Miracle-dz/UniFAR-FTUs huggingface dataset:
Numerical Investigation on Fatigue Problem of Cable Net Structure of Five-Hundred-Meter Aperture Spherical Radio Telescope

The reflector of Five-hundred-meter Aperture Spherical radio Telescope (FAST) is supported by cable-net structure, so that to enable its reflector surface to form a paraboloid from a sphere in real time through active control. However, such form-changing operation would lead to about 500MPa stress range for the cable-net structure. Such stress range is nearly twice as much of that defined by the relative standard. So the cable-net structure is the most critical and expendable part of FAST reflector system. So, the service life of FAST would directly depend on the residual fatigue life of its cable-net structure. The present paper would make an effort to find a more appropriate deformation strategy to decrease the stress amplitude of the cable during form-changing operation.
Analysis of Yellow Striped Mutants of Zea mays Reveals Novel Loci Contributing to Iron Deficiency Chlorosis

The micronutrient iron (Fe) is essential for photosynthesis, respiration, and many other processes, but it is only sparingly soluble in aqueous solution, making adequate acquisition by plants a serious challenge. Fe is a limiting factor for plant growth on approximately 30% of the world’s arable lands. Moreover, Fe deficiency in humans is a global health issue, affecting 1.62 billion people, or about 25% of the world’s population. It is imperative that we gain a better understanding of the mechanisms that plants use to regulate iron homeostasis, since these will be important targets for future biofortification and crop improvement strategies. Grasses and non-grasses have evolved independent mechanisms for primary iron uptake from the soil. The grasses, which include most of the world’s staple grains, have evolved a distinct ‘chelation’ mechanism to acquire iron from the soil. Strong iron chelators called phytosiderophores (PSs) are synthesized by grasses and secreted into the rhizosphere where they bind and solubilize Fe(III). The Fe(III)-PS complex is then taken up into root cells via transporters specific for the Fe(III)-PS complex. In this study, 31 novel, uncharacterized striped maize mutants available through the Maize Genetics Cooperation Stock Center (MGCSC) were analyzed to determine whether their mutant phenotypes are caused by decreased iron. Many of these proved to be either pale yellow or white striped mutants. Complementation tests were performed by crossing the MGCSC mutants to ys1 and ys3 reference mutants. This allowed assignment of 10 ys1 alleles and 4 ys3 alleles among the novel mutants. In addition, four ys∗ mutant lines were identified that are not allelic to either ys1 or ys3. Three of these were characterized as being non-allelic to each other and as having low iron in leaves. These represent new genes involved in iron acquisition by maize, and future cloning of these genes may reveal novel aspects of the grass iron acquisition mechanism.
Tightened constraints on the time-lag between Antarctic temperature and CO 2 during the last deglaciation

Antarctic ice cores provide clear evidence of a close coupling between variations in Antarctic tempera- ture and the atmospheric concentration of CO2 during the glacial/interglacial cycles of at least the past 800-thousand years. Precise information on the relative timing of the tem- perature and CO2 changes can assist in refining our under- standing of the physical processes involved in this coupling. Here, we focus on the last deglaciation, 19 000 to 11 000 yr before present, during which CO2 concentrations increased by 80 parts per million by volume and Antarctic temper- ature increased by 10 C. Utilising a recently developed proxy for regional Antarctic temperature, derived from five near-coastal ice cores and two ice core CO2 records with high dating precision, we show that the increase in CO2 likely lagged the increase in regional Antarctic temperature by less than 400 yr and that even a short lead of CO2 over tem- perature cannot be excluded. This result, consistent for both CO2 records, implies a faster coupling between temperature and CO2 than previous estimates, which had permitted up to millennial-scale lags.
A Propensity-Score Matched Comparison of Perioperative and Early Renal Functional Outcomes of Robotic versus Open Partial Nephrectomy

Objectives To compare the perioperative and early renal functional outcomes of RPN with OPN for kidney tumors. Materials and Methods A total of 209 RPN or OPN patients with availability of preoperative cross-sectional imaging since 2009 at our center were included. To adjust for potential baseline confounders propensity-score matching was performed, which resulted in 94 OPNs matched to 51 RPNs. Perioperative and early renal functional outcomes were compared. Results In propensity-score matched analysis, RPN procedures were well tolerated and resulted in significant decreases in postoperative analgesic time (24 vs. 48 hr, p<0.001) and visual analog pain scale (3 vs. 4, p<0.001). Besides, the RPN patients had a significantly shorter LOS (9 vs. 11 days, p = 0.008) and less EBL (100 vs. 200 ml, p<0.001), but median operative time was significantly longer (229 vs. 182 min, p<0.001). Ischemia time, transfusion rates, complication rates, percentage eGFR decline and CKD upstaging were equivalent after RPN versus OPN. In multivariable logistic regression analysis, RPN patients were less likely to have a prolonged LOS (odds ratio [OR]: 0.409; p = 0.016), while more likely to experience a longer operative time (OR: 4.296; p = 0.001). However, the statistical significance for the protective effect of RPN versus OPN in EBL was not confirmed by examining the risk of EBL≥400 ml (OR: 0.488; p = 0.212). Conclusions When adjusted for potential selection biases, RPN offers comparable perioperative and early renal functional outcomes to those of OPN, with the added advantage of improved postoperative pain control and a shorter LOS.
Detection of cocaine and benzoylecgonine in formalin fixed rat tissues

The stability of drugs in formalin solution is an important factor in forensic investigation. Tissues (liver, lung, kidney, brain) taken from rats, which have been poisoned acutely with cocaine, were preserved in two different conditions, analyzed by GC-MS, and then compared. Organs of the first group were preserved and stored at −20°C without adding formalin, whereas the organs of the second group were preserved and stored in formalin solution at room temperature (25°C). Serum samples were taken immediately after poisoning and studied as well. In specimens stored at −20°C, cocaine and its metabolite benzoylecgonine were detected in the tissues. Only benzoylecgonine was detected both in tissues and their formalin solution. It was observed that the distribution of cocaine in tissues had differed depending on the preservation conditions. The formalin solution in which benzoylecgonine was mostly detected was from liver. As a result, cocaine was detected in tissues stored at −20°C. It is recommended that both the formalin-fixed tissues and formalin solution should be analyzed concurrently to assure the accurate results (LOD = 3 ng/ml).
Identification of the Sex Chromosomes of Brown Trout (Salmo trutta) and Their Comparison with the Corresponding Chromosomes in Atlantic Salmon (Salmo salar) and Rainbow Trout (Oncorhynchus mykiss)

Males are the heterogametic sex in salmonid fishes. In brown trout (Salmo trutta) the sex-determining locus, SEX, has been mapped to the end of linkage group BT-28, which corresponds to linkage group AS-8 and chromosome SSA15 in Atlantic salmon (Salmo salar). We set out to identify the sex chromosomes in brown trout. We isolated Atlantic salmon BAC clones containing microsatellite markers that are on BT-28 and also on AS-8, and used these BACs as probes for fluorescent in situ hybridization (FISH) analysis. SEX is located on the short arm of a small subtelocentric/acrocentric chromosome in brown trout, which is consistent with linkage analysis. The acrocentric chromosome SSA15 in Atlantic salmon appears to have arisen by a centric fusion of 2 small acrocentric chromosomes in the common ancestor of Salmo sp. We speculate that the fusion process that produced Atlantic salmon chromosome SSA15 disrupted the ancestral sex-determining locus in the Atlantic salmon lineage, providing the impetus either for the relocation of SEX or selection pressure for a novel sex-determining gene to arise in this species. Thus, the sex-determining genes may differ in Atlantic salmon and brown trout.
Insights into esophagus tissue architecture using two-photon confocal microscopy

In this paper, microstructures of human esophageal mucosa were evaluated using the two-photon laser scanning confocal microscopy (TPLSCM), based on two-photon excited fluorescence (TPEF) and second harmonic generation (SHG). The distribution of epithelial cells, muscle fibers of muscularis mucosae has been distinctly obtained. Furthermore, esophageal submucosa characteristics with cancer cells invading into were detected. The variation of collagen, elastin and cancer cells is very relevant to the pathology in esophagus, especially early esophageal cancer. Our experimental results indicate that the MPM technique has the much more advantages for label-free imaging, and has the potential application in vivo in the clinical diagnosis and monitoring of early esophageal cancer.
Mast cells mediate early neutrophil recruitment and exhibit anti‐inflammatory properties via the formyl peptide receptor 2/lipoxin A4 receptor

In recent years, studies have focused on the resolution of inflammation, which can be achieved by endogenous anti‐inflammatory agonists such as Annexin A1 (AnxA1). Here, we investigated the effects of mast cells (MCs) on early LPS‐induced neutrophil recruitment and the involvement of the AnxA1‐formyl peptide receptor 2/ALX (FPR2/ALX or lipoxin A4 receptor) pathway.
Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5′ UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing).
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing

The number of microbial and metagenomic studies has increased drastically due to advance-ments in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates. Additionally, the compositional nature of current amplicon and metagenomic data differs from many other biological data types adding another challenge to the data analysis. To address these challenges in human microbiome research, we introduce a novel probabilistic approach to explicitly model overdispersion and sampling zeros by considering the temporal correlation between nearby time points using Gaussian Processes. The proposed Temporal Gaussian Process Model for Compositional Data Analysis (TGP-CODA) shows superior modeling performance compared to commonly used Dirichlet-multinomial, multinomial, and non-parametric regression models on real and synthetic data. We demonstrate that the nonreplicative nature of human gut microbiota studies can be partially overcome by our method with proper experimental design of dense temporal sampling. We also show that different modeling ap-proaches have a strong impact on ecological interpretation of the data, such as stationarity, persistence, and environmental noise models. A Stan implementation of the proposed method is available under MIT license at https://github.com/tare/GPMicrobiome.
Unscented Kalman Filter for Non-Linear Identification of a New Prototype of Bidirectional Tuned Vibration Absorber: A Numerical Investigation

Several nonlinear system identification methods have been presented in the past, such as the Extended Kalman Filter, the H filter and the Sequential Monte Carlo methods. One of the most promising ones is the Unscented Kalman Filter (UKF) recently proposed for the on-line identification of structural parameters. In the present study the UKF is proposed to the purpose of the nonlinear identification of a new prototype of rolling-pendulum tuned vibration absorber which, relying on an optimal three-dimensional guiding receptacle, can simultaneously control the response of the supporting structure along two orthogonal horizontal directions. Unlike existing ball vibration absorbers, mounted on spherical recesses and used in axial-symmetrical structures, the new device can be bidirectionally tuned to both fundamental structural modes even when the corresponding natural frequencies are different, by virtue of the optimum shape of the rolling cavity. Based on preliminary numerical simulations, the UKF is shown to be effective in identifying the structural parameters of the new device and particularly the nonlinear rolling friction dissipation mechanism at the interface between the ball bearing and the rolling surface.
Role of muscle stem cells in sarcopenia

Purpose of reviewThe review is an update on recent research investigating the role of skeletal muscle stem cells (also known as satellite cells) during muscle fiber regeneration and growth in animal and human skeletal muscle, with an emphasis on their role in age-related sarcopenia. Recent findingsStudies indicate clear impairments in satellite cell function with aging, resulting in an impaired muscle fiber regenerative response. The autophagy-mediated switch to an irreversible presenescent state of geriatric satellite cells appears to play a key role in age-related impaired satellite cell function. In addition, inadequate muscle fiber vascularization may be a crucial factor underlying impaired regulation of satellite cells in older adults. Controversy remains on the actual contribution of satellite cells to the development of sarcopenia in later life, this clearly requires further research. Nevertheless, exercise training remains to be a potent intervention strategy, mediated through satellite cells or not, to counteract the ill effects of sarcopenia. SummaryAlthough important strides are made investigating the importance of satellite cells in the development and/or treatment of sarcopenia, the idea that satellite cell function is a therapeutic target to treat sarcopenia remains controversial.
Are rare variants really independent?

Recent advances in genotyping with high‐density markers allow researchers access to genomic variants including rare ones. Linkage disequilibrium (LD) is widely used to provide insight into evolutionary history. It is also the basis for association mapping in humans and other species. Better understanding of the genomic LD structure may lead to better‐informed statistical tests that can improve the power of association studies. Although rare variant associations with common diseases (RVCD) have been extensively studied recently, there is very limited understanding, and even controversial view of LD structures among rare variants and between rare and common variants. In fact, many popular RVCD tests make the assumptions that rare variants are independent. In this report, we show that two commonly used LD measures are not capable of detecting LD when rare variants are involved. We present this argument from two perspectives, both the LD measures themselves and the computational issues associated with them. To address these issues, we propose an alternative LD measure, the polychoric correlation, that was originally designed for detecting associations among categorical variables. Using simulated as well as the 1000 Genomes data, we explore the performances of LD measures in detail and discuss their implications in association studies.
Solar Oscillations and Convection. II. Excitation of Radial Oscillations

Solar p-mode oscillations are excited by the work of stochastic, nonadiabatic, pressure fluctuations on the compressive modes. We evaluate the expression for the radial mode excitation rate derived by Nordlund & Stein using numerical simulations of near-surface solar convection. We first apply this expression to the three radial modes of the simulation and obtain good agreement between the predicted excitation rate and the actual mode damping rates as determined from their energies and the widths of their resolved spectral profiles. These radial simulation modes are essentially the same as the solar modes at the resonant frequencies, where the solar modes have a node at the depth of the bottom of the simulation domain. We then apply this expression for the mode excitation rate to the solar modes and obtain excellent agreement with the low ℓ damping rates determined from data obtained by the "global oscillations at low frequencies" (GOLF) instrument on SOHO. Excitation occurs close to the surface, mainly in the intergranular lanes and near the boundaries of granules (where turbulence and radiative cooling are large). The nonadiabatic pressure fluctuations near the surface are produced by small instantaneous local imbalances between the divergence of the radiative and convective fluxes near the solar surface. Below the surface, the nonadiabatic pressure fluctuations are produced primarily by turbulent-pressure fluctuations (Reynolds stresses). The frequency dependence of the mode excitation is due to effects of the mode structure and the pressure fluctuation spectrum. Excitation is small at low frequencies because of mode properties—the mode compression decreases and the mode mass increases at low frequency. Excitation is small at high frequencies because of the pressure fluctuation spectrum—pressure fluctuations become small at high frequencies because they are due to convection, which is a long-timescale phenomenon compared with the dominant p-mode periods.
Diverging Progression of Network Disruption and Atrophy in Alzheimer’s Disease and Semantic Dementia

The progression of cognitive deficits in Alzheimer’s disease and semantic dementia is accompanied by grey matter atrophy and white matter deterioration. The impact of neuronal loss on the structural network connectivity in these dementia subtypes is, however, not well understood. In order to gain a more refined knowledge of the topological organization of white matter alterations in dementia, we used a network-based approach to analyze the brain’s structural connectivity network. Diffusion-weighted and anatomical MRI images of groups with eighteen Alzheimer’s disease and six semantic dementia patients, as well as twenty-one healthy controls were recorded to reconstruct individual connectivity networks. Additionally, voxel-based morphometry, using grey and white matter volume, served to relate atrophy to altered structural connectivity. The analyses showed that Alzheimer’s disease is characterized by decreased connectivity strength in various cortical regions. An overlap with grey matter loss was found only in the inferior frontal and superior temporal areas. In semantic dementia, significantly reduced network strength was found in the temporal lobes, which converged with grey and white matter atrophy. Therefore, this study demonstrated that the structural disconnection in early Alzheimer’s disease goes beyond grey matter atrophy and is independent of white matter volume loss, an observation that was not found in semantic dementia.
A Reaction Zone Hypothesis for the Effects of Particle Size and Water‐to‐Cement Ratio on the Early Hydration Kinetics of C3S

The hydration kinetics of tricalcium silicate (C3S) has been the subject of much study, yet the experimentally observed effects of the water-to-cement (w/c) ratio and particle size distribution have been difficult to explain with models. Here, we propose a simple hypothesis that provides an explanation of the lack of any significant effect of w/c on the kinetics and for the strong effect of the particle size distribution on the amount of early hydration associated with the main hydration peak. The hypothesis is that during the early hydration period the calcium–silicate–hydrate product forms only in a reaction zone close to the surface of the C3S particles. To test the hypothesis, a new microstructure-based kinetics (MBK) model has been developed. The MBK model treats the C3S particle size distribution in a statistical way to save computation time and treats the early hydration as essentially a boundary nucleation and growth process. The MBK model is used to fit kinetic data from two published studies for C3S with different size distributions, one for alite (impure C3S) pastes and one for stirred C3S suspensions. The model is able to fit all the data sets with parameters that show no significant trend with particle size, providing support for the reaction zone hypothesis.
Advances in diagnostics for transplant rejection

ABSTRACT Introduction: Identification of allograft injury, including acute clinical and subclinical injury, is vital in increasing the longevity of the transplanted organ. Acute rejection, which occurs as a result of a variety of immune and non-immune factors including the infiltration of immune cells and antibodies to the donor specific epitopes, poses a significant risk to the organ. Recent years have marked an increase in the discovery of new genomic, transcriptomic, and proteomic biomarkers in molecular diagnostics, which offer better potential for personalized management of the transplanted organ by providing earlier detection of rejection episodes. Areas covered: This review was compiled from key word searches of full-text publications relevant to the field. Expert commentary: Many of the recent advancements in the molecular diagnostics of allograft injury show much promise, but before they can be fully realized further validation in larger sample sets must be conducted. Additionally, for better informed therapeutic decisions, more work must be completed to differentiate between different causes of injury. Moreover, the diagnostics field is looking at methodologies that allow for multiplexing, the ability to identify multiple targets simultaneously, in order to provide more robust biomarkers and better understanding.