Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated microbiome and metabolomics analysis reveal a closer relationship between soil metabolites and bacterial community than fungal community in pecan plantations

Understanding soil metabolic diversity and the chemical signals that shape rhizosphere microbial activity is important for protecting plants and improving forest productivity. At present, little information is known about the metabolites in the rhizosphere soil of pecan (Carya illinoinensis) plantation. Based on technologies of untargeted metabolomics and high‐throughput sequencing, we investigated differences in the metabolic profiles of rhizosphere and bulk soils and the relationship between metabolites and microorganisms in pecan plantations. The results showed that the abundance of metabolites in rhizosphere soil was significantly higher than that in bulk soil (p < 0.05), especially reflected in plant secondary metabolites and lipids. Orientaloside and marmesin rutinoside were significantly enriched in rhizosphere soil metabolites of pecan at three pecan ages (VIP >1, p < 0.05). The linoleic acid and α‐linolenic acid metabolic pathways were significantly enriched in the differential metabolic set (p < 0.01). In addition, tryptophan metabolism, starch and sucrose metabolism, and galactose metabolism were also important factors affecting the rhizosphere metabolic spectrum. Differential metabolites between bulk and rhizosphere soils were more closely associated with bacteria than with fungal communities, particularly in young pecans. With the increasing age of pecans, new significant enrichment of plant secondary metabolites such as cyanidin, 3‐trans‐caffeoyltormentic acid, N‐(1‐Deoxy‐1‐fructosyl) serine and piperdia emerged in the rhizosphere soil. 3‐trans‐caffeoyltormentic acid was positively related to Saitozyma and Protoglossum. Phenylacetaldehyde was positively correlated with Gaiellaceae, Tausonia, and Tuber. This study provides new insights into the mechanisms of interaction between pecans and microorganisms.
Wave radiation and wave diffraction from a submerged body in a uniform current

Radiation and diffraction of free-surface waves due to a submerged body in a uniform current is considered. The fluid layer is infinitely deep and the motion is two-dimensional. Applying the method of integral equations, the radiation problem and the diffraction problem for a submerged circular cylinder are examined. For small speed U of the current a forced motion of a given frequency will give rise to four waves. It is shown, however, that, for a circular cylinder, an incoming harmonic wave gives rise to two waves only. Depending on the frequency, the new generated wave may be considered as a transmitted or a reflected wave. The mean second-order force is computed. For the radiation problem the first-order damping force is also obtained. It is shown that, for some values of the parameters, the damping force is negative. This result is closely related to the fact that a harmonic wave travelling upstream with a phase velocity less than U conveys negative energy downstream. The forces remain finite as Uσ/g (σ ≡ the frequency, g ≡ the acceleration due to gravity) approaches ¼.
Secure formation control for resilient multi‐agent cyber‐physical systems under DoS attacks and faults

A distributed cyber‐security and fault tolerance formation problem is considered in this paper. This is done though a multi‐agent system in which all agents concentrate on a formation reference function and accomplish a desired time‐varying formation even in the presence of malicious attacks and multiple faults. To achieve the resilient control task, a distributed control protocol using an event‐triggered technique and active reconfigurable strategy is proposed in the face of adverse effects for the overall system. When denial of service is launched by adversaries, the attack parameters are bounded by analyzing the Lyapunov stability theorem and the property of the Laplacian matrix. To improve the capability of fault‐tolerance, an observer‐based fault estimator is used to calculate fault values. The simulation results validate that the presented scheme can perfectly address the distributed formation issue with faults over attack intervals.
Genetic Characteristics and Long-Term Follow-Up of Slovenian Patients with RPGR Retinal Dystrophy

Genetic characteristics and a long-term clinical follow-up of 18 Slovenian retinitis pigmentosa GTPase regulator (RPGR) patients from 10 families with retinitis pigmentosa (RP) or cone/cone-rod dystrophy (COD/CORD) are reported. RP (eight families) was associated with two already known (p.(Ser407Ilefs*46) and p.(Glu746Argfs*23)) and five novel variants (c.1245+704_1415-2286del, p.(Glu660*), p.(Ala153Thr), c.1506+1G>T, and p.(Arg780Serfs*54)). COD (two families) was associated with p.(Ter1153Lysext*38). The median age of onset in males with RP (N = 9) was 6 years. At the first examination (median age of 32 years), the median best corrected visual acuity (BCVA) was 0.30 logMAR, and all patients had a hyperautofluorescent ring on fundus autofluorescence (FAF) encircling preserved photoreceptors. At the last follow-up (median age of 39 years), the median BCVA was 0.48 logMAR, and FAF showed ring constriction transitioning to patch in 2/9. Among females (N = 6; median age of 40 years), two had normal/near-normal FAF, one had unilateral RP (male pattern), and three had a radial and/or focal pattern of retinal degeneration. After a median of 4 years (4–21) of follow-up, 2/6 exhibited disease progression. The median age of onset in males with COD was 25 years. At first examination (median age of 35 years), the median BCVA was 1.00 logMAR, and all patients had a hyperautofluorescent FAF ring encircling foveal photoreceptor loss. At the last follow-up (median age of 42 years), the median BCVA was 1.30 logMAR, and FAF showed ring enlargement. The majority of the identified variants (75%; 6/8) had not been previously reported in other RPGR cohorts, which suggested the presence of distinct RPGR alleles in the Slovenian population.
Marginalized, silenced, and struggling: Understanding the plights of Chinese graduate teaching assistants

Pursuing equity and diversity on internationalized higher education campuses has become an urgent agenda. Chinese Graduate Teaching Assistants (GTAs) do not always have smooth experiences with this internationalization. While they are often overlooked in racial discussion in the U.S., they cannot escape the racial and cultural inequalities in the same context. Using Bronfenbrenner’s bioecological systems (2005) and Lee’s neo-racism (2020) as analytical lenses, this study revealed the racial and cultural challenges experienced by 21 Chinese at micro-, meso-, exo-, macro-, and chrono-levels. The study helps educators charged with the complexity of Chinese GTAs’ plights by considering contextual influences using critical concepts (e.g., neo-racism). This study is significant in addressing unique equity and diversity issues in globalized higher education using both phenomenological and critical perspectives. Finally, we call for actions on the part of higher education institutions to create more equitable and caring systems to improve all students’ academic and sociocultural experiences.
A numerical comparison of several unconditional exact tests in problems of equivalence based on the difference of proportions

In order to compare two independent proportions (p 1 and p 2) there are several useful tests for the parameter d=p 2−p 1:H SG:d≤δ vs. K SG:d>δ, H SG2:d=δ vs. K SG2:d≠δ (where−1Δ (where Δ≥0) and H PE:|d|≥Δ vs. K PE:|d|0). The exact unconditional test requires an ordering statistic, which is usually the z-pooled statistic, to be defined. The paper gives the definition of 10 new ordering statistics with a similar computational time, and compares the number of points which each introduces into the critical region obtained to error α=5%. The article reaches the conclusion that the most generally powerful statistics are: the z-pooled one with a small continuity correction (c=1/N if n 1≠n 2 or c=2/N if n 1=n 2, where N={n 1+1} {n 2+1} and n i are the sample sizes) and those z-pooled with Yates’ continuity correction (c={n 1+n 2}/{2n 1 n 2} ). In the paper the authors also show that Barnard's two classic convexity conditions are redundant, because when one of them is verified the other is also verified. The programs for these tests may be obtained free of charge from the site http://www.ugr. es/local/bioest/software.htm.
Association of Systemic Immune Inflammation Index with Estimated Pulse Wave Velocity, Atherogenic Index of Plasma, Triglyceride-Glucose Index, and Cardiovascular Disease: A Large Cross-Sectional Study

In the U.S. general population, there is a lack of understanding regarding the association between the systemic immune inflammation (SII) index and estimated pulse wave velocity (ePWV), atherogenic index of plasma (AIP), and triglyceride-glucose (TyG) index and cardiovascular disease (CVD). As a result, the objective of our research was to investigate the association between the SII index and ePWV, AIP, and TyG index and incident CVD. We used the National Health and Nutrition Examination Survey (NHANES) data from 1999 to 2018 to conduct this study. The correlation between the SII index and ePWV, AIP, and TyG index was examined using generalized additive models with smooth functions. In addition, the association between SII index and triglyceride (TC), high-density lipoprotein cholesterol (HDL-C), and fast glucose (FBG) also were explored. Finally, we further performed multivariable logistic regression analysis, restricted cubic spline (RCS) plots, and subgroup analysis to study the connection between the SII index and CVD. Our analysis included 17389 subjects from the NHANES database. A substantial positive association existed between SII, WV, and the TyG index. In addition, with the increase of the SII index, AIP showed a trend of decreasing first, then rising, and then decreasing. The SII index was inversely and linearly associated with triglyceride (TG), while positively and linearly associated with fast glucose (FBG). However, high-density lipoprotein cholesterol (HDL-C) had a tendency of first declining, then climbing, and finally falling with the rise in the SII index. After adjusting for potential confounders, compared with the lowest quartiles, the odds ratios with 95% confidence intervals for CVD across the quartiles were 0.914 (0.777, 1.074), 0.935 (0.779, 1.096), and 1.112 (0.956, 1.293) for SII index. The RCS plot showed an inverse U-shaped curve relationship between the SII index and CVD. Overall, this study found a strong correlation between a higher SII index and ePWV and the TyG index. Additionally, these cross-sectional data also revealed a U-shaped connection between the SII index and CVD.
Stochastic factorizations, sandwiched simplices and the topology of the space of explanations

We study the space of stochastic factorizations of a stochastic matrix V, motivated by the statistical problem of hidden random variables. We show that this space is homeomorphic to the space of simplices sandwiched between two nested convex polyhedra, and use this geometrical model to gain some insight into its structure and topology. We prove theorems describing its homotopy type, and, in the case where the rank of V is 2, we give a complete description, including bounds on the number of connected components, and examples in which these bounds are attained. We attempt to make the notions of topology accessible and relevant to statisticians.
Tillage with straw incorporation reduces the optimal nitrogen rate for maize production by affecting crop uptake, utility efficiency, and the soil balance of nitrogen

Understanding the combined effects of tillage and straw incorporation on grain yield and nitrogen (N) fertilizer utilization is vital for sustainable agriculture in northeastern China. How various tillage patterns with straw incorporation affect soil N balance and optimal N rate for crop production remains largely unknown. A four‐year (2015–2018) field experiment was conducted to assess the impact of rotary tillage with maize straw incorporation (RTS) and plough tillage with straw incorporation (PTS) combined with different N fertilizer rates (0, 112, 187, 262, and 337 kg N ha−1) on maize yield, N uptake, soil N balance, nitrogen use efficiency, and optimal N rate. In general, higher straw N uptake and lower N partial factor productivity, N use efficiency, and recovery of applied N in grains were obtained under PTS than under RTS. Moreover, grain yield and both straw and grain N uptake increased with the N application rate. However, no further increase in grain yield was observed when the applied N exceeded 187 kg N ha−1. PTS resulted in a higher level of unaccounted N from applied N fertilizer (38–81 kg N ha−1) than RTS. A high N fertilizer input (>262 kg N ha−1) combined with straw incorporation resulted in a high soil mineral N profit and substantially increased unaccounted N (614–715 kg N ha−1) over the four‐year field trial period. The optimal N input required for the highest maize yield could be reduced by 35.0%–44.6% using tillage with straw return. Nevertheless, PTS was more effective than RTS at lowering the optimal N application rate. Overall, the results of this short‐term maize field study conducted in northeastern China suggest that the amount of N fertilizer input required for maize production could be reduced by using tillage with continuous straw incorporation.
Nuclear accent F0 peak location: Effects of rate, vowel, and number of following syllables

Reported here are results from an investigation of the alignment of speech segments with the fundamental frequency (F0) contour at the end of an intonational phrase. Findings suggest that the F0 peak on the main sentence stress (nuclear stress) occurs at some proportion of the length of the vowel, instead of at a fixed distance into the vowel. The vowel may be shortened by a faster speaking rate, an intrinsically shorter vowel, and added post‐nuclear syllables. The F0 peak delay, however, is shortened by faster speaking rate and intrinsically shorter vowels, but lengthened or unaffected by added syllables. Thus vowel length and post‐nuclear syllables interact to determine the location of the F0 peak.
An Overview of Human Anti-HIV-1 Neutralizing Antibodies against Diverse Epitopes of HIV-1

In this Review, we have addressed some recent developments in the discovery and applications of anti-human immunodeficiency virus type− 1 (HIV−1) broadly neutralizing antibodies (bnAbs) isolated from infected adults and children. The recent developments in human antibody isolation technologies have led to the discovery of several highly potent anti-HIV-1 bnAbs. Herein, we have discussed the characteristics of recently identified bnAbs directed at distinct epitopes of HIV-1, in addition to the existing antibodies, from adults and children and have shed light on the benefits of multispecific HIV-1 bnAbs and their role in the design of polyvalent vaccines.
Re-entrant corner flows of Oldroyd-B fluids

The method of matched asymptotic expansions is used to construct solutions for the planar steady flow of Oldroyd-B fluids around re-entrant corners of angles π/α (1/2≤α<1). Two types of similarity solutions are described for the core flow away from the walls. These correspond to the two main dominant balances of the constitutive equation, where the upper convected derivative of stress either dominates or is balanced by the upper convected derivative of the rate of strain. The former balance gives the incompressible Euler or inviscid flow equations and the latter balance the incompressible Navier–Stokes equations. The inviscid flow similarity solution for the core is that first derived by Hinch (Hinch 1993 J. Non-Newtonian Fluid Mech. 50, 161–171) with a core stress singularity that depends upon the corner angle and radial distance as O(r−2(1−α)) and a velocity behaviour that vanishes as O(rα(3−α)−1). Extending the analysis of Renardy (Renardy 1995 J. Non-Newtonian Fluid Mech. 58, 83–39), this outer solution is matched to viscometric wall behaviour for both upstream and downstream boundary layers. This structure is shown to hold for the majority of the retardation parameter range. In contrast, the similarity solution associated with the Navier–Stokes equations has a velocity behaviour O(rλ) where λ∈(0,1) satisfies a nonlinear eigenvalue problem, dependent upon the corner angle and an associated Reynolds number defined in terms of the ratio of the retardation and relaxation times. This similarity solution is shown to hold as an outer solution and is matched into stress boundary layers at the walls which recover viscometric behaviour. However, the matching is restricted to values of the retardation parameter close to the relaxation parameter. In this case the leading order core stress is Newtonian with behaviour O(r−(1−λ)).
Bandwidth packing: a tabu search approach

The bandwidth packing (BWP) problem is a combinatorially difficult problem arising in the area of telecommunications. The problem consists of assigning calls to paths in a capacitated graph, such that capacities are not violated and the total profit is maximized. In this paper we discuss the development of a tabu search (TS) method for the BWP problem. The method makes use of an efficient implementation of the k-shortest path algorithm, that allows the identification of a controlled set of feasible paths for each call. A tabu search is then performed to find the best path assignment for each call. The TS method developed here incorporates a number of features that have proved useful for obtaining optimal and near optimal solutions to difficult combinatorial problems. We establish the effectiveness of our approach by comparing its performance in speed and solution quality to other specialized heuristics and to a standard optimization package applied to a 0-1 integer programming formulation of the problem.
Dissipation of Primordial Turbulence and Thermal History of the Universe

The assumption that in the early stage of the universe there existed turbulence of photons and plasma dragged by them can explain the formation of galaxies plausibly. Using simple expressions to represent the decay law of the primordial turbulence, the thermal history of gas at the pre-galactic stage is followed and the residual ionization degree of hydrogen is computed. It is found that maximum temperatures attainable are about 104 oK for a wide range of heating paramaters. This is because a kind of thermostat that keeps gas temperature below 104 OK operates: the increase of temperature above 10 4 oK is prevented by the increase of the ionization degree and the resultant increase of cooling rate. Therefore, it can be concluded that galaxies cannot be formed through the thermal instability due to the heating by the primordial turbulence.
Preference queries processing over imprecise data

With the increasing availability of various data sources, the preference queries are essential to find the relevant results to users. Several preference functions has been introduced in literature including: top-k [1], skylines [2], distributed skyline [3], spatial skyline [4], multi-objective [5], k-dominance [6], k-frequency [7], and ranked skylines [8], k-representative dominance [9], distance-based dominance [10], e-skylines [11], top-k dominance [12], and stochastic skyline [13]. With the growing number of applications that generate imprecise data, e.g., sensor readings, human reading errors, and data imperfection, it has become essential to support preference queries of various types over imprecise data. Imprecise data can be classified into two categories: incomplete and uncertain data. Unfortunately, existing work for preference queries for the imprecise data are limited and isolated. This thesis addresses efficiently extending DBMS to be preference-aware over imprecise data. First, we address the problem of skyline queries over incomplete data where multi-dimensional data items are missing some values of their dimensions. We show that with incomplete data, the dominance relation among data points may not be transitive, thus, almost all existing techniques for skyline queries are not applicable. We propose an efficient algorithm to compute the skyline over incomplete data. Then, we define preference queries over uncertain data, represented as a continuous range. We propose a novel, efficient framework to answer these preference queries. Then, we present PrefJoin, an efficient preference-aware join query operator, designed specifically to deal with preference queries where the set of preferred attributes reside in more than one relation. The main idea of PrefJoin is to make the join operator aware of the required preference functionality. Finally, we extend PrefJoin framework to realize an efficient preference-aware operator which support imprecise data. The extended framework is denoted as UPrefJoin.
Moisture Vertical Structure, Column Water Vapor, and Tropical Deep Convection

Abstract The vertical structure of the relationship between water vapor and precipitation is analyzed in 5 yr of radiosonde and precipitation gauge data from the Nauru Atmospheric Radiation Measurement (ARM) site. The first vertical principal component of specific humidity is very highly correlated with column water vapor (CWV) and has a maximum of both total and fractional variance captured in the lower free troposphere (around 800 hPa). Moisture profiles conditionally averaged on precipitation show a strong association between rainfall and moisture variability in the free troposphere and little boundary layer variability. A sharp pickup in precipitation occurs near a critical value of CWV, confirming satellite-based studies. A lag–lead analysis suggests it is unlikely that the increase in water vapor is just a result of the falling precipitation. To investigate mechanisms for the CWV–precipitation relationship, entraining plume buoyancy is examined in sonde data and simplified cases. For several differe.
Large-Amplitude Magnetohydrodynamic Waves in Nonhomogeneous Plasmas

We consider the propagation of large-amplitude magnetohydrodynamic (MHD) waves in an anisotropic nonhomogeneous plasma. A classical MHD formulation is adopted, and, by means of a sequence of transformations and use of Elsässer's variables, we derive an exact nonlinear system of equations in compact form that describes such waves. The system incorporates compressibility of the plasma and an arbitrary polarization for the waves. Accordingly, the system provides for the analysis of parallel-propagating, nonlinear Alfvén waves and magnetosonic waves in a general space plasma context, including the solar wind. We obtain a new large-amplitude incompressible Alfvén wave solution to the system, and also show how to construct Riemann solutions that are valid under broad assumptions. Brief consideration is given to Alfvén wave propagation in a stationary plasma, and we show that the equation of propagation reduces to classical second-order partial differential equations in two special cases. For the special case in which the Alfvén speed depends linearly on the spatial coordinate, a simple, exact Riemann solution is presented.