Miracle-dz/UniFAR-FTUs huggingface dataset:
Flowering Phenology Shifts in Response to Functional Traits, Growth Form, and Phylogeny of Woody Species in a Desert Area

Climatic factors are considered the major driving forces for variation of flowering phenology among species. Yet, whether flowering phenology of woody species varies with functional traits, growth form, and phylogeny in arid regions is unknown. In the present study, we evaluated the relationships of three characteristics of flowering phenology (i.e., first flowering date, end of flowering date, and flowering duration) against functional traits, growth form, and phylogeny across 59 woody plant species across 3 years in Ürümqi city of the Xinjiang Autonomous Region, in Northwest China. The results showed that, plant functional traits and growth form had significant influences on the variability of flowering phenology among species. The contributions of fruit type (34.7–43.5%) and flower color (30.1–30.7%) to the variability of flowering phenology were larger than those of pollination mode (4.6–14.4%), life form (8.4–14%) and maximum plant height (9.7–13.1%). Trees had the significant correlations in terms of flowering duration against first flowering date and end of flowering date, while shrubs showed the opposite pattern. The values of phylogenetic signal (Blomberg’s K) of the three characteristics of flowering phenology ranged from 0.36 to 0.43, which were significantly lower than the expectation of the Brownian motion model. Our results suggested that functional traits, growth form and phylogeny all affected variability of flowering phenology among species. Our results provide a new perspective for correctly evaluating the relationship between global climate change and plant reproduction.
Oxidative Stress-Induced Axon Fragmentation Is a Consequence of Reduced Axonal Transport in Hereditary Spastic Paraplegia SPAST Patient Neurons

Hereditary spastic paraplegia (HSP) is a group of inherited disorders characterized by progressive spasticity and paralysis of the lower limbs. Autosomal dominant mutations in SPAST gene account for ∼40% of adult-onset patients. We have previously shown that SPAST patient cells have reduced organelle transport and are therefore more sensitive to oxidative stress. To test whether these effects are present in neuronal cells, we first generated 11 induced pluripotent stem (iPS) cell lines from fibroblasts of three healthy controls and three HSP patients with different SPAST mutations. These cells were differentiated into FOXG1-positive forebrain neurons and then evaluated for multiple aspects of axonal transport and fragmentation. Patient neurons exhibited reduced levels of SPAST encoded spastin, as well as a range of axonal deficits, including reduced levels of stabilized microtubules, lower peroxisome transport speed as a consequence of reduced microtubule-dependent transport, reduced number of peroxisomes, and higher density of axon swellings. Patient axons fragmented significantly more than controls following hydrogen peroxide exposure, suggesting for the first time that the SPAST patient axons are more sensitive than controls to the deleterious effects of oxidative stress. Treatment of patient neurons with tubulin-binding drugs epothilone D and noscapine rescued axon peroxisome transport and protected them against axon fragmentation induced by oxidative stress, showing that SPAST patient axons are vulnerable to oxidative stress-induced degeneration as a consequence of reduced axonal transport.
Inflammaging and Complement System: A Link Between Acute Kidney Injury and Chronic Graft Damage

The aberrant activation of complement system in several kidney diseases suggests that this pillar of innate immunity has a critical role in the pathophysiology of renal damage of different etiologies. A growing body of experimental evidence indicates that complement activation contributes to the pathogenesis of acute kidney injury (AKI) such as delayed graft function (DGF) in transplant patients. AKI is characterized by the rapid loss of the kidney’s excretory function and is a complex syndrome currently lacking a specific medical treatment to arrest or attenuate progression in chronic kidney disease (CKD). Recent evidence suggests that independently from the initial trigger (i.e., sepsis or ischemia/reperfusions injury), an episode of AKI is strongly associated with an increased risk of subsequent CKD. The AKI-to-CKD transition may involve a wide range of mechanisms including scar-forming myofibroblasts generated from different sources, microvascular rarefaction, mitochondrial dysfunction, or cell cycle arrest by the involvement of epigenetic, gene, and protein alterations leading to common final signaling pathways [i.e., transforming growth factor beta (TGF-β), p16ink4a, Wnt/β-catenin pathway] involved in renal aging. Research in recent years has revealed that several stressors or complications such as rejection after renal transplantation can lead to accelerated renal aging with detrimental effects with the establishment of chronic proinflammatory cellular phenotypes within the kidney. Despite a greater understanding of these mechanisms, the role of complement system in the context of the AKI-to-CKD transition and renal inflammaging is still poorly explored. The purpose of this review is to summarize recent findings describing the role of complement in AKI-to-CKD transition. We will also address how and when complement inhibitors might be used to prevent AKI and CKD progression, therefore improving graft function.
Outlier Detection

Over the past decade, we have witnessed an enormous amount of research effort dedicated to the design of efficient outlier detection techniques while taking into consideration efficiency, accuracy, high-dimensional data, and distributed environments, among other factors. In this article, we present and examine these characteristics, current solutions, as well as open challenges and future research directions in identifying new outlier detection strategies. We propose a taxonomy of the recently designed outlier detection strategies while underlying their fundamental characteristics and properties. We also introduce several newly trending outlier detection methods designed for high-dimensional data, data streams, big data, and minimally labeled data. Last, we review their advantages and limitations and then discuss future and new challenging issues.
Latency-efficient Data Collection Scheduling in Battery-free Wireless Sensor Networks

The lifetime of battery-powered Wireless Sensor Networks (WSNs) are limited by the batteries equipped in sensors. The appearance of Battery-free Wireless Sensor Networks (BF-WSNs) breaks through this limitation, in which battery-free sensors harvest energy from sustainable but uncontrollable energy sources in ambient environment, such as solar power, wind power, radio frequency signal power, and so on. The energy characteristics of BF-WSNs make it more challenging for data collection scheduling in BF-WSNs. Latency of data collection is a crucial measurement to evaluate the performance of data collection schedules. In this article, we study the problem of generating data collection schedules with minimum latency for BF-WSNs and propose latency-efficient data collection scheduling algorithms for line BF-WSNs and general BF-WSNs, respectively. Theoretical analysis and extensive simulations are conducted to verify the efficiency and effectiveness of the proposed algorithms.
Efficacy and Safety of Intraoperative Lumbar Drain in Endoscopic Skull Base Tumor Resection: A Meta-Analysis

Objectives: This study aims to evaluate the efficacy and safety of lumbar drainage (LD) in preventing cerebrospinal fluid (CSF) leaks after endoscopic skull base tumor resection. Methods: A systematic online search was conducted using PubMed, Embase, Scopus, Web of Science, and Cochrane Library from January 2006 to July 2019. Data analyses were performed by the Cochrane Collaboration's Review Manager 5.3 software. Results: Eight studies, including two randomized controlled trials and six observational studies, met the inclusion criteria. No significant difference was found in the post-operative CSF leak rate between the LD group and the non-LD group [odds ratio (OR), 0.80; 95%CI, 0.37–1.74; I2 = 37%; P = 0.57). Subgroup analysis of the intraoperative high-flow leaks, including 4 studies and 313 patients, showed that LD was associated with reduced likelihood of post-operative CSF leak (OR, 0.37; 95%CI, 0.17–0.83; I2 = 0%; P = 0.02). The placement of LD was related to increased risk of headache compared with non-LD use, and no significant difference was found in the occurrence of deep vein thromboses and pulmonary emboli between two groups. Conclusion: LD is not recommended in all patients undergoing endoscopic skull base tumor resection. However, for patients with intraoperative high-flow leaks, LD is effective and safe in reducing risk of CSF leak.
Relationship Between Buddhist Belief and Suicide Risk in Chinese Persons Undergoing Methadone Maintenance Therapy for Heroin Dependence

Background In western countries, there is a negative association between religious belief and suicide risk, while in China this association is positive. Nevertheless, few data are available on the association between one specific type of religion and suicide risk, which might be different from the overall positive religion-suicide association in China. This study examined the association between Buddhist belief and suicide risk in Chinese persons receiving methadone maintenance therapy (MMT) for heroin dependence. Methods In total, 61 Buddhist believers and 425 age, gender, and clinic frequency-matched non-religious believers were selected from a sample of patients with heroin dependence treated in three MMT clinics in Wuhan, China. The suicidality module of the Chinese version of the Mini-international Neuropsychiatric Interview 5.0 was used to assess current suicide risk. Patients' demographic and clinical characteristics were also collected. Multiple ordinary logistic regression was used to analyze the association between Buddhist belief and current suicide risk, controlling for the confounding effects of demographic and clinical factors. Results In Chinese patients receiving MMT for heroin dependence, Buddhist believers had significantly higher levels of current suicide risk than non-religious believers (low: 45.9% vs. 24.7%, medium: 4.9% vs. 3.5%, high: 19.7% vs. 12.5%, P < 0.001). After adjusting for demographic and clinical covariates (including depressive symptoms), Buddhist belief was still significantly associated with an increase in the level of current suicide risk (OR: 2.98, P < 0.001). Conclusion Buddhist belief is significantly associated with elevated current suicide risk in Chinese patients receiving MMT for heroin independence. In Chinese MMT clinics, patients with Buddhist belief may have a high current suicide risk and a timely psychiatric assessment and crisis intervention (when necessary) should be provided to these patients.
Unraveling the Diversity of Eukaryotic Microplankton in a Large and Deep Perialpine Lake Using a High Throughput Sequencing Approach

The structure of microbial communities, microalgae, heterotrophic protozoa and fungi contributes to characterize food webs and productivity and, from an anthropogenic point of view, the qualitative characteristics of water bodies. Traditionally, in freshwater environments many investigations have been directed to the study of pelagic microalgae (“phytoplankton”) and periphyton (i.e., photosynthetic and mixotrophic protists) through the use of light microscopy (LM). While the number of studies on bacterioplankton communities have shown a substantial increase after the advent of high-throughput sequencing (HTS) approaches, the study of the composition, structure, and spatio-temporal patterns of microbial eukaryotes in freshwater environments was much less widespread. Moreover, the understanding of the correspondence between the relative phytoplankton abundances estimated by HTS and LM is still incomplete. Taking into account these limitations, this study examined the biodiversity and seasonality of the community of eukaryotic microplankton in the epilimnetic layer of a large and deep perialpine lake (Lake Garda) using HTS. The analyses were carried out at monthly frequency during 2014 and 2015. The results highlighted the existence of a rich and well diversified community and the presence of numerous phytoplankton taxa that were never identified by LM in previous investigations. Furthermore, the relative abundances of phytoplankton estimated by HTS and LM showed a significant relationship at different taxonomic ranks. In the 2 years of investigation, the temporal development of the whole micro-eukaryotic community showed a clear non-random and comparable distribution pattern, with the main taxonomic groups coherently distributed in the individual seasons. In perspective, the results obtained in this study highlight the importance of HTS approaches in assessing biodiversity and the relative importance of the main protist groups along environmental gradients, including those caused by anthropogenic impacts (e.g., eutrophication and climate change).
Enhancing Employer Brand Evaluation with Collaborative Topic Regression Models

Employer Brand Evaluation (EBE) is to understand an employer’s unique characteristics to identify competitive edges. Traditional approaches rely heavily on employers’ financial information, including financial reports and filings submitted to the Securities and Exchange Commission (SEC), which may not be readily available for private companies. Fortunately, online recruitment services provide a variety of employers’ information from their employees’ online ratings and comments, which enables EBE from an employee’s perspective. To this end, in this article, we propose a method named Company Profiling–based Collaborative Topic Regression (CPCTR) to collaboratively model both textual (i.e., reviews) and numerical information (i.e., salaries and ratings) for learning latent structural patterns of employer brands. With identified patterns, we can effectively conduct both qualitative opinion analysis and quantitative salary benchmarking. Moreover, a Gaussian processes--based extension, GPCTR, is proposed to capture the complex correlation among heterogeneous information. Extensive experiments are conducted on three real-world datasets to validate the effectiveness and generalizability of our methods in real-life applications. The results clearly show that our methods outperform state-of-the-art baselines and enable a comprehensive understanding of EBE.
Influence of Compliant Joints in Four-Legged Robots

Legged animals are capable of rapid movements, are efficient from the energy point of view, and are able to adapt their gaits to environmental conditions. Motions like walking, trotting, galloping, and jumping, are difficult to evaluate and replicate due to their being consequences of complex interactions of different systems (such as the musculoskeletal system and the central and peripheral nervous systems, including also the influence of the environment). In this paper, we analyzed the behavior of a four-legged robot constituted by one active DOF in each leg (using commercial servomotors) and one passive DOF in each knee and in the spine (using springs). Our objective was to increase the motion performances of the robot by varying the stiffness of the springs. The results obtained from the simulation underline how the stiffness of the spine influences the performance of the robot by increasing the speed and reducing the energy required by the servomotors.
Poultry and coloured light

Poultry have four types of cone in the retina of the eye, and this means that they probably see colour differently from trichromatic humans. Notwithstanding the fact that humans and birds have maximum sensitivity in a similar part of the spectrum (545–575nm), poultry are likely to perceive light from various types of lamp at a different intensity from humans because they are more sensitive to the blue and red parts of the spectrum. Although colour has been confounded with illuminance in many trials, wavelength has an unquestionable effect on poultry production and behaviour. Growth and behaviour responses depend principally on retinal photoreception, whereas photosexual responses are mainly influenced by hypothalamic light reception. In turkeys and chickens growth under red illumination is inferior to that under blue or green light, and this may be a result of birds exposed to red light being more active and showing more aggression than birds exposed to shorter wavelength radiation. In contrast, the easier penetration of longer wavelength radiation to the hypothalamus makes red light more sexually stimulatory than blue or green, although the hypothalamic photoreceptors are more sensitive to blue/green light when illuminated directly. Egg production traits, however, appear to be minimally affected by wavelength.
Practical Accuracy Estimation for Efficient Deep Neural Network Testing

Deep neural network (DNN) has become increasingly popular and DNN testing is very critical to guarantee the correctness of DNN, i.e., the accuracy of DNN in this work. However, DNN testing suffers from a serious efficiency problem, i.e., it is costly to label each test input to know the DNN accuracy for the testing set, since labeling each test input involves multiple persons (even with domain-specific knowledge) in a manual way and the testing set is large-scale. To relieve this problem, we propose a novel and practical approach, called PACE (which is short for Practical ACcuracy Estimation), which selects a small set of test inputs that can precisely estimate the accuracy of the whole testing set. In this way, the labeling costs can be largely reduced by just labeling this small set of selected test inputs. Besides achieving a precise accuracy estimation, to make PACE more practical it is also required that it is interpretable, deterministic, and as efficient as possible. Therefore, PACE first incorporates clustering to interpretably divide test inputs with different testing capabilities (i.e., testing different functionalities of a DNN model) into different groups. Then, PACE utilizes the MMD-critic algorithm, a state-of-the-art example-based explanation algorithm, to select prototypes (i.e., the most representative test inputs) from each group, according to the group sizes, which can reduce the impact of noise due to clustering. Meanwhile, PACE also borrows the idea of adaptive random testing to select test inputs from the minority space (i.e., the test inputs that are not clustered into any group) to achieve great diversity under the required number of test inputs. The two parallel selection processes (i.e., selection from both groups and the minority space) compose the final small set of selected test inputs. We conducted an extensive study to evaluate the performance of PACE based on a comprehensive benchmark (i.e., 24 pairs of DNN models and testing sets) by considering different types of models (i.e., classification and regression models, high-accuracy and low-accuracy models, and CNN and RNN models) and different types of test inputs (i.e., original, mutated, and automatically generated test inputs). The results demonstrate that PACE is able to precisely estimate the accuracy of the whole testing set with only 1.181%∼2.302% deviations, on average, significantly outperforming the state-of-the-art approaches.
Intrapulmonary (i.pulmon.) Pull Immunization With the Tuberculosis Subunit Vaccine Candidate H56/CAF01 After Intramuscular (i.m.) Priming Elicits a Distinct Innate Myeloid Response and Activation of Antigen-Presenting Cells Than i.m. or i.pulmon. Prime Immunization Alone

Understanding the in vivo fate of vaccine antigens and adjuvants and their safety is crucial for the rational design of mucosal subunit vaccines. Prime and pull vaccination using the T helper 17-inducing adjuvant CAF01 administered parenterally and mucosally, respectively, has previously been suggested as a promising strategy to redirect immunity to mucosal tissues. Recently, we reported a promising tuberculosis (TB) vaccination strategy comprising of parenteral priming followed by intrapulmonary (i.pulmon.) mucosal pull immunization with the TB subunit vaccine candidate H56/CAF01, which resulted in the induction of lung-localized, H56-specific T cells and systemic as well as lung mucosal IgA responses. Here, we investigate the uptake of H56/CAF01 by mucosal and systemic innate myeloid cells, antigen-presenting cells (APCs), lung epithelial cells and endothelial cells in mice after parenteral prime combined with i.pulmon. pull immunization, and after parenteral or i.pulmon. prime immunization alone. We find that i.pulmon. pull immunization of mice with H56/CAF01, which are parenterally primed with H56/CAF01, substantially enhances vaccine uptake and presentation by pulmonary and splenic APCs, pulmonary endothelial cells and type I epithelial cells and induces stronger activation of dendritic cells in the lung-draining lymph nodes, compared with parenteral immunization alone, which suggests activation of both innate and memory responses. Using mass spectrometry imaging of lipid biomarkers, we further show that (i) airway mucosal immunization with H56/CAF01 neither induces apparent local tissue damage nor inflammation in the lungs, and (ii) the presence of CAF01 is accompanied by evidence of an altered phagocytic activity in alveolar macrophages, evident from co-localization of CAF01 with the biomarker bis(monoacylglycero)phosphate, which is expressed in the late endosomes and lysosomes of phagocytosing macrophages. Hence, our data demonstrate that innate myeloid responses differ after one and two immunizations, respectively, and the priming route and boosting route individually affect this outcome. These findings may have important implications for the design of mucosal vaccines intended for safe administration in the airways.
Oogenesis in Dacus tryoni (Frogg.) (Diptera: Trypetidae)

Oogenesis in D. tryoni is typical of cyclorrhaphous Diptera. The ovariolar germarium produces a linear succession of 16-cell cysts enclosed by follicle cells. The cells of a cyst are interconnected by cytoplasmic canals and differentiate as 15 nurse cells and a posterior oocyte. Previtellogenesis occupies 3 days, vitellogenesis 1 day. The oocyte grows slowly during previtellogenesis, with little differentiation, rapidly during vitellogenesis, when protein and fatty yolk deposition, axial differentiation, and nuclear breakdown to first maturation metaphase, take place. The nurse cells grow rapidly during previtellogenesis and early vitellogenesis, developing large polytene nuclei and RNA-rich cytoplasm, and pour an RNA-rich nutrient stream into the oocyte during early vitellogenesis. The stream also contains P.A. S. -positive material, lipid droplets, possibly protein precursors, and nucleotides. Later, the nurse cells degenerate. Both growth and degeneration of the nurse cells are polarized, the posterior cells leading the more anterior cells. The follicular epithelium, cuboidal during previtellogenesis, differentiates as columnar around the oocyte, squamous outside the nurse cells, and anteriorly as border cells which migrate between the nurse cells to the anterior end of the oocyte. Late in vitellogenesis, the follicular epithelium secretes the chorion and vitelline membrane. It is not yet possible to discern in oogenesis the establishment in the oocyte of the prepattern essential for normal epigenesis.