPA can be neuroprotective even when given 3 hours after TBI. This expanded TW has significant implications for the design of the clinical trial.
Nesting Emergences and Other Terrestrial Movements of Macrochelys (Testudines: Chelydridae)

Abstract - Alligator snapping turtles (genus Macrochelys) are the largest freshwater turtles in North America. Despite strong interest in their conservation, we still lack a comprehensive understanding of their natural history, including behaviors associated with terrestrial activity. We reviewed the literature and solicited unpublished observations of terrestrial movements of these highly aquatic turtles. We compiled 206 observations of terrestrial activity from 9 states. The majority of observations were associated with nesting behavior. Observations expanded our knowledge regarding the spatial extent and timing of terrestrial movements and the nesting season. In addition, we compiled observations of terrestrially foraging animals, as well as males and juveniles traveling overland and crossing roads. Collectively, this information clarifies the extent of terrestrial movement by Macrochelys, behaviors that should be considered in conservation plans.
Determining Sexual Size Dimorphism in an Alligator Snapping Turtle (Macrochelys temminckii) Population in Southwest Georgia: Use of Morphometrics, Ultrasonography, and Testosterone

Abstract - We studied the determination of sex for intermediate size classes and adult sexual dimorphism in a Georgia population of Macrochelys temminckii (Alligator Snapping Turtle). We sexed turtles when possible based on size and morphometrics. We took blood samples from captured individuals and measured plasma testosterone using enzyme-linked immunoassay. We examined females and individuals for which sex was unknown using ultrasound to determine sex and reproductive status. We used testosterone concentration to confirm individual sex assignments. For all biometric measurements, adult males were larger than females. Testosterone concentrations were higher in adult and subadult males than in females. Head width did not differ between the sexes when adjusted for body size. Plastron-to-vent length (cm) and testosterone concentrations were significantly greater in adult and subadult male turtles compared to females and were valuable in determining sex of smaller adults >25 cm straight-midline carapace length.
Diet of Montagu's Harriers Circus pygargus Wintering in India: Analysing Seasonal, Regional and Sex Differences Using Web-Sourced Photographs and Pellet Contents

Abstract. Studies on the diet composition of bird species provide valuable insights on their habitat use, trophic interactions and prey selection. Prey abundance can drive movements of raptors in their wintering grounds. But such links have been difficult to establish due to the lack of dietary information for most raptor species. Estimating the wintering diet of raptors is a challenge that requires extensive fieldwork across a large geographical area which is often not possible. The methods used in breeding sites such as nest observations are not available in the non-breeding regions. Recently, several studies have demonstrated the use of web-sourced photographs as a tool for understanding the diet of raptors and also the need for combining multiple approaches to get a comprehensive overview of diet. In this study, we use a novel approach by using web-sourced photographs and pellets to estimate the variations in the diet of Montagu's Harrier Circus pygargus, a species in decline, across its wintering range in India. A total of 232 photographs and 391 pellets collected across western India, Deccan and south India during autumn, winter and early spring seasons were analysed. About 53% of photographs and 71% of pellets contained orthopterans, forming the major component of the harrier's diet. The proportion of reptiles, eggs and birds in the diet were similar across both methods. Presence of other insects in the diet was better estimated by photographs (23%) than pellets (8%) while rodent presence was higher in pellets (17%) than photographs (4%). Pellet analysis and photographs showed similar variation in diet across seasons while only pellets showed variation in diet across regions. Photographs also showed that there is significant variation in diet between the sexes of the species, with higher presence of insects and reptiles in the diet of males than females. Our results suggest that a combination of photographs and pellet analysis provide better estimates of wintering diet of Montagu's Harriers.
On the Steady-State Performance of the Poisson Double GWMA Control Chart

Abstract This article presents a control chart called “Poisson double GWMA” (PDGWMA) chart for monitoring Poisson-distributed processes. Using simulation, the steady-state average run length (SSARL) of PDGWMA chart is evaluated and compared with those of other control charts including Poisson EWMA, Poisson GWMA and Poisson double EWMA (PDEWMA). It is shown that this chart is always more sensitive than other control charts in detecting an out-of-control signal. The PDGWMA chart is a generalized model for which the PDEWMA chart is a special case and also is an effective control chart in situations where the quality deterioration (upward shift) and the quality improvement (downward shift) can be detected agilely, which is important to a modern advanced system.
Separated and vortical flow in aircraft aerodynamics: a CFD perspective

Abstract In the early era of aviation, Frederick Lanchester was both an inventor and a theoretician driven by the need for a theory of flight that would reduce the guesswork in designing new aircraft. His book Aerodynamics in 1907 laid down the early foundations of such a theory. The theory with contributions from others, notably Ludwig Prandtl, was refined to become the basis for the sleek designs of WWII aircraft brought about with little guesswork. New technology changed aircraft design radically with the increased speed of jet propulsion reaching into the transonic range with nonlinear aerodynamics. In the late 1940s and early 1950s substantial guesswork returned to aircraft design. The legacy of Lanchester et al., however, lived on with the development of computational fluid dynamics (CFD) that could guide designers through nonlinear transonic effects. This article presents a historical sketch of how CFD developed, illustrated with examples explaining some of the difficulties overcome in the design of the first-generation swept-wing transonic fighters. The historical study is forensic CFD in search for the likely explanation of the designer’s choice for the wing shape that went into production a long time ago. The capability of current CFD applied to the aerodynamics of aircraft with slender wings is surveyed. The cases discussed involve flow patterns with coherent vortices over hybrid wings and wings of moderate sweep. Vortex-flow aerodynamics pertains to understanding the interaction of concentrated vortices with aircraft components. Modern Reynolds-Averaged Navier-Stokes (RANS) technology is useful to predict attached flow. But vortex interaction with other vortices and breakdown lead to unsteady, largely separated flow which has been found out of scope for RANS. Direct simulation of the Navier-Stokes equations is out of computational reach in the foreseeable future, and the need for better physical modeling is evident. Both cruise performance and stalling characteristics are influenced by strong interactions. Two important aspects of wing-flow physics are discussed: separation from a smooth surface that creates a vortex, and vortex bursting, the abrupt breakdown of a vortex with a subsequent loss of lift. Vortex aerodynamics of not-so-slender wings encounter particularly challenging problems, and it is shown how the design of early-generation operational aircraft surmounted these difficulties. Through use of forensic CFD, the article concludes with two case studies of aerodynamic design: how the Saab J29A wing maintains control authority near stall, and how the Saab J32 mitigates pitch-up instability at high incidence.
Radiative corrections to parity nonconservation in atoms and test of the standard model

Recent progress in calculations of QED radiative corrections to parity nonconservation in atoms is reviewed. The QED vacuum polarization, the self-energy corrections and the vertex corrections are shown to be described very reliably by different methods used by different groups. All new calculations have recently converged to very close final results. Each separate radiative correction is very large, above 1% for heavy atoms, but, having different signs, they partly compensate each other. Our results for the radiative corrections for all atoms are presented. The corrections are −0.5% for 133Cs and −0.70% for 205Tl, 208Pb and 209Bi. The result for 133Cs reconciles the most accurate atomic experimental data for the 6s–7s parity nonconservation amplitude in 133Cs of Wood et al (1997 Science 275 1759) with the standard model.
Stable Stress‐Drop Measurements and their Variability: Implications for Ground‐Motion Prediction

We estimate the a rms‐stress drop, ! [Graphic][1] , (Hanks, 1979) using acceleration time records of 59 earthquakes from two earthquake sequences in eastern Honshu, Japan. These acceleration‐based static stress drops compare well to stress drops calculated for the same events by Baltay et al. (2011) using an empirical Green’s function (eGf) approach. This agreement supports the assumption that earthquake acceleration time histories in the bandwidth between the corner frequency and a maximum observed frequency can be considered white, Gaussian, noise. Although the ! [Graphic][2] is computationally simpler than the eGf‐based ! [Graphic][3] ‐stress drop, and is used as the “stress parameter” to describe the earthquake source in ground‐motion prediction equations, we find that it only compares well to the ! [Graphic][4] at source‐station distances of ∼20 km or less because there is no consideration of whole‐path anelastic attenuation or scattering. In these circumstances, the correlation between the ! [Graphic][5] and ! [Graphic][6] is strong. Events with high and low stress drops obtained through the eGf method have similarly high and low ! [Graphic][7] . We find that the inter‐event standard deviation of stress drop, for the population of earthquakes considered, is similar for both methods, 0.40 for the ! [Graphic][8] method and 0.42 for the ! [Graphic][9] , in log10 units, provided we apply the ∼20 km distance restriction to ! [Graphic][10] . This indicates that the observed variability is inherent to the source, rather than attributable to uncertainties in stress‐drop estimates. Online Material: Earthquake catalog including additional source parameters. [1]: /embed/inline-graphic-1.gif [2]: /embed/inline-graphic-2.gif [3]: /embed/inline-graphic-3.gif [4]: /embed/inline-graphic-4.gif [5]: /embed/inline-graphic-5.gif [6]: /embed/inline-graphic-6.gif [7]: /embed/inline-graphic-7.gif [8]: /embed/inline-graphic-8.gif [9]: /embed/inline-graphic-9.gif [10]: /embed/inline-graphic-10.gif
Configurational Condition of Mode of Multiple Taylor Vortex Flow. (In the case of a symmetric condition).

The Taylor vortex flow exhibits several flow patterns (modes) under the same conditions at small aspect ratios. The primary mode that is formed by increasing Re gradually from zero has a unique pattern with two normal cells having inward flow direction on the plate, and the secondary modes that are formed by increasing Re rapidly have several flow patterns with the normal cell or one or two anomalous cells that flow outward on the end plate. We used the flow visualization technique for the Taylor vortex flow and counted the number of modes appearing according to the various ways of increasing Re. The entropy was calculated, and the complication of the bifurcation of the modes was clarified. Finally, the processes of the formation of modes were illustrated and discussed.
Cell type-specific weighting-factors to solve solid organs-specific limitations of single cell RNA-sequencing

While single-cell RNA-sequencing (scRNA-seq) is a popular method to analyze gene expression and cellular composition at single-cell resolution, it harbors shortcomings: The failure to account for cell-to-cell variations of transcriptome-size (i.e., the total number of transcripts per cell) and also cell dissociation/processing-induced cryptic gene expression. This is particularly a problem when analyzing highly heterogeneous solid tissues/organs, which requires cell dissociation for the analysis. As a result, there exists a discrepancy between bulk RNA-seq result and virtually reconstituted bulk RNA-seq result using its composite scRNA-seq data. To fix this problem, we propose a computationally calculated coefficient, “cell type-specific weighting-factor (cWF)”. Here, we introduce a concept and a method of its computation and report cWFs for 76 cell-types across 10 solid organs. Their fidelity is validated by more accurate reconstitution and deconvolution of bulk RNA-seq data of diverse solid organs using the scRNA-seq data and the cWFs of their composite cells. Furthermore, we also show that cWFs effectively predict aging-progression, implicating their diagnostic applications and also their association with aging mechanism. Our study provides an important method to solve critical limitations of scRNA-seq analysis of complex solid tissues/organs. Furthermore, our findings suggest a diagnostic utility and biological significance of cWFs.
Soil chemical and microbial gradients determine accumulation of root exuded secondary metabolites and plant-soil feedbacks in the field

Introduction Harnessing positive plant-soil feedbacks via crop rotations is a promising strategy for sustainable agriculture. Plants can influence soil properties including microbes by exuding specialized metabolites. However, the effects are often context dependent and variable. If and how local soil heterogeneity may explain this variation is unknown. Benzoxazinoids are specialized metabolites that are released in high quantities by cereals such as wheat and maize. Benzoxazinoids can alter rhizosphere microbiota and the performance of plants subsequently growing in the exposed soils and are thus an excellent model to study agriculturally relevant plant-soil feedbacks in the field, and to assess how soil factors affect their outcome. Materials & methods To understand the importance of local variation in soil properties on benzoxazinoid-mediated plant-soil feedbacks, we conditioned plots with wild-type maize and benzoxazinoid-deficient bx1 mutant plants in a grid pattern across an arable field. We then grew winter wheat across the entire field in the following season. We determined accumulation of benzoxazinoids, root-associated microbial communities, abiotic soil properties and wheat performance in each plot. We also determined benzoxazinoid conversion dynamics in a labelling experiment under controlled conditions, and then assessed associations between soil chemical variation and benzoxazinoid-mediated plant-soil feedbacks. Results Across the field, we detected a marked gradient in soil chemical and microbial community composition. This gradient resulted in significant differences in benzoxazinoid accumulation. These differences were explained by differential benzoxazinoid degradation rather than exudation. Benzoxazinoid exudation modulated alpha diversity of root and rhizosphere bacteria and fungi during maize growth, but not during subsequent wheat growth, while the chemical fingerprint of benzoxazinoid accumulation persisted. Averaged across the field, we detected no significant feedback effects of benzoxazinoid conditioning on wheat performance and defence, apart from a transient decrease in biomass during vegetative growth. Closer analysis however, revealed pronounced feedback effects along the chemical and microbial gradient of the field, with effects gradually changing from negative to positive along the gradient. Conclusion Overall, this study revealed that plant-soil feedbacks differ in strength and direction within a field, and that this variation can be explained by standing chemical and microbial gradients, which strongly affect benzoxazinoid accumulation in the soil. Understanding within-field soil heterogeneity is crucial for the future exploitation of plant-soil feedbacks in sustainable precision agriculture.
Robust estimation in the additive hazards model

ABSTRACT In the additive hazards model the hazard function of a survival variable T is modeled additively as , where λ0(t) is a common non parametric baseline hazard function and is a vector of independent variables. For this model, the pioneering work of Lin and Ying (1994) develops a closed-form estimator for the regression parameter from a new estimating equation. That equation has a similar structure to the corresponding partial likelihood score function for the multiplicative model (Cox 1972) in that it exploits a martingale structure and it allows estimation of separate from the baseline hazard function. Their estimator is asymptotically normal and highly efficient. However, a potential drawback is that it is very sensitive to outliers. In this paper we propose a family of robust alternatives for estimation of the parameter in the additive hazards model which is robust to outliers and still highly efficient and asymptotically normal. We prove Fisher-consistency, obtain the influence function, and illustrate the estimation with simulated and real data. The latter corresponds to the time-honored Welsh Nickels Refiners dataset first introduced by Doll et al. (1970) and subsequently analyzed by Breslow and Day (1987) and Lin and Ying (1994), among others.