Miracle-dz/UniFAR-FTUs huggingface dataset:
The interplay between lumen pressure and cell proliferation determines organoid morphology in a multicellular phase field model

Organoids are ideal systems to predict the phenotypes of organs. However, there is currently a lack of understanding regarding the generalized rules that enable use of simple cellular principles to make morphological predictions of entire organoids. Therefore, we employed a phase field model with the following basic components: the minimum conditions for the timing and volume of cell division, lumen nucleation rules, and lumenal pressure. Through our model, we could compute and generate a myriad of organoid phenotypes observed till date. We propose morphological indices necessary to characterize the shapes and construct phase diagrams and show their dependencies on proliferation time and lumen pressure. Additionally, we introduced the lumen-index parameter, which helped in examining the criteria to maintain organoids as spherical structures comprising a single layer of cells and enclosing an intact lumen. Finally, we predict a star-like organoid phenotype that did not undergo differentiation, suggesting that the volume constraint during cell division may determine the final phenotype. In summary, our approach provides researchers with guidelines to test the mechanisms of self-organization and predict the shape of organoid. Author summary In nature, a wide variety of organ morphologies are observed. Owing to the complexity of the process underlying the acquisition of organs’ morphology, it is challenging to investigate the mechanisms that lead to such variations. A promising approach to study these variations is the use of “computational organoid” study, which is the computational-based study of self-organizing shapes in multicellular assemblies and fluid-filled cavities called lumens that develop from a few proliferating cells. This study explores general mechanisms that dictate how various mechanical factors affect the growing self-organized multicellular assembly. We relied on computer simulations of the mathematical model called multicellular phase-field model with lumens and explored the mechanical factor effects, such as the lumen pressure while considering the time and volume conditions required for cell division. These simulations generated and categorized a wide range of organoid phenotypes based on the varying lumen pressure and cell division conditions. These phenotypes were characterized into seven distinct classes, based on the morphological index sets, including a cellular monolayer/multilayer surrounding single or multiple lumens and branch formation. These phenotypes were obtained without the assumption of differentiation. Our study elucidates the mechanisms underlying the organoid and organ formation with different shapes, thereby highlighting the significance of mechanical forces in shaping these complex biological structures.
CD56-mediated activation of human natural killer cells is triggered by Aspergillus fumigatus galactosaminogalactan

Invasive aspergillosis causes significant morbidity and mortality in immunocompromised patients. Natural killer (NK) cells are pivotal for antifungal defense. Thus far, CD56 is the only known pathogen recognition receptor on NK cells triggering potent antifungal activity against Aspergillus fumigatus. However, the underlying cellular mechanisms and the fungal ligand of CD56 have remained unknown. Using purified cell wall components, biochemical treatments, and A. fumigatus mutants with altered cell wall composition, we herein found that CD56 interacts with the A. fumigatus cell wall carbohydrate galactosaminogalactan (GAG). This interaction induced NK cell activation, degranulation, and secretion of immune-enhancing chemokines and cytotoxic effectors. Supernatants from GAG-stimulated NK cells elicited antifungal activity and enhanced antifungal effector responses of polymorphonuclear cells. In conclusion, we identified A. fumigatus GAG as a ligand of CD56 on human primary NK cells, stimulating potent antifungal effector responses and activating other immune cells.
Double mutation of open syntaxin and UNC-18 P334A leads to excitatory-inhibitory imbalance and impairs multiple aspects of C. elegans behavior

SNARE and Sec/Munc18 proteins are essential in synaptic vesicle exocytosis. Open form t-SNARE syntaxin and UNC-18 P334A are well-studied exocytosis-enhancing mutants. Here we investigate the interrelationship between the two mutations by generating double mutants in various genetic backgrounds in C. elegans. While each single mutation rescued the motility of CAPS/unc-31 and synaptotagmin/snt-1 mutants significantly, double mutations unexpectedly worsened motility or lost their rescuing effects. Electrophysiological analyses revealed that simultaneous mutations of open syntaxin and gain-of-function P334A UNC-18 induces a strong imbalance of excitatory over inhibitory transmission. In liposome fusion assays performed with mammalian proteins, the enhancement of fusion caused by the two mutations individually was abolished when the two mutations were introduced simultaneously, consistent with what we observed in C. elegans. We conclude that open syntaxin and P334A UNC-18 do not have additive beneficial effects, and this extends to C. elegans’ characteristics such as motility, growth, offspring bared, body size, and exocytosis, as well as liposome fusion in vitro. Our results also reveal unexpected differences between the regulation of exocytosis in excitatory versus inhibitory synapses.
Decidability of difference logics with unary predicates

We investigate the decidability of a family of logics mixing difference-logic constraints and unary uninterpreted predicates. The focus is set on logics whose domain of interpretation is R , but the language has a recognizer for integer values. We first establish the decidability of the logic allowing unary uninterpreted predicates, order constraints between real and integer variables, and difference-logic constraints between integer variables. Afterwards, we prove the undecidability of the logic where unary uninterpreted predicates and difference-logic constraints between real variables are allowed.
Variabilité basse fréquence de l'Atlantique Tropical: Rôle de la dynamique océanique équatoriale et Influence d'El Niño Southern Oscillation

L'objectif de cette these est l'etude de la variabilite interannuelle en Atlantique tropical : nous etudions les roles des processus couples lies a la dynamique lineaire et ceux lies a l'influence de la variabilite du Pacifique tropical de type El Nino. Les resultats obtenus suggerent que la variabilite associee aux propagations d'ondes de Kelvin et de Rossby joue un role essentiel dans l'ajustement oceanique au forcage par le vent et plus generalement dans les processus couples ocean-atmosphere en Atlantique equatorial. Les resultats de simulations couplees montrent que l'energie dans la bande de frequences 1-3 ans est en partie liee aux interactions locales air-mer, tandis que la variabilite associee au Pacifique tropical domine les basses frequences (3-7 ans). Nos resultats soulignent la complexite du systeme ocean-atmosphere en Atlantique equatorial, dont la predictibilite depend fortement de la variabilite du Pacifique tropical et de la variabilite atmospherique intra-saisonniere.
Numerical modelling of an acoustically-driven bubble : the growth and collapse near a wall.

The acoustically-driven collapse of a bubble results from the oscillating position of an ultrasound transducer face in a liquid medium. Existing fully-compressible models of bubble collapse have been applied to represent the Rayleigh collapse and the shock-induced collapse. These applications may not adequately represent the conditions associated with the acoustically-driven collapse. The current work presents a fully-compressible model that is the first to capture the collapse of a bubble set in a liquid medium subjected to an ultrasound transducer. The oscillating transducer face is represented by an immersed moving reflective boundary. The flow is simulated using a conservative interface capturing method, which includes the use of a high-order WENO reconstruction, a maximum-principle-satisfying and positivity-preserving limiter, and the HLLC approximate Riemann flux. The numerical method is verified by quantitative comparison to the benchmark shock-bubble problem. The bubble growth, before the bubble collapse, is considered using a Rayleigh-Plesset (RP) approximation. The RP growth initialised collapse (RPGI) model is used to investigate the collapse of a near-wall cavitation bubble. The RPGI model is also used to investigate the influence of common growth assumptions, like neglecting surface tension, on the subsequent collapse of the bubble. The direct simulation of both the growth and collapse, which we refer to as the acoustically-driven growth and collapse (ADGC) model, is used to investigate the dynamics of the bubble growth and the subsequent collapse with varying standoff distance from the near-wall. The ADGC model is also modified to capture the influence of nearby bubbles on the growth and collapse of the single bubble, providing insight into bubble cloud dynamics.
Single center blind testing of a US multi-center validated diagnostic algorithm for Kawasaki disease in Asia

Kawasaki disease (KD) is the leading cause of acquired heart disease in children. A key objective of research in KD is to reduce the risk of long-term cardiovascular sequelae by expediting timely diagnosis. The major challenge in KD diagnosis is that it shares clinical signs with other childhood febrile illnesses. Our previously single-center developed computer-based two-step algorithm was further tested by a five-center validation in US. This first blinded multi-center trial validated our approach, with sufficient sensitivity and positive predictive value, to identify most patients with KD diagnosed at centers across the US. We sought to determine if our algorithmic approach applied to an Asian cohort. This study involved 418 KD and 259 febrile controls (FC) from the Chang Gung Memorial Hospital in Taiwan. Our diagnostic algorithm retained sensitivity (379 of 418; 90.7%), specificity (223 of 259; 86.1%), PPV (379 of 409; 92.7%), and NPV (223 of 247; 90.3%) comparable to previous US 2016 single center and US 2020 fiver center results. Only 4.7% (15 of 418) of KD and 2.3% (6 of 259) of FC patients were identified as indeterminate. The algorithm identified 18 of 50 (36%) KD patients who presented 2 or 3 principal criteria. Of 418 KD patients, 157 were infants younger than one year and 89.2% (140 of 157) were classified correctly. Of the 44 patients with KD who had coronary artery abnormalities, our diagnostic algorithm correctly identified 43 (97.7%) including all patients with dilated coronary artery but one who found to resolve in 8 weeks. We assessed the performance of our KD diagnostic algorithm with a single center Asian cohort. This work demonstrates the applicability of our algorithmic approach and diagnostic portability, providing evidence to support the launch of an adequately powered, multicenter study for future Asian application in the emergency department setting. If deployed in Asia, our tool promises a cost-effective diagnostic approach to allow the timely management of Asian KD patients even in the absence of KD experts, to potentially enhance the outcome for KD patients and reduce the risk of coronary artery aneurysms.
Primary myelofibrosis: 2017 update on diagnosis, risk‐stratification, and management

Disease overview: Primary myelofibrosis (PMF) is a myeloproliferative neoplasm (MPN) characterized by stem cell‐derived clonal myeloproliferation that is often but not always accompanied by JAK2, CALR or MPL mutation, abnormal cytokine expression, bone marrow fibrosis, anemia, splenomegaly, extramedullary hematopoiesis (EMH), constitutional symptoms, cachexia, leukemic progression and shortened survival.
Etude experimentale des phenomenes turbulents generes par une houle reguliere sur un dispositif multi-ecrans

L'objet de cette etude experimentale est d'analyser les mecanismes energetiques determinant le transfert et la dissipation d'energie au voisinage d'une structure multi-ecrans composee de spheres (de diametre d) soumis a l'action de la houle. Des visualisations ont ete realisees, et les champs cinematiques ont ete obtenus par velocimetrie doppler laser. Une etude preliminaire fait apparaitre une zone perturbee proche de la structure qui s'etend sur un diametre de sphere. L'analyse fine du champ des vitesses met en evidence l'apparition d'un lacher tourbillonnaire a partir d'un rapport amplitude de houle-diametre sensiblement egal a 1. La variation des parametres hydrauliques se repercute egalement sur l'amplitude des mecanismes energetiques de l'ecoulement, notamment sur le transfert et la dissipation d'energie au voisinage de la structure. En utilisant des techniques v. D. L. , on a pu mettre en evidence l'influence de la phase de la houle sur les dimensions des echelles spatiales de turbulences, celles-ci ayant ete obtenues par la determination des coefficients de correlation spatiaux dans la zone perturbee. L'approche d'une structure bi-couche fait apparaitre l'influence de l'ecartement entre les ecrans sur le fonctionnement global du dispositif, une distance de l'ordre de un diametre annihilant l'interaction mutuelle de chaque couche. Le fonctionnement compare de chaque ecran au sein de la structure bi-couche est directement influence par la distance entre les parois, celles-ci presentant des caracteristiques d'absorption pour une gamme d'ecartements comprise entre 0,5d et 3/4d.
Economic stress in childhood and adulthood , and self-rated health : a population based study concerning risk accumulation , critical period and social mobility

Background: Research in recent decades increasingly indicates the importance of conditions in early life for health in adulthood. Only few studies have investigated socioeconomic conditions in both childhood and adulthood in relation to health testing the risk accumulation, critical period, and social mobility hypotheses within the same setting. This study investigates the associations between economic stress in childhood and adulthood, and self-rated health with reference to the accumulation, critical period and social mobility hypotheses in life course epidemiology, taking demographic, social support, trust and lifestyle factors into account. Methods: The public health survey in Skåne (southern Sweden) in 2008 is a cross-sectional postal questionnaire study based on a random sample, in which 28,198 persons aged 18–80 years participated (55% participation). Logistic regression models were used to investigate associations between economic stress in childhood and adulthood, and self-rated health. Results: Three life-course socioeconomic models concerning the association between economic stress and self-rated health (SRH) were investigated. The results showed a graded association between the combined effect of childhood and adulthood economic stress and poor SRH in accordance with the accumulation hypothesis. Furthermore, upward social mobility showed a protecting effect and downward mobility increased odds ratios of poor SRH in accordance with the social mobility hypothesis. High/severe economic stress exposures in both stages of life were independently associated with poor SRH in adulthood. Furthermore, stratifying the study population into six age groups showed similar odds ratios of poor SRH regarding economic stress exposure in childhood and adulthood in all age groups among both men and women. Conclusions: The accumulation and social mobility hypotheses were confirmed. The critical period model was confirmed in the sense that both economic stress in childhood and adulthood had independent effects on poor SRH. However, it was not confirmed in the sense that a particular window in time (in childhood or adulthood) had a specifically high impact on self-rated health.
Exploiting Code Generation for Efficient LIKE Pattern Matching

Efficiently evaluating text pattern matching is one of the most common computationally expensive tasks in data processing pipelines. Especially when dealing with text-heavy real-world data, evaluating even simple LIKE predicates is costly. Despite the abundance of text and the frequency of string-handling expressions in real-world queries, processing is an afterthought for most systems. We argue that we must instead properly integrate text processing into the flow of DBMS query execution. In this work, we propose a code generation approach that specifically tailors the generated code to the given pattern and matching algorithm and integrates cleanly into DBMS query compilation. In addition, we introduce a generalized SSE search algorithm that uses a sequence of SSE instructions to compare packed strings in the generated code to efficiently locate longer input patterns. Our approach of generating specialized code for each pattern eliminates the overhead of interpreting the pattern for each tuple. As a result, we improve the performance of LIKE pattern matching by up to 2.5×, demonstrating that code generation can significantly improve the efficiency of LIKE predicate evaluation in DBMSs.
Borassus Aethiopum Ripe Fruits’ Dried Pulp Powder Optimum Incorporation Rate in White Corn-Based Diets for Egg Yolk Colouration

: The study assessed the optimum incorporation rate of Borassus aethiopum ( Ba ) ripe fruits’ dried pulp in laying hens’ feed. So, 72 Isa Brown laying hens of 37-week-old were allotted into 9 groups of 8 hens each. Then, 3 control diets including 60% yellow corn (60%YC), 55.2% yellow corn (55.2%YC) and 60% white corn (60%WC) were formulated. Additionally, 6 test diets were made by substituting 5%; 7.5%; 10%; 12.5% and 15% of 60%WC by Ba ripe fruits’ dried pulp. Then, randomly each hens’ group received one diet. The experiment lasted 90 days, week-39 - week-50. Each day, the eggs were weighed, and each week 3 eggs of similar weight were used per diet for analyses. So, the eggs shell, yolk, and albumen were weighed. Moreover, yolk colours were assessed according to their components L*, a* and b*. Finally, yolks total cholesterol contents were determined. In results, the laying rates fluctuated between 60.86±1.9% for 60%WC and 76.19±2.69% for WC+12.5% Ba , and egg weights fluctuated between 57.71±0.30 and 61.63±0.22 g, within 4 groups (p<0.001). Although WC+12.5% Ba generated the weightless yolks for 14.31±0.2 g compared to 15.14±0.14 for 55.2%YC, its yolks were well coloured. Also, yolk yellowness (b*) revealed 2 groups, and the good was from 60%YC, and 55.2%YC for 153.94±3.27 and 140.28±3.27, respectively (p=0.07). In the second group, WC+12.5% Ba got 90.17±5.17, and the colour was visually good. Finally, looking at the egg yolks total cholesterols contents, 55.2%YC got 30.90±1.47 mg/g, and WC+12.5% Ba exhibited 34.71±3.19 mg/g (p=0.838). To conclude, WC+12.5% Ba was the best incorporation rate.
The current distribution and status of the Hermann’s tortoise, Testudo hermanni boettgeri (Reptilia, Testudines, Testudinidae) in Croatia

Hermann’s tortoise ( Testudo hermanni ) is listed as “Near threatened” in the IUCN Red list of endangered species. The importance of protecting the Hermann’s tortoise populations and its habitats have led to the inclusion of the species within CITES Convention (Annex II), Annex A of EU Wildlife Trade Regulation, Annex II of the Bern Convention and Annexes II and IV of the EU Habitats Directive. To assess the distribution and status of the eastern Hermann’s tortoise ( Testudo hermanni boettgeri ) in Croatia, historical and recent records were gathered and analyzed. The species was recorded in all three biogeographical regions in the country, but it’s native to the Mediterranean and a small part of the Alpine region. With the increase of recent surveys and the use of citizen science platforms, the known range of the species in Croatia was increased by 35.8% and is now encompassing 123 10 × 10 km EEA reference grid cells. Most records (66%) originate from lower elevations (up to 199 m), and the highest was recorded at 570 m. Sparse forests are the most preferred habitats, followed by semi-open habitats, such as grasslands and shrubs. The most serious threat to the species is natural succession due to the increased abandonment of traditional farming and grazing. Other threats include touristic infrastructure and urban development, transportation, illegal collecting, and invasive species. The Area of Occupancy calculated using 2 × 2 km grids resulted in an AOO of 1,372.00 km 2 , while Extent of Occurrence (EOO) is calculated to be 18,145.07 km 2 . The current network of National protected areas includes 14% of the species’ AOO while the designated Natura 2000 areas include 29.30% of its AOO. We propose to designate an additional 10 Natura 2000 areas to help with the long-term protection of the species.
Investigating causes of regional variations in atmospheric CO2 concentrations

OF DISSERTATION INVESTIGATING CAUSES OF REGIONAL VARIATIONS IN ATMOSPHERIC CO2 CONCENTRATIONS Atmospheric CO2 concentrations are rapidly increasing due to anthropogenic activities; however, only about half of the emissions have accumulated in the atmosphere, and the fate of the remaining half remains uncertain. Since atmospheric CO2 concentrations contain information regarding carbon sources and sinks, it is important to understand CO2 variability. This study investigated causes of atmospheric CO2 variability, focusing on the relationship between CO2 concentrations and clouds, the impact of heterogeneous land cover and agricultural production, and the effect of redistributing fossil fuel emissions. Due to global coverage and sheer data volume, satellite CO2 concentrations will be used in inverse models to improve carbon source and sink estimates. Satellite concentrations will only retrieve CO2 measurements in clear conditions, and it is important to understand how CO2 concentrations vary with cloud cover in order to optimally utilize these data. This study evaluated differences between clear-sky and mean concentrations on local, regional, and global scales. Analyses of in situ data, regional model simulations, and global model output all revealed clear-sky differences that were regionally coherent on sub-continental scales and that varied both with time and location. In the mid-latitudes, clear-sky CO2 concentrations were systematically lower than on average, and these differences were not due to biology, but rather to frontal convergence of large-scale gradients that were covered by clouds. Instead of using satellite data to represent temporal averages, inverse models and data assimilation systems that use satellite data to calculate carbon