Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene expression differentiation in the reproductive tissues of Drosophila willistoni subspecies and their hybrids

Early lineage diversification is central to understand what mutational events drive species divergence. Particularly, gene misregulation in interspecific hybrids can inform about what genes and pathways underlie hybrid dysfunction. In Drosophila hybrids, how regulatory evolution impacts different reproductive tissues remains understudied. Here, we generate a new genome assembly and annotation in Drosophila willistoni and analyse the patterns of transcriptome divergence between two allopatrically evolved D. willistoni subspecies, their male sterile and female fertile hybrid progeny across testis, male accessory gland, and ovary. Patterns of transcriptome divergence and modes of regulatory evolution were tissue‐specific. Despite no indication for cell‐type differences in hybrid testis, this tissue exhibited the largest magnitude of expression differentiation between subspecies and between parentals and hybrids. No evidence for anomalous dosage compensation in hybrid male tissues was detected nor was a differential role for the neo‐ and the ancestral arms of the D. willistoni X chromosome. Compared to the autosomes, the X chromosome appeared enriched for transgressively expressed genes in testis despite being the least differentiated in expression between subspecies. Evidence for fine genome clustering of transgressively expressed genes suggests a role of chromatin structure on hybrid gene misregulation. Lastly, transgressively expressed genes in the testis of the sterile male progeny were enriched for GO terms not typically associated with sperm function, instead hinting at anomalous development of the reproductive tissue. Our thorough tissue‐level portrait of transcriptome differentiation between recently diverged D. willistoni subspecies and their hybrids provides a more nuanced view of early regulatory changes during speciation.
IL-37 Attenuates Platelet Activation and Thrombosis Through IL-1R8 Pathway

Background: IL-37 (interleukin-37), a natural suppressor of innate inflammatory and immune responses, is increased in patients with myocardial infarction. Platelets play an important role in the progress of myocardial infarction, but the direct effects of IL-37 on platelet activation and thrombosis, as well as the underlying mechanisms, still remain unclear. Methods: We evaluated the direct effects of IL-37 on agonists-induced platelet activation and thrombus formation, as well as revealed the underlying mechanisms using platelet-specific IL-1R8 (IL-1 receptor 8)–deficient mice. Using myocardial infarct model, we explored the effects of IL-37 on microvascular obstruction and myocardial injury. Results: IL-37 directly inhibited agonists-induced platelet aggregation, dense granule ATP release, P-selectin exposure, integrin αIIbβ3 activation, platelet spreading, and clot retraction. IL-37 inhibited thrombus formation in vivo in a FeCl3-injured mesenteric arteriole thrombosis mouse model and ex vivo in a microfluidic whole-blood perfusion assay. Mechanistic studies using platelet-specific IL-1R8–deficient mice revealed that IL-37 bound to platelet IL-1R8 and IL-18Rα, and IL-1R8 deficiency impaired the inhibitory effects of IL-37 on platelet activation. Using PTEN (phosphatase and tensin homolog)-specific inhibitor and PTEN-deficient platelets, we found that IL-37 combined with IL-1R8 to enhance PTEN activity, inhibit Akt (protein kinase B), mitogen-activated protein kinases, and spleen tyrosine kinase pathways, as well as decrease the generation of reactive oxygen species to regulate platelet activation. Exogenous IL-37 injection suppressed microvascular thrombosis to protect against myocardial injury in wild-type mice but not in platelet-specific IL-1R8–deficient mice after permanent ligation of the left anterior descending coronary. Finally, a negative correlation between plasma IL-37 concentration and platelet aggregation was observed in patients with myocardial infarction. Conclusions: IL-37 directly attenuated platelet activation, thrombus formation, and myocardial injury via IL-1R8 receptor. Accumulated IL-37 in plasma inhibited platelet activation to ameliorate atherothrombosis and infarction expansion, and thus may have therapeutic advantages as potential antiplatelet drugs.
CEGPairGen: An Automated Tool for Generating Pairwise Tests from Cause-Effect Graphs

Pairwise testing is known to be effective in finding errors while considering only a small fraction of input space. Recently, a new testing technique that generates pairwise tests from the cause-effect graph has been presented. This technique assumes the use of the Alloy analyzer to generate pairwise tests from the cause-effect graph. Since, however, the Alloy analyzer does not support APIs that build and manipulate the Alloy formulas, the task of test generation may be tedious and error-prone. In this paper, we introduce a tool named CEGPairGen that automates the process of generating pairwise tests from the cause-effect graph without any human intervention. CEGPairGen produces a test generator written in Java KodKod APIs that generates pairwise tests from a given causeeffect graph. KodKod has been designed to efficiently construct, manipulate, and solve constraints. CEGPairGen takes an incremental test generation strategy for situations where the number of pairs to be covered grows quickly. We show a case study where experimental assessment of tests produced by CEGPairGen has been carried out.
Iterated calculation of global implications and recursive learning in combinational equivalence checking

Boolean satisfiability and recursive learning have been used in solving the combinational equivalence-checking problem. In this paper, we extend the recursive learning procedure and integrate it with global implications calculated in an iterative way to reduce the time needed for the solution. We also propose a variable ordering scheme to minimize the number of iterations needed to calculate the implications.
Physical Realism in the Analysis of Stellar Magnetic Fields. III. Flux Tubes and Multicomponent Atmospheres

Several important tests of likely systematic effects in the analysis of Zeeman broadening on cool stars have been performed. The effects of different atmospheric structures inside and outside of magnetic regions are considered, and the effects of field gradients within flux tubes and of errors in the assumed spectral type of a star are considered. It is found that substantial effects are possible which render the results of one-component analyses somewhat uncertain, with systematic errors potentially as great as 40 percent in the derived magnetic flux. However, it appears that two-component models consisting of quiet and flux tube regions may be oversimplified, since the predicted line profiles tend to be shallower than those observed. 39 refs.
Self-limiting behavior of the grain growth in lead zirconate titanate thin films

During the lateral grain-growth process in lead zirconate titanate (PZT) thin films by selectively nucleated lateral crystallization using PZT seed, it was found that the lateral growth was saturated with the annealing temperature. The saturation of lateral growth was analyzed by the interface energy, which appeared during the crystallization process. The factors affecting the saturation of lateral growth were found to be the interface energy between the perovskite phase and the pyrochlore phase, and the one between the PZT thin film and the bottom Pt electrode. When the ion damage was introduced to the growth-saturated PZT thin films, further lateral growth was observed. Pt bottom electrode thickness was changed to control the interface energy between the PZT thin film and the Pt bottom electrode. PZT grain size increased according to the Pt thickness, because the lattice parameter of Pt films increased with the thickness of the Pt films. The incubation time for nucleation in the PZT thin films increased.
Nonlinear and non-Markovian fluctuation-dissipation processes : a Fokker-Planck treatment

This paper is devoted to the derivation of the Fokker–Planck equation in a case where the external potential acting on the system and the coupling between system and bath are not harmonic. This problem has already the subject of many preceding investigations, which left open, however, the problem of deriving the Fokker–Planck equation with no assumption but the Born approximation. Within the present treatment the problem of the derivation of the Fokker–Planck equation is solved with no limitation on the bath time scale.
The right ventricle systolic force ratio could predict the severity of the tricuspid regurgitation‐RIVIERA ratio

For assessing the severity of tricuspid regurgitation (TR), there is no gold standard. We developed a parameter, the right ventricular systolic force ratio—RIVIERA, using the continious wave Doppler analysis of TR and pulsed‐wave analysis of the right ventricle outflow tract. We hypothesized that the RIVIERA would facilitate the ability to identify severe TR in clinical settings.
Alginate encapsulation improves probiotics survival in carbonated sodas and beers

Probiotic functionalization of non-dairy beverages has been garnering interest to provide dairy-sensitive populations with greater probiotic product varieties. The addition of probiotics into popularly consumed beverages–carbonated sodas and beers, presents an interesting challenge as the presence of acidic pH, hops-derived compounds, and ethanol have highly deleterious effects. Herein, alginate encapsulation was proposed to improve probiotics viability within sodas and beers. Three probiotics, namely Lacticaseibacillus rhamnosus GG, Escherichia coli Nissle 1917, and Bifidobacterium longum were encapsulated in alginate spheres and exposed to Coca-Cola, 7-Up, Tiger Beer, and Guinness under refrigerated, room temperature and simulated gastric fluid conditions. Results demonstrate that alginate encapsulation significantly improved the viabilities of all three probiotics in various beverages and conditions. Refrigerated storage better preserved probiotic viabilities and reduced the formation of the probiotic metabolic by-product, L-lactate, than at room temperature storage. Findings here could provide beverage manufacturers with a novel way to develop probiotic-sodas and probiotic-beers through encapsulation.
Micromachined silicon plates for sensing molecular interactions

A micromachined surface stress sensor based on a thin suspended crystalline silicon circular plate measures differential surface stress changes associated with vapor phase chemisorption of an alkanethiol self-assembled monolayer. The isolated face of the suspended silicon plate serves as the sensing surface treated with a receptor layer sensitive to a target molecule, in this case Au(111). Chemisorption of an alkanethiol on the gold coated silicon surfaces results in plate bending. Plate displacements, measured with a phase scanning interferometer, indicate a differential surface stress change $\Delta \sigma_s$=-0.72 +/- 0.02 N m(-1) for 1-dodecanethiol.
Privacy Policies across the Ages: Content of Privacy Policies 1996–2021

It is well known that most users do not read privacy policies but almost always tick the box to agree with them. While the length and readability of privacy policies have been well studied and many approaches for policy analysis based on natural language processing have been proposed, existing studies are limited in their depth and scope, often focusing on a small number of data practices at single point in time. In this article, we fill this gap by analyzing the 25-year history of privacy policies using machine learning and natural language processing and presenting a comprehensive analysis of policy contents. Specifically, we collect a large-scale longitudinal corpus of privacy policies from 1996 to 2021 and analyze their content in terms of the data practices they describe, the rights they grant to users, and the rights they reserve for their organizations. We pay particular attention to changes in response to recent privacy regulations such as the GDPR and CCPA. We observe some positive changes, such as reductions in data collection post-GDPR, but also a range of concerning data practices, such as widespread implicit data collection for which users have no meaningful choices or access rights. Our work is an important step toward making privacy policies machine readable on the user side, which would help users match their privacy preferences against the policies offered by web services.
An Efficient and Accurate Detection of Fake News Using Capsule Transient Auto Encoder

Fake news is “news reports that are deliberatively and indisputably fake. ” News that uses fake information is becoming a threat. It becomes challenging for humans to distinguish between fake and actual news. It has become necessary to detect fake news, which seeks to determine whether a news document can be believed. Detection of fake news faces challenges in accurate classification, making existing detection algorithms ineffective. In these issues, this article uses a novel Adaptive Capsule Transient Auto Encoder (ACTAE) for effectively detecting fake news. ACTAE is a combined approach of a classifier named Capsule Auto Encoder and an algorithm called Adaptive Transient Search Optimization Algorithm. The overall detection process is performed in various stages, including preprocessing, feature withdrawal, feature selection, and classification and optimization of weight parameters of the classifier for better results. The overall process is executed in Python, proving that ACTAE detects fake news with higher accuracy (99%) and lower error rate.
Optimization design of crude oil distillation unit using bi-level surrogate model

Crude Oil Distillation Unit (CDU) is one of the most important separation installations in the petroleum refinery industries. In this work, a Bi-level Surrogate column model Aided Constrained Optimization Design (Bi-SACOD) is proposed for time-consuming objectives and constraints in the evolutionary optimization design of CDUs. The main components of Bi-SACOD include bi-level surrogate model construction (Bi-SMC), bi-level model management (Bi-MM), and particle swarm optimization (PSO) mixed-integer constrained evolutionary (PSO-MICE) search. Bi-SMC implements surrogate column model construction and feasible domain identification. Bi-MM combines surrogate column models with rigorous CDU simulations to perform model management, and PSO-MICE implements optimum search works. The optimization results of the CDUs indicate that Bi-SACOD outperforms the single-level surrogate column model approaches, and are more consistent with the rigorous CDU model optimization approach, whereas the evaluation numbers of the time-consuming rigorous models are significantly reduced.
Application of Aerosondes to Melt-Pond Observations over Arctic Sea Ice

Abstract Continuous observation of sea ice using a small robotic aircraft called the Aerosonde was made over the Arctic Ocean from Barrow, Alaska, on 20–21 July 2003. Over a region located 350 km off the coast of Barrow, images obtained from the aircraft were used to characterize the sea ice and to determine the fraction of melt ponds on both multiyear and first-year ice. Analysis of the data indicates that melt-pond fraction increased northward from 20% to 30% as the ice fraction increased. However, the fraction of ponded ice was over 30% in the multiyear ice zone while it was about 25% in the first-year ice zone. A comparison with a satellite microwave product showed that the ice concentration derived from the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E) has a negative bias of 7% due to melt ponds. These analyses demonstrate the utility of recent advances in unmanned aerial vehicle (UAV) technology for monitoring and interpreting the spatial variations in the sea ice wi.
New champions of preferential trade? Two-level games in China’s and India’s shifting commercial strategies

Abstract Following decades of relative isolation, China and India have become the world’s largest new traders. In this paper, we focus on their Preferential Trade Agreements (PTAs). While the two economies initially followed similar paths, with a growing number of PTAs signed in the first decade of the 21st Century, since 2011 India has taken a U-turn and stopped completing them. China, on the other hand, has widened and deepened its trade agreements. We present a novel theoretical framework to analyze international economic negotiations by emerging economies and use it to study the puzzling divergence of the trade policies of China and India. By adapting the two-level game framework to emerging economies, we argue that there are key differences in the political economies of countries like China and India (compared to Western industrialized ones), which requires a more specific focus on the domestic side of the two-level game. We show that accounting for non-legislative domestic ratification processes and for iterative games and experiential learning by domestic actors are crucial in understanding the trade strategies of emerging economies. While much of the literature explains large emerging economies by looking at external systemic factors, we instead suggest that their domestic politics trumps international politics.
Regional fire occurrence in Southern Africa using BFAST iterative break detection in seasonal and trend components of a MODIS time series

ABSTRACT Fire is an integral part of southern African savannas, but despite being well-studied, complex relationships among fire, humans, climate and ecological systems remain poorly understood across much of the region. Analyses that provide information on fire trends in diverse regional contexts are essential for informing fire management and monitoring change. Harmonic seasonal patterns, linear time-series trends and breakpoints in fire occurrence (BFAST) were analysed for 2001–2018 in Botswana using remotely sensed fire occurrence measurements. Regional classification schemes were organized by human land-use, annual precipitation zones and vegetation communities. At the regional scale, mean annual precipitation, land-use and vegetation type influenced fire occurrence magnitude. Seasonality and variability were most clearly organized according to mean annual precipitation. Variability in seasonal and long-term fire trends were observed across the different classification schemes apart from mean annual precipitation zones above 600 mm. The methodology used effectively identified key differences in fire variability across regional classification schemes. However, the spatial resolution and classification scheme may be less effective for human land use and small fires. Overall, MODIS fire data analysed with BFAST is a promising and accessible method for analysing regional savanna fire regimes.
Interoperable Private Attribution: A Distributed Attribution and Aggregation Protocol

Measuring people’s interactions that span multiple websites can provide unique insight that enables better products and improves people’s experiences, but directly observing people’s individual journeys creates privacy risks that conflict with the newly emerging privacy model for the web. We propose a protocol that uses the combination of multi-party computation and differential privacy that enables the processing of peoples’ data such that only aggregate measurements are revealed, strictly limiting the information leakage about individual people. Our primary application of this protocol is measuring, in aggregate, the effectiveness of digital advertising without enabling cross-site tracking of individuals. In this paper we formalize our protocol, Interoperable Private Attribution (IPA), and analyze its security. IPA is proposed in the W3C’s Private Advertising Technology Community Group (PATCG) [8]. We have implemented our protocol in the malicious honest majority MPC setting for three parties where network costs dominate compute costs. For processing a query with 1M records it uses around 18GB of network which at $0.08 per GB leads to a network cost of $1.44.
Ruffle: Rapid 3-party shuffle protocols

Secure shuffle is an important primitive that finds use in several applications such as secure electronic voting, oblivious RAMs, secure sorting, to name a few. For time-sensitive shuffle-based applications that demand a fast response time, it is essential to design a fast and efficient shuffle protocol. In this work, we design secure and fast shuffle protocols relying on the techniques of secure multiparty computation. We make several design choices that aid in achieving highly efficient protocols. Specifically, we consider malicious 3-party computation setting with an honest majority and design robust ring-based protocols. Our shuffle protocols provide a fast online (i.e., input-dependent) phase compared to the state-of-the-art for the considered setting. To showcase the efficiency improvements brought in by our shuffle protocols, we consider two distinct applications of anonymous broadcast and secure graph computation via the GraphSC paradigm. In both cases, multiple shuffle invocations are required. Hence, going beyond standalone shuffle invocation, we identify two distinct scenarios of multiple invocations and provide customised protocols for the same. Further, we showcase that our customized protocols not only provide a fast response time, but also provide improved overall run time for multiple shuffle invocations. With respect to the applications, we not only improve in terms of efficiency, but also work towards providing improved security guarantees, thereby outperforming the respective state-of-the-art works. We benchmark our shuffle protocols and the considered applications to analyze the efficiency improvements with respect to various parameters.
Evidence for a high-density amorphous form in indomethacin from Raman scattering investigations

Pressure-induced transformation of $\ensuremath{\gamma}$-IMC [1-($p$-chlorobenzoyl)-5-methoxy-2-methylindole-3-acetic acid] is analyzed from Raman scattering investigations in the low-frequency range of $10\char21{}250\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$ and the high frequency region between 1550 and $1750\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$, where $\mathrm{C}\mathrm{O}$ stretching vibrations are usually observed. At room temperature, by pressurization from atmospheric pressure up to $4\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$, $\ensuremath{\gamma}$-IMC undergoes a collapse transformation into a high-pressure crystalline form, induced by large rearrangement in the hydrogen-bonded network associated with molecular conformational changes. The Raman spectrum of the high-pressure crystal is similar to that of the $\ensuremath{\alpha}$ form, which is denser than the $\ensuremath{\gamma}$ form and metastable with respect to $\ensuremath{\gamma}$-IMC at atmospheric pressure. Upon further compression a solid-state amorphization is observed via the breakdown of hydrogen bonds. The Raman line shape of the high-pressure amorphous form is different from that of the vitreous state (or thermal glass obtained by quenching the liquid), suggesting the existence of a high-density amorphous state. By release of pressure, this high-density amorphous state transforms into the thermal glass. This transformation can be interpreted as a transformation between a high-density amorphous to a low-density amorphous state, which could be associated with a polyamorphic transformation.