Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Artemisia argyi Levl. et Van is an important Asteraceae species with a high medicinal value. There are abundant A. argyi germplasm resources in Asia, especially in China, but the evolutionary relationships of these varieties and the systematic localization of A. argyi in the family Asteraceae are still unclear. In this study, the chloroplast (cp) genomes of 72 A. argyi varieties were systematically analyzed. The 72 varieties originated from 47 regions in China at different longitudes, latitudes and altitudes, and included both wild and cultivated varieties. The A. argyi cp genome was found to be ∼151 kb in size and to contain 114 genes, including 82 protein-coding, 28 tRNA, and 4 rRNA genes. The number of short sequence repeats (SSRs) in A. argyi cp genomes ranged from 35 to 42, and most of them were mononucleotide A/T repeats. A total of 196 polymorphic sites were detected in the cp genomes of the 72 varieties. Phylogenetic analysis demonstrated that the genetic relationship between A. argyi varieties had a weak relationship with their geographical distribution. Furthermore, inverted repeat (IR) boundaries of 10 Artemisia species were found to be significantly different. A sequence divergence analysis of Asteraceae cp genomes showed that the variable regions were mostly located in single-copy (SC) regions and that the coding regions were more conserved than the non-coding regions. A phylogenetic tree was constructed using 43 protein-coding genes common to 67 Asteraceae species. The resulting tree was consistent with the traditional classification system; Artemisia species were clustered into one group, and A. argyi was shown to be closely related to Artemisia lactiflora and Artemisia montana. In summary, this study systematically analyzed the cp genome characteristics of A. argyi and compared cp genomes of Asteraceae species. The results provide valuable information for the definitive identification of A. argyi varieties and for the understanding of the evolutionary relationships between Asteraceae species.
Design, Implementation and Preliminary Analysis of General Multidimensional Trees

In this thesis, a new multidimensional data structure, the q-kd tree, for storing points lying in a multidimensional space is defined, implemented and experimentally analyzed. This new data structure has k-d trees and quad-trees as particular cases. The main difference between q-kd trees and either kd-trees or quad-trees is the way in which discriminants are assigned to each node of the tree. While this is fixed for kd-trees and quad-trees, it is variable for q-kd trees. We propose two different ways for assigning discriminants to nodes, the heuristics: Split Tendency and Prob-of-1. These heuristics allow us to build what we call quasi-optimal q-kd trees and randomly-split q-kd trees respectively. Experimentally we show that our variants of q-kd trees are in between quad-trees and k-d trees concerning the memory space and internal path length, and that by proper parameter settings it is possible to construct q-kd trees taylored to the space and time restrictions we can have.
Mitigating to user cold-start issue in Recommendations System

This research paper uses a brand new popular model to resolve users' side issues within the recommendation process. the primary cold problem occurs when the target user doesn't have a rating history within the system. Today, the recommendation system has been utilized in various fields. However, they still suffer from various ailments, including cold sores and sparsity problems. The aim of the model is to recommend the highest five items to the user and therefore the performance of the model is evaluated
On the Conditioning of the Nonsymmetric Eigenproblem: Theory and Software

This report reviews the theory and practical estimation of condition numbers for the nonsymmetric eigenvalue problem. The report provides a manual for using LAPACK subroutines STRSNA and STRSEN to estimate condition numbers for individual eigenvalues and eigenvectors, multiple (or clustered) eigenvalues, and invariant subspaces. The authors acknowledge the financial support of NSF, grant ASC-8715728. The first author acknowledges DARPA, grant F49620-87-C0065. The second author is also a Presidential Young Investigator.
P-smoother: efficient PBWT smoothing of large haplotype panels

Abstract Motivation As large haplotype panels become increasingly available, efficient string matching algorithms such as positional Burrows-Wheeler transformation (PBWT) are promising for identifying shared haplotypes. However, recent mutations and genotyping errors create occasional mismatches, presenting challenges for exact haplotype matching. Previous solutions are based on probabilistic models or seed-and-extension algorithms that passively tolerate mismatches. Results Here, we propose a PBWT-based smoothing algorithm, P-smoother, to actively ‘correct’ these mismatches and thus ‘smooth’ the panel. P-smoother runs a bidirectional PBWT-based panel scanning that flips mismatching alleles based on the overall haplotype matching context, which we call the IBD (identical-by-descent) prior. In a simulated panel with 4000 haplotypes and a 0.2% error rate, we show it can reliably correct 85% of errors. As a result, PBWT algorithms running over the smoothed panel can identify more pairwise IBD segments than that over the unsmoothed panel. Most strikingly, a PBWT-cluster algorithm running over the smoothed panel, which we call PS-cluster, achieves state-of-the-art performance for identifying multiway IBD segments, a challenging problem in the computational community for years. We also showed that PS-cluster is adequately efficient for UK Biobank data. Therefore, P-smoother opens up new possibilities for efficient error-tolerating algorithms for biobank-scale haplotype panels. Availability and implementation Source code is available at github.com/ZhiGroup/P-smoother.
T-Cell Depleted Haploidentical Transplantation in Children With Hematological Malignancies: A Comparison Between CD3+/CD19+ and TCRαβ+/CD19+ Depletion Platforms

Background T-cell depleted (TCD) haploidentical transplantation using CD3+/CD19+ and TCRαβ+/CD19+ depletion techniques has been increasingly used in children with hematological malignancies. We present a retrospective study aimed to compare transplant outcomes in children with leukemia receiving a TCD haploidentical transplant using either CD3+/CD19+ or TCRαβ+/CD19+ platforms. Methods A total of 159 children with leukemia (ALL=80) (AML=79) that received a TCD haploidentical transplantation using either CD3+/CD19+ (n=79) or TCRαβ+/CD19+ (n=80) platforms between 2005 and 2020 were included. Median age was 9 years in both groups. There were no differences in patient, donor, and transplant characteristics between groups except for donor KIR B genotype more frequent in the TCRαβ+/CD19+ group (91%) than in the CD3+/CD19+ group (76%) (p=0.009) and a high number of NK+ cells and lower CD19+ cells infused in the TCRαβ+/CD19+ group (35.32x106/kg and 0.06 x106/Kg) than in the CD3+/CD19 group (24.6x106/Kg and 0.25 x106/Kg) (p=0.04 and p=0.0001), respectively. Conditioning was based on TBF. Median follow-up for survivors was 11 years (range; 8-16 y) in CD3+/CD19+ group and 5 years (range; 2-9 y) in the TCRαβ+/CD19+ group. Results Engraftment kinetics were similar in both groups (13 days for neutrophils and 10 days for platelets). There was no difference in the incidence of acute GvHD II-IV (29 ± 5% in the CD3+/CD19+ group vs 38 ± 5% in the TCRαβ+/CD19+ group) and chronic GvHD (32 ± 5% vs 23 ± 4%, respectively). NRM was 23 ± 5% in the CD3+/CD19+group vs 21 ± 4% in the TCRαβ+/CD19+group. Relapse incidence was also similar, 32 ± 5% vs 34 ± 6%, respectively. DFS and OS were not different (45 ± 5% vs 45 ± 6% and 53 ± 6% vs 58 ± 6% respectively). As there were no differences on transplant outcomes between groups, we further analyzed all patients together for risk factors associated with transplant outcomes. On multivariate analysis, we identified that early disease status at transplant (HR: 0.16; 95%CI (0.07-0.35) (p=0.0001), presence of cGvHD (HR: 0.38; 95%CI (0.20-0.70) (p= 0.002), and donor KIR-B genotype (HR: 0.50; 95%CI (0.32-0.90) (p=0.04) were associated with better DFS. Conclusions Our data suggest that there are no advantages in transplant outcomes between TCD platforms. Risk factors for survival are dependent on disease characteristic, donor KIR genotype, and chronic GvHD rather than the TCD platform used.
In vitro and in vivo anticancer studies of n-butanol fraction from ethanol extract of annona muricata leaves

Background: Cancer is a leading life threatening disease that adversely affects millions of people in a year worldwide. The growing concerns on the impact of cancer treatment such as surgery, radio & chemotherapy has been notably redirected to the usage of natural bioactive compounds having potential anticancer activity. Annona muricataLinn, a tropical plant belonging to Annonaceae family, was broadly investigated for the ethno medical property. The leaves of the plant was found to contain acetogenins that showed the significant anticancer activity. Objectives: To employ n-butanol fractionation to get the abundance of alkaloid phytochemicals from ethanolic extract of Annona muricata leaves and to study the extract In- vitro and In-vivo for anticancer activity. Methods: MTT assay was performed in-vitro to analyze the cytotoxicity of the extract.The invivo studies were performed with albino mice and the effect of n-butanol extract was studied on the body weight, hematological & biochemical parameter, hepatic enzymes, antioxidant proteins of the experimental animals. Results: The cytotoxic potential of the n-butanol extract using MTT assayshowed the IC50 value of 50 µg/mL inferring 50% of inhibition to MCF-7 adenocarcinoma cells.
Climate Change and Downstream Water Quality in Agricultural Production: The Case of Nutrient Runoff to the Gulf of Mexico

45 Nitrogen (N) fertilizer use in agricultural production is a significant determinant 46 of surface water quality. As climate changes, agricultural producers are likely to adapt 47 at extensive and intensive margins in terms of planted acreage and per ha input use, 48 including fertilizers. These changes can affect downstream water quality. We 49 investigate the effect of climate-driven land productivity changes on water quality in 50 the Gulf of Mexico using an integrated hydro-economic agricultural land use (IHEAL) 51 model. Our results indicate that land and N use adaptation in agricultural production 52 to climate change increases N delivery to the Gulf of Mexico by 0.5%-1.6% (1,690 53 -5,980 metric tons) relative to the baseline scenario with no climate change. 54
Wheat yield estimation based on analysis of UAV images at low altitude

Information about the yield of wheat crops makes it possible to correctly assess their productivity and choose apropriate agronomic procedures to maximize yield. However, determining yields based on manual ear counts is labor intensive. Recently UAVs demonstrated high efficiency for rapid yield estimation. This paper presents a software package WDS (Wheat Detection System) for ears counting in wheat crops based on RGB images obtained from UAVs. WDS creates the flight plan, for the acquired images carries out automatic georeferencing to the appropriate fragment of the field, counts ears using the neural network models, reconstructs the density of ears in the crop and visualizes it as a heat map in the interactive web application. Based on the field experiment the accuracy of ears counting in plots was assessed: Spearman and Pearson correlation coefficients between the ears density counted manually and using WDS were 0.618 and 0.541, respectively (p-value < 0.05). WDS avaliable at https://github.com/Sl07h/wheat_detection.
Analytical Method for High-Precision Seabed Surface Modelling Combining B-Spline Functions and Fourier Series

Abstract High-accuracy seabed surface modelling provides multi-source high-precision fundamental geographic datasets for marine visual computing, seabed topography detection, marine biology, marine engineering and other fields. Proposed in this paper is a high-precision seabed surface model, which combines B-spline functions and Fourier-series, referred to as the Spline-Fourier-series (S-FS) method. Firstly, the mathematical relationship between the B-spline functions and Fourier-series in the modelling process is explored in depth, deducing the non-recursive basis functions of the Spline-Fourier-series model and the specific representation of the two dimensional Spline-Fourier-series model. Furthermore, using a publicly available Large-area bathymetric dataset, extensive experiments are conducted for comparisons with traditional methods (nearest-neighbor, bilinear, bicubic) and traditional Fourier-series, which generally shows the S-FS method has higher accuracy, better convergence and stronger robustness. Finally, based on its mathematically theoretical model, three characteristics (dimensionality reduction, multi-resolution expression and multi-scale visualization) of the S-FS method for constructing high-precision seabed surface are analyzed visually and deeply. Compared with B-spline function, the basic functions of the S-FS method inherit its prioritized compactly-supported performance and do not need to be recursively calculated anymore, thereby further showing its feasibility and extensibility in the field of high-precision seabed surface modelling.
The normalization of the scattering matrix

Let us start with considering the following simple scattering experiment [see Fig. 1]. A parallel beam of light is incident on a cloud (ensemble) of randomly oriented particles that scatter the incoming quasi-monochromatic light independently in all directions and without changing the wavelength. Particles and their mirror particles occur in equal numbers. Hence the cloud constitutes a macroscopically isotropic medium with mirror symmetry (see [1, section 2.7]). We assume the cloud to be optically thin so that multiple scattering can be neglected. The light scattered in a direction that makes an angle Θ (the scattering angle) with the direction of the incident beam is, in general, polarized. The properties of this scattered light, i.e. the flux and state of polarization, are measured by a detector at a distance, D, of the center of the cloud. The plane through the directions of incidence and scattering is called the scattering plane and we use this plane as a plane of reference for defining Stokes parameters as in Van de Hulst [2], Hovenier and Van der Mee [3] and Hovenier et al. [1]. The incident parallel beam of light is characterized by a flux vector πΦ0. This is a column vector with four elements that are Stokes parameters in such a way that the first element is the net flux (irradiance) expressible in WmHz or similar units. Similarly the flux vector of the light falling on the detector is the column vector πΦ, the first element of which is the net flux detected at a distance
Aldehyde Dehydrogenase 2 (ALDH2) Elicits Protection against Pulmonary Hypertension via Inhibition of ERK1/2-Mediated Autophagy

Pulmonary hypertension (PH) is caused by chronic hypoxia that induces the migration and proliferation of pulmonary arterial smooth muscle cells (PASMCs), eventually resulting in right heart failure. PH has been related to aberrant autophagy; however, the hidden mechanisms are still unclear. Approximately 40% East Asians, equivalent to 8% of the universal population, carry a mutation in Aldehyde dehydrogenase 2 (ALDH2), which leads to the aggregation of noxious reactive aldehydes and increases the propensity of several diseases. Therefore, we explored the potential aspect of ALDH2 in autophagy associated with PH. In vitro mechanistic studies were conducted in human PASMCs (HPASMCs) after lentiviral ALDH2 knockdown and treatment with platelet-derived growth factor-BB (PDGF-BB). PH was induced in wild-type (WT) and ALDH2-knockout (ALDH2−/−) mice using vascular endothelial growth factor receptor inhibitor SU5416 under hypoxic conditions (HySU). Right ventricular function was assessed using echocardiography and invasive hemodynamic monitoring. Histological and immunohistochemical analyses were performed to evaluate pulmonary vascular remodeling. EdU, transwell, and wound healing assays were used to evaluate HPASMC migration and proliferation, and electron microscopy and immunohistochemical and immunoblot assays were performed to assess autophagy. The findings demonstrated that ALDH2 deficiency exacerbated right ventricular pressure, hypertrophy, fibrosis, and right heart failure resulting from HySU-induced PH. ALDH2−/− mice exhibited increased pulmonary artery muscularization and 4-hydroxynonenal (4-HNE) levels in lung tissues. ALDH2 knockdown increased PDGF-BB-induced PASMC migration and proliferation and 4-HNE accumulation in vitro. Additionally, ALDH2 deficiency increased the number of autophagosomes and autophagic lysosomes together with autophagic flux and ERK1/2-Beclin-1 activity in lung tissues and PASMCs, indicating enhanced autophagy. In conclusion, the study shows that ALDH2 has a protective role against the migration and proliferation of PASMCs and PH, possibly by regulating autophagy through the ERK1/2-Beclin-1 pathway.
THE EFFECT OF PARENTS’ STRESS LEVELS RELATED TO THE COVID-19 PANDEMIC ON DIGITAL PARENTING AWARENESS, IN TURKEY

Aims: The research was conducted to determine the effect of parents' stress levels related to the COVID-19 pandemic on digital parenting awareness. Materials: This descriptive study was conducted between November 2020-January 2021 with 452 parents residing in Turkey, whose children attended primary school. The data were collected online with a data collection tool consisting of the PSS and the DPAS. Results: It was found that the variables of occupation and number of children of the parents participating in the research are influence the mean scores of DPAS, while the variables of occupation, age, income perception, adaptation to the pandemic process, time spent with the child and the way the relationship with family members are perceived are influence the mean scores of PSS. It was found that, among the characteristics of using digital tools, the parent's phone/tablet usage time, the parent's daily phone/tablet usage time, and the child's status of having his/her own tablet were effective on the mean DPAS score; the variables of parents not knowing their children's use of smart phones/tablets for playing games, homework or educational purposes and not knowing the usage for what purpose were effective variables the mean PSS score. The total mean score of DPAS was determined to be 45.13±9.06, and the mean total score of PSS was determined to be 13.82±2.82. Conclusion: As a result of the research, it was determined that the stress levels perceived by the parents had an effect on digital parenting awareness.
Hexanal combined with decanal mediate host location by the bamboo powderpost beetle, Dinoderus minutus

The bamboo powderpost beetle, Dinoderus minutus (Fabricius) (Coleoptera: Bostrichidae), is the major post‐harvest pest of several bamboo species worldwide. Conspecific adults colonize injured bamboo stems, primarily those with low moisture content. Here, the volatiles from dry cut stems of Bambusa vulgaris Schrad. ex J.C. Wendl (Poaceae) were identified and field‐tested for attraction of adults of D. minutus. Analyses of headspace volatile extracts from these stems revealed 22 compounds, of which hexanal was the most abundant, followed by heptanal, octanal, nonanal, decanal, and 2‐pentylfuran. Together, these six compounds comprised >94% of the total abundance of airborne volatiles from dry cut bamboo stems. The biological activity of these compounds was tested in three consecutive field‐trapping trials in Brazil. Broadly speaking, the binary blend of hexanal and decanal was the optimal attractant for both male and female D. minutus adults, whereas hexanal alone was not attractive and the presence of heptanal, octanal, nonanal, and 2‐pentylfuran in some tested blends proved to be redundant or disruptive in attracting conspecific beetles. Traps baited with hexanal and decanal could be used for surveillance and monitoring of D. minutus at countries' points‐of‐entry and for integrated pest management (IPM) at storage facilities of post‐harvest bamboo stems and related products.
Physical-World Attack towards WiFi-based Behavior Recognition

Behavior recognition plays an essential role in numerous behavior-driven applications (e.g., virtual reality and smart home) and even in the security-critical applications (e.g., security surveillance and elder healthcare). Recently, WiFi-based behavior recognition (WBR) technique stands out among many behavior recognition techniques due to its advantages of being non-intrusive, device-free, and ubiquitous. However, existing WBR research mainly focuses on improving the recognition precision, while neglecting the security aspects. In this paper, we reveal that WBR systems are vulnerable to manipulating physical signals. For instance, our observation shows that WiFi signals can be changed by jamming signals. By exploiting the vulnerability, we propose two approaches to generate physically online adversarial samples to perform untargeted attack and targeted attack, respectively. The effectiveness of these attacks are extensively evaluated over four real-world WBR systems. The experiment results show that our attack approaches can achieve 80% and 60% success rates for untargeted attack and targeted attack in physical world, respectively. We also propose three methods to mitigate the hazard of such attacks.
Engineering Trainee-Teachers’ Attitudes Toward Technology Use in Pedagogical Practices: Extending Computer Attitude Scale (CAS)

The current study examined the trainee teachers’ attitudes toward technology adoption and use in tertiary engineering education. The Computer Attitude Scale (CAS) was extended by including the social influence component, to examine whether social norms affect the acceptance of technology by teachers. Findings from 110 trainee-teachers revealed that their attitudes toward technology are positive. These attitudes constitute the way they like and intend to use technology, their perception of its usefulness in their daily tasks, and the control they perceived to have over technology while using it in engineering disciplines. The findings also confirm that social influence is an important predictor of trainee teachers’ attitudes toward using technology. Overall, the study provides a new influential factor (social) that could be merged with the other four major components (affect, perceived usefulness, perceived control, and behavioral intention) of CAS in conducting future research. The results of this study further provide useful knowledge that extends prior arguments concerning teachers’ attitudes toward using technology in teaching with respect to age, gender, and disciplines. More specifically, the study, theoretically, contributes to research practice in technology acceptance, by extending the computer attitude scale (CAS), with social influence as an additional important factor to be considered when conducting future research. Therefore, an extended CAS is established for exploring newer research in this domain. Policymakers and designers of teacher professional development will be informed of these findings that will accelerate initiatives of technology integration of engineering education in developing countries and other similar contexts.