Miracle-dz/UniFAR-FTUs huggingface dataset:
Dilemmas in generic delimitation of Senegalia and allies (Caesalpinioideae, mimosoid clade): how to reconcile phylogenomic evidence with morphology and taxonomy?

Abstract Senegalia comprises 219 species distributed in tropical and subtropical regions of North and South America, Africa, Asia and Australia. Two sections are currently recognised within Senegalia and these are most readily distinguished by the differences in disposition of their cauline prickles, i.e. sect. Senegalia with prickles at or near leaf nodes and sect. Monacanthea with mostly internodal prickles. Previous phylogenetic studies, based primarily on small numbers of plastid DNA loci, found Senegalia to be monophyletic with two large subclades corresponding to the sections. Here, we present new phylogenomic evidence from 997 single-copy nuclear gene sequences for a small, but representative set of species. These new analyses show that Senegalia is non-monophyletic, but instead, forms a grade that is paraphyletic with respect to the remainder of the ingoid clade (i.e. Ingeae + Acacia s.s. + Acaciella), comprising two well-supported subclades most likely representing the same clades as found in previous phylogenetic studies of the genus and, interspersed between these, a third, moderately supported clade, comprising the genera Mariosousa, Pseudosenegalia and Parasenegalia. In marked contrast to the nuclear phylogeny, the two Senegalia clades are sister groups in the plastid phylogeny, based on analyses of 72 chloroplast genes, rendering the genus monophyletic, based on plastid data alone. We discuss this new evidence that Senegalia is non-monophyletic in relation to the marked cytonuclear discordance, high gene tree conflict and lack of resolution across this senegalioid grade and review the consistency of the key morphological characters distinguishing the two sections of Senegalia. We conclude that it is likely that Senegalia will need to be split into two (or possibly more) genera: a re-circumscribed Senegalia s.s. that corresponds to the existing Senegaliasect.Senegalia plus the S.ataxacantha group (Senegaliasect.Monacanthea s.s.; future studies may show that this group warrants generic status) and a new genus corresponding to the remainder of sect. Monacanthea (here designated as Senegaliasect.Monacanthea p.p.). However, re-delimiting Senegalia now would be premature given that the key morphological characters are not fully congruent with the two sections and pending denser phylogenetic sampling of taxa. A judiciously selected list of critical taxa is presented to facilitate future phylogenomic studies. Finally, we discuss the identity of Albizialeonardii, which is also placed in this senegalioid grade in these new phylogenomic analyses and place it in synonymy with Parasenegaliavogeliana.
VISCOUS VORTEX FLOW IN SUPERCONDUCTORS WITH PARAMAGNETIC IMPURITIES.

An expression for the conductivity of a vortex lattice in fields H << Hc 2 is obtained on the basis of the nonstationary equations for superconductors with paramagnetic impurities. The case of high temperatures (small paramagnetic impurity concentrations) leads effectively to a conductivity greater than in the low temptlrature region. This agrees qualitatively with the experiments with ordinary alloys. Macroscopic electrodynamics equations are written down for vortex-structure superconductors.
The Occurrence and Co-Occurrence of Regulated, Emerging, and Masked Mycotoxins in Rice Bran and Maize from Southeast Asia

Raw feed materials are often contaminated with mycotoxins, and co-occurrence of mycotoxins occurs frequently. A total of 250 samples i.e., rice bran and maize from Cambodia, Laos, Myanmar, and Thailand were analysed using state-of-the-art liquid chromatography-mass spectrometry (LC-MS/MS) for monitoring the occurrence of regulated, emerging, and masked mycotoxins. Seven regulated mycotoxins – aflatoxins, ochratoxin A, fumonisin B1, deoxynivalenol, zearalenone, HT-2, and T-2 toxin were detected as well as some emerging mycotoxins, such as beauvericin, enniatin type B, stachybotrylactam, sterigmatocystin, and masked mycotoxins, specifically zearalenone-14-glucoside, and zearalenone-16-glucoside. Aspergillus and Fusarium mycotoxins were the most prevalent compounds identified, especially aflatoxins and fumonisin B1 in 100% and 95% of samples, respectively. Of the emerging toxins, beauvericin and enniatin type B showed high occurrences, with more than 90% of rice bran and maize contaminated, whereas zearalenone-14-glucoside and zearalenone-16-glucoside were found in rice bran in the range of 56–60%. Regulated mycotoxins (DON and ZEN) were the most frequent mycotoxin combination with emerging mycotoxins (BEA and ENN type B) in rice bran and maize. This study indicates that mycotoxin occurrence and co-occurrence are common in raw feed materials, and it is critical to monitor mycotoxin levels in ASEAN’s feedstuffs so that mitigation strategies can be developed and implemented.
Time Series: Applications to Finance with R and S-Plus

List of Figures. List of Tables. Preface. Preface to the First Edition. 1 Introduction. 1.1 Basic Description. 1.2 Simple Descriptive Techniques. 1.3 Transformations. 1.4 Example. 1.5 Conclusions. 1.6 Exercises. 2 Probability Models. 2.1 Introduction. 2.2 Stochastic Processes. 2.3 Examples. 2.4 Sample Correlation Function. 2.5 Exercises. 3 Autoregressive Moving Average Models. 3.1 Introduction. 3.2 Moving Average Models. 3.3 Autoregressive Models. 3.4 ARMA Models. 3.5 ARIMA Models. 3.6 Seasonal ARIMA. 3.7 Exercises. 4 Estimation in the Time Domain. 4.1 Introduction. 4.2 Moment Estimators. 4.3 Autoregressive Models. 4.4 Moving Average Models. 4.5 ARMA Models. 4.6 Maximum Likelihood Estimates. 4.7 Partial ACF. 4.8 Order Selections. 4.9 Residual Analysis. 4.10 Model Building. 4.11 Exercises. 5 Examples in SPLUS and R. 5.1 Introduction. 5.2 Example 1. 5.3 Example 2. 5.4 Exercises. 6 Forecasting. 6.1 Introduction. 6.2 Simple Forecasts. 6.3 Box and Jenkins Approach. 6.4 Treasury Bill Example. 6.5 Recursions. 6.6 Exercises. 7 Spectral Analysis. 7.1 Introduction. 7.2 Spectral Representation Theorems. 7.3 Periodogram. 7.4 Smoothing of Periodogram. 7.5 Conclusions. 7.6 Exercises. 8 Nonstationarity. 8.1 Introduction. 8.2 Nonstationarity in Variance. 8.3 Nonstationarity in Mean: Random Walk with Drift. 8.4 Unit Root Test. 8.5 Simulations. 8.6 Exercises. 9 Heteroskedasticity. 9.1 Introduction. 9.2 ARCH. 9.3 GARCH. 9.4 Estimation and Testing for ARCH. 9.5 Example of Foreign Exchange Rates. 9.6 Exercises. 10 Multivariate Time Series. 10.1 Introduction. 10.2 Estimation of mu and GAMMA. 10.3 Multivariate ARMA Processes. 10.4 Vector AR Models. 10.5 Example of Inferences for VAR. 10.6 Exercises. 11 State Space Models. 11.1 Introduction. 11.2 State Space Representation. 11.3 Kalman Recursions. 11.4 Stochastic Volatility Models. 11.5 Example of Kalman Filtering of Term Structure. 11.6 Exercises. 12 Multivariate GARCH. 12.1 Introduction. 12.2 General Model. 12.3 Quadratic Form. 12.4 Example of Foreign Exchange Rates. 12.5 Conclusions. 12.6 Exercises. 13 Cointegrations and Common Trends. 13.1 Introduction. 13.2 Definitions and Examples. 13.3 Error Correction Form. 13.4 Granger's Representation Theorem. 13.5 Structure of Cointegrated Systems. 13.6 Statistical Inference for Cointegrated Systems. 13.7 Example of Spot Index and Futures. 13.8 Conclusions. 13.9 Exercises. 14 Markov Chain Monte Carlo Methods. 14.1 Introduction. 14.2 Bayesian Inference. 14.3 Markov Chain Monte Carlo. 14.4 Exercises. 15 Statistical Arbitrage. 15.1 Introduction. 15.2 Pairs Trading. 15.3 Cointegration. 15.4 Simple Pairs Trading. 15.5 Cointegrations and Pairs Trading. 15.6 Hang Seng Index Components Example. 15.7 Exercises. 16 Answers to Selected Exercises. 16.1 Chapter 1. 16.2 Chapter 2. 16.3 Chapter 3. 16.4 Chapter 4. 16.5 Chapter 5. 16.6 Chapter 6. 16.7 Chapter 7. 16.8 Chapter 8. 16.9 Chapter 9. 16.10 Chapter 10. 16.11 Chapter 11. 16.12 Chapter 12. 16.13 Chapter 13. 16.14 Chapter 14. 16.15 Chapter 15. References. Subject Index. Author Index.
Estimation of intrinsic and extrinsic capacitances of graphene self-switching diode using conformal mapping technique

Due to a very high carrier concentration and low band gap, graphene based self-switching diodes do not demonstrate a very high rectification ratio. Despite that, it takes the advantage of graphene’s high carrier mobility and has been shown to work at very high microwave frequencies. However, the AC component of these devices is hidden in the very linear current–voltage characteristics. Here, we extract and quantitatively study the device capacitance that determines the device nonlinearity by implementing a conformal mapping technique. The estimated value of the nonlinear component or curvature coefficient from DC results based on Shichman–Hodges model predicts the rectified output voltage, which is in good agreement with the experimental RF results.
A Localized and Minimally Invasive Tumor Treatment Based on a Frequency Adjustable Microwave Ablation Method

As a minimally invasive surgery, microwave ablation (MWA) has been widely used in tumor treatment. However, the electromagnetic properties of tissue will change with temperature during operation, which may lead to unstable performance or even failure of the antenna. In this paper, we preliminarily verified the feasibility of improving the stability of microwave ablation antenna by adjusting the frequency. Experimental results show that the ablation zone is change form 16 mm × 40 mm to 20 mm × 35 mm with frequency adjustment, showing larger and more localized ablation zone. In addition, the $S_{11}$ keeps remaining lower than −10dB during the operation, while the $S_{11}$ at 2.45 GHz without frequency adjustment is expanded to −8.5dB at the end of the experiment.
Usability of Two New Interactive Game Sensor-Based Hand Training Devices in Parkinson’s Disease

This pilot cross-sectional study aimed to evaluate the usability of two new interactive game sensor-based hand devices (GripAble and Smart Sensor Egg) in both healthy adults as well as in persons with Parkinson’s Disease (PD). Eight healthy adults and eight persons with PD participated in this study. Besides a standardised usability measure, the state of flow after one training session and the effect of cognitive abilities on flow were evaluated. High system usability scores (SUS) were obtained both in healthy participants (72.5, IQR = 64.375–90, GripAble) as well as persons with PD (77.5, IQR = 70–80.625, GripAble; 77.5, IQR = 75–82.5, Smart Sensor Egg). Similarly, high FSSOT scores were achieved after one training session (42.5, IQR = 39.75–50, GripAble; 50, IQR = 47–50, Smart Sensor Egg; maximum score 55). Across both groups, FSSOT scores correlated significantly with SUS scores (r = 0.52, p = 0.039). Finally, MoCA did not correlate significantly with FSSOT scores (r = 0.02, p = 0.9). The present study shows high usability for both interactive game sensor-based hand training devices, for persons with PD and healthy participants.
A Bombyx mori Infection Model for Screening Antibiotics against Staphylococcus epidermidis

Simple Summary The use and misuse of antibiotics in the past decades have contributed to the wide spread of antibiotic resistance, which currently represents a major issue and threat to human health. Consequently, the discovery of new anti-infective molecules is of primary importance. In vivo studies are crucial for testing the efficacy of novel antibiotics. Invertebrate models look promising to reduce the large-scale use of mammalians, which is mainly limited by high costs and ethical concerns. In this scenario, the silkworm proved to be an interesting alternative among insects. Here, we developed a silkworm infection model by challenging the larvae with Staphylococcus epidermidis, one common cause of infections in hospitals, and assessing the curative effects of three life-saving glycopeptide antibiotics that are used to treat infections caused by multidrug-resistant Gram-positive pathogens. Abstract The increasing number of microorganisms that are resistant to antibiotics is prompting the development of new antimicrobial compounds and strategies to fight bacterial infections. The use of insects to screen and test new drugs is increasingly considered a promising tool to accelerate the discovery phase and limit the use of mammalians. In this study, we used for the first time the silkworm, Bombyx mori, as an in vivo infection model to test the efficacy of three glycopeptide antibiotics (GPAs), against the nosocomial pathogen Staphylococcus epidermidis. To reproduce the human physiological temperature, the bacterial infection was performed at 37 °C and it was monitored over time by evaluating the survival rate of the larvae, as well the response of immunological markers (i.e., activity of hemocytes, activation of the prophenoloxidase system, and lysozyme activity). All the three GPAs tested (vancomycin, teicoplanin, and dalbavancin) were effective in curing infected larvae, significantly reducing their mortality and blocking the activation of the immune system. These results corroborate the use of this silkworm infection model for the in vivo studies of antimicrobial molecules active against staphylococci.
The latency validation of the optical link for the ATLAS Liquid Argon Calorimeter Phase-I trigger upgrade

Two optical data link data transmission Application Specific Integrated Circuits (ASICs), the baseline and its backup, have been designed for the ATLAS Liquid Argon (LAr) Calorimeter Phase-I trigger upgrade. The latency of each ASIC and that of its corresponding receiver implemented in a back-end Field-Programmable Gate Array (FPGA) are critical specifications. In this paper, we present the latency measurements and simulation of two ASICs. The measurement results indicate that both ASICs achieve their design goals and meet the latency specifications. The consistency between the simulation and measurements validates the ASIC latency characterization.
End-to-End Neural Network for Autonomous Steering using LiDAR Point Cloud Data

Although numerous studies on end-to-end autonomous driving systems based on deep learning have been conducted, many of them used shallow feedforward neural networks, which are unsuitable for extracting useful information from complicated contexts and are mainly focused on video frames. This study investigates a LiDAR point cloud-based end-to-end autonomous steering problem in structured roads. The control command to the vehicle is focused on the steering angle of the wheel, which is discretized into continuous integers as the direction category. The problem is then converted into a classification task, which is a mapping connection between the original point cloud data and the driving direction category. On the basis of the PointNet++ framework, we propose using K-means, KNN, and weighted sampling, to perform the steering decision making. Using the CARLA simulation environment, we have shown that the proposed approach is performing effective autonomous decision making with a rate strictly higher than 91% while requiring less inference speed compared to benchmarks.
Energetics of vacancy segregation to symmetric tilt grain boundaries in hexagonal closed pack materials

Molecular static simulations of 190 symmetric tilt grain boundaries in hexagonal closed pack metals were used to understand the energetics of vacancy segregation, which is important for designing stable interfaces in harsh environments. Simulation results show that the local arrangements of grain boundaries and the resulting structural units have a significant influence on the magnitude of vacancy binding energies, and the site-to-site variation within each boundary is substantial. Comparing the vacancy binding energies for each site in different c/a ratio materials shows that the binding energy increases significantly with an increase in c/a ratio. For example, in the [12¯10] tilt axis, Ti and Zr with c/a = 1.5811 have a lower vacancy binding energy than the Mg with c/a = 1.6299. Furthermore, when the grain boundary energies of all 190 boundaries in all three elements are plotted against the vacancy binding energies of the same boundaries, a highly negative correlation (r = −0.7144) is revealed that has .
A Newly Isolated Alcaligenes faecalis ANSA176 with the Capability of Alleviating Immune Injury and Inflammation through Efficiently Degrading Ochratoxin A

Ochratoxin A (OTA) is one of the most prevalent mycotoxins that threatens food and feed safety. Biodegradation of OTA has gained much attention. In this study, an Alcaligenes faecalis strain named ANSA176, with a strong OTA-detoxifying ability, was isolated from donkey intestinal chyme and characterized. The strain ANSA176 could degrade 97.43% of 1 mg/mL OTA into OTα within 12 h, at 37 °C. The optimal levels for bacterial growth were 22–37 °C and pH 6.0–9.0. The effects of ANSA176 on laying hens with an OTA-contaminated diet were further investigated. A total of 36 laying hens were assigned to three dietary treatments: control group, OTA (250 µg/kg) group, and OTA + ANSA176 (6.2 × 108 CFU/kg diet) group. The results showed that OTA decreased the average daily feed intake (ADFI) and egg weight (EW); meanwhile, it increased serum alanine aminopeptidase (AAP), leucine aminopeptidase (LAP), β2-microglobulin (β2-MG), immunoglobulin G (IgG), tumor necrosis factor-α (TNF-α), and glutathione reductase (GR). However, the ANSA176 supplementation inhibited or attenuated the OTA-induced damages. Taken together, OTA-degrading strain A. faecalis ANSA176 was able to alleviate the immune injury and inflammation induced by OTA.
Comparative analysis of physico-chemical properties and fatty acid composition of linseed (Linum usitatissimum L.) oils of Indian accessions

The aim of the current study was to investigate the variation in oil content, fatty acid composition, and physico- chemical characteristics of different accessions of linseed oil ( Linum usitatissimum L.). Significant variations in fatty acid composition, oil content and physico-chemical properties were observed in linseed accessions, among them, unsaturated and saturated fatty acid compositions were ranged from 79.23–86.66% to 12.61–19.99%, respectively, in total fatty acid compositions. The highest content of alpha-linolenic acid (ALA) was found to be major in BHU-A (53.39%) accession followed by BHU-B (53.14%) accessions, whereas the lowest one was found in the accession IC 564631 (38.07%). The current investigation found varying results for the physico-chemical characteristics of linseed oil, such as Iodine value (173.39–178.83 g Iodine/100 g), acid value (2.10–3.04 mg KOH/g), saponification value (192.16–193.49 mg KOH/g), peroxide value (1.52–2.12 meq/Kg), refractive index (1.471–1.472 RI at 40°C), and viscosity (23.37–27.95 at 40°C (cSt)). The findings of our current investigation revealed that linseed oil is a valuable source of ALA which could be potential applications in the food and pharmaceutical industries. Therefore, comparative and characterization analysis of different linseed accessions aids in selecting a good quality linseed oil and provides new breeding resources for linseed accessions.
Hydroxychloride‐Bearing Fluid Inclusions in Ultramafic Rocks From New Caledonia: Implications for Serpentinization in Saline Environments on Earth and Beyond

Serpentinization produces H2 and synthesizes CH4 that can support nonphotosynthetic habitability on Earth and possibly beyond. Although fluids on Earth and beyond that may participate in serpentinization are extensively saline with elevated levels of chlorine, chloride minerals are generally not considered to be a crucial component of serpentinization. In this study, we report the formation of kuliginite, a recently discovered hydroxychloride mineral with the ideal formula of Fe3Mg(OH)6Cl2, during internal serpentinization within olivine‐hosted fluid inclusions in ultramafic rocks from New Caledonia, southwest Pacific. It is inferred that kuliginite may form during serpentinization by Cl‐rich saline fluids under certain conditions on celestial bodies, which is largely unrevealed due to our insufficient knowledge about kuliginite. As a mineral containing ∼57 wt. % FeO that is mainly ferrous, kuliginite, even in minor amounts, may play an important role in iron partitioning during serpentinization, with a great influence on the production of H2 and synthesis of CH4. In a word, stabilization of kuliginite retards iron oxidation, whereas further hydration of kuliginite supplements canonical pathways of iron oxidation. In addition, as a hydroxychloride, kuliginite may have a significant weight in the chlorine budget of serpentinite. Therefore, kuliginite in the serpentinized fluid inclusions presented in this study may have general implications for serpentinization in certain saline environments on Earth and beyond, which needs to be further explored in the future.
Mixing time and cutoff for the adjacent transposition shuffle and the simple exclusion

In this paper, we investigate the mixing time of the adjacent transposition shuffle for a deck of cards. We prove that around time N^2\log N/(2\pi^2), the total-variation distance to equilibrium of the deck distribution drops abruptly from 1 to 0, and that the separation distance has a similar behavior but with a transition occurring at time (N^2\log N)/\pi^2. This solves a conjecture formulated by David Wilson. We present also similar results for the exclusion process on a segment of length N with k particles.
Human Pulmonary Tuberculosis: Understanding the Immune Response in the Bronchoalveolar System

Mycobacterium tuberculosis, the causal agent of one of the most devastating infectious diseases worldwide, can evade or modulate the host immune response and remain dormant for many years. In this review, we focus on identifying the local immune response induced in vivo by M. tuberculosis in the lungs of patients with active tuberculosis by analyzing data from untouched cells from bronchoalveolar lavage fluid (BALF) or exhaled breath condensate (EBC) samples. The most abundant resident cells in patients with active tuberculosis are macrophages and lymphocytes, which facilitate the recruitment of neutrophils. The cellular response is characterized by an inflammatory state and oxidative stress produced mainly by macrophages and T lymphocytes. In the alveolar microenvironment, the levels of cytokines such as interleukins (IL), chemokines, and matrix metalloproteinases (MMP) are increased compared with healthy patients. The production of cytokines such as interferon (IFN)-γ and IL-17 and specific immunoglobulin (Ig) A and G against M. tuberculosis indicate that the adaptive immune response is induced despite the presence of a chronic infection. The role of epithelial cells, the processing and presentation of antigens by macrophages and dendritic cells, as well as the role of tissue-resident memory T cells (Trm) for in situ vaccination remains to be understood.
Beliefs-Preferences Gauge Symmetry and Dynamic Replication in a General Market Environment

Although symmetries play a major role in physics, their use in finance is relatively new and, to the best of our knowledge, can be traced to 1995 when Kholodnyi introduced the beliefs-preferences gauge symmetry. One of the main outcomes of the beliefs-preferences gauge symmetry is that it allows for the valuation and dynamic replication of contingent claims in a general market environment, that is, in the case of a general, not necessarily diffusion Markov process for the prices of underlying securities. This valuation and dynamic replication is based on the novel ideas of symmetry in contrast to the standard approach which uses stochastic calculus. The practical applications of the beliefs-preferences gauge symmetry range from the detection of a new type of true arbitrage to the beliefs-preferences independent valuation and dynamic replication of contingent claims in a general market environment.