Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitochondrial genome of the Japanese honeybee, Apis cerana japonica (Insecta: Hymenoptera: Apidae)

Abstract In this study, we analyzed the complete mitochondrial genome of the Japanese honeybee Apis cerana japonica. The mitochondrial genome of A. c. japonica is a circular molecule of 15 917 bp and is similar to that of A. c. cerana. It contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one A + T-rich control region. All protein-coding genes are initiated by ATT and ATG codons and are terminated by the typical stop codon TAA or TAG, except for the start codon of ATP8 which ends with C. All tRNA genes typically form a cloverleaf secondary structure, except for tRNA-Ser (AGN).
Survey of Models for Acquiring the Optical Properties of Translucent Materials

The outset of realistic rendering is a desire to reproduce the appearance of the real world. Rendering techniques therefore operate at a scale corresponding to the size of objects that we observe with our naked eyes. At the same time, rendering techniques must be able to deal with objects of nearly arbitrary shapes and materials. These requirements lead to techniques that oftentimes leave the task of setting the optical properties of the materials to the user. Matching the appearance of real objects by manual adjustment of optical properties is however nearly impossible. We can render objects with a plausible appearance in this way but cannot compare the appearance of a manufactured item to that of its digital twin. This is especially true in the case of translucent objects, where we need more than a goniometric measurement of the optical properties. In this survey, we provide an overview of forward and inverse models for acquiring the optical properties of translucent materials. We map out the efforts in graphics research in this area and describe techniques available in related fields. Our objective is to provide a better understanding of the tools currently available for appearance specification when it comes to digital representations of real translucent objects.
A Survey on Sketch Based Content Creation: from the Desktop to Virtual and Augmented Reality

Sketching is one of the most natural ways for representing any object pictorially. It is however, challenging to convert sketches to 3D content that is suitable for various applications like movies, games and computer aided design. With the advent of more accessible Virtual Reality (VR) and Augmented Reality (AR) technologies, sketching can potentially become a more powerful yet easy‐to‐use modality for content creation. In this state‐of‐the‐art report, we aim to present a comprehensive overview of techniques related to sketch based content creation, both on the desktop and in VR/AR. We discuss various basic concepts related to static and dynamic content creation using sketches. We provide a structured review of various aspects of content creation including model generation, coloring and texturing, and finally animation. We try to motivate the advantages that VR/AR based sketching techniques and systems can offer into making sketch based content creation a more accessible and powerful mode of expression. We also discuss and highlight various unsolved challenges that current sketch based techniques face with the goal of encouraging future research in the domain.
Heritability and genetic potential of upland cotton genotypes for morpho-yield traits.

The studies determining genetic variability and heritability in upland cotton were carried out in a randomized complete block (RCB) design with three replications during 2008 at the NWFP Agricultural University Peshawar, Pakistan. The breeding material comprised of eight Gossypium hirsutum cultivars viz., SLH-284, CIM-446, CIM-473, CIM-496, CIM-499, CIM-506, CIM-554 and CIM-707. The cultivars manifested highly significant differences (p<0.01) for plant height, monopodia and sympodia plant and seed cotton yield plant, while merely significant (p<0.05) for days to first flowering and boll weight. However, first internode length showed non-significant variation among the cultivars. The cultivar CIM-506 was found top promising by having maximum seed cotton yield plant, sympodia plant, short stature plants, and medium early maturity and boll weight as compared to other seven cultivars. The cultivars CIM-707 and CIM-554 also showed comparable yield contributing traits and seed cotton yield. The heritability broad sense (bs) was high for the traits days to first flowering (0.96), plant height (0.95), monopodia plant (0.88), sympodia plant (0.89), boll weight (0.97) and seed cotton yield plant (0.91) while first internode length (0.36) revealed low heritability. For majority of the traits the genetic variances were also greater than environmental variances and were found high heritable. Therefore, the said breeding material has the room for further improvement of morpho-yield traits and can safely be used in future breeding programmes.
Characteristics in Polyploid Meiwa Kumquat (Fortunella crassifolia Swingle) Induced by Colchicine Treatment to Nucellar Embryos and Their Utilization for Triploid Breeding

ニンポウキンカン種子へのコルヒチン処理から得た四倍体6系統（No.5，No.6，No.8，No.12，No.18およびNo. 19）の倍数性と発生起源の確認，樹体および果実の特性調査を行うとともに，二倍体との交雑による三倍体の作出を試みた．これら6系統は，CMA染色による核型分析により，すべて珠心胚由来であることが推察された．倍数性解析を行ったところ，No.8は二倍体と四倍体の倍数性キメラであり，その他5系統は四倍体であった．四倍体5系統は，二倍体と比較して葉，花および花粉が大きく，花粉稔性が低くなるなどの四倍体特有の形質を示した．一方，果実は二倍体と比較して四倍体の方が厚皮，高糖度および少核となり，キンカンにとって望ましい形質を有していた．No.8は表皮系が二倍体同様の特徴を示したものの，その他の特性は四倍体と類似した．二倍体との正逆交雑におけるほとんどの交雑組合せで三倍体が得られた．
ON OUTGROUPS

Abstract— The relations among polarity, outgroups and rooting are clarified. The “outgroup algorithm” and “outgroup substitution method” are irrelevant forms of relaxed parsimony. They should be discarded in favor of unconstrained, simultaneous analysis of all terminals. A revised outgroup method is described both in text and with a computer‐generated flowchart. Lundberg rooting is consistent with cladistic parsimony only under specific circumstances involving hypothetical ancestors.
The State of the Art in Enhancing Trust in Machine Learning Models with the Use of Visualizations

Machine learning (ML) models are nowadays used in complex applications in various domains, such as medicine, bioinformatics, and other sciences. Due to their black box nature, however, it may sometimes be hard to understand and trust the results they provide. This has increased the demand for reliable visualization tools related to enhancing trust in ML models, which has become a prominent topic of research in the visualization community over the past decades. To provide an overview and present the frontiers of current research on the topic, we present a State‐of‐the‐Art Report (STAR) on enhancing trust in ML models with the use of interactive visualization. We define and describe the background of the topic, introduce a categorization for visualization techniques that aim to accomplish this goal, and discuss insights and opportunities for future research directions. Among our contributions is a categorization of trust against different facets of interactive ML, expanded and improved from previous research. Our results are investigated from different analytical perspectives: (a) providing a statistical overview, (b) summarizing key findings, (c) performing topic analyses, and (d) exploring the data sets used in the individual papers, all with the support of an interactive web‐based survey browser. We intend this survey to be beneficial for visualization researchers whose interests involve making ML models more trustworthy, as well as researchers and practitioners from other disciplines in their search for effective visualization techniques suitable for solving their tasks with confidence and conveying meaning to their data.
SeqDynamics: Visual Analytics for Evaluating Online Problem‐solving Dynamics

Problem‐solving dynamics refers to the process of solving a series of problems over time, from which a student's cognitive skills and non‐cognitive traits and behaviors can be inferred. For example, we can derive a student's learning curve (an indicator of cognitive skill) from the changes in the difficulty level of problems solved, or derive a student's self‐regulation patterns (an example of non‐cognitive traits and behaviors) based on the problem‐solving frequency over time. Few studies provide an integrated overview of both aspects by unfolding the problem‐solving process. In this paper, we present a visual analytics system named SeqDynamics that evaluates students ‘problem‐solving dynamics from both cognitive and non‐cognitive perspectives. The system visualizes the chronological sequence of learners’ problem‐solving behavior through a set of novel visual designs and coordinated contextual views, enabling users to compare and evaluate problem‐solving dynamics on multiple scales. We present three scenarios to demonstrate the usefulness of SeqDynamics on a real‐world dataset which consists of thousands of problem‐solving traces. We also conduct five expert interviews to show that SeqDynamics enhances domain experts’ understanding of learning behavior sequences and assists them in completing evaluation tasks efficiently.
Displacement‐Correlated XFEM for Simulating Brittle Fracture

We present a remeshing‐free brittle fracture simulation method under the assumption of quasi‐static linear elastic fracture mechanics (LEFM). To achieve this, we devise two algorithms. First, we develop an approximate volumetric simulation, based on the extended Finite Element Method (XFEM), to initialize and propagate Lagrangian crack‐fronts. We model the geometry of fracture explicitly as a surface mesh, which allows us to generate high‐resolution crack surfaces that are decoupled from the resolution of the deformation mesh. Our second contribution is a mesh cutting algorithm, which produces fragments of the input mesh using the fracture surface. We do this by directly operating on the half‐edge data structures of two surface meshes, which enables us to cut general surface meshes including those of concave polyhedra and meshes with abutting concave polygons. Since we avoid triangulation for cutting, the connectivity of the resulting fragments is identical to the (uncut) input mesh except at edges introduced by the cut. We evaluate our simulation and cutting algorithms and show that they outperform state‐of‐the‐art approaches both qualitatively and quantitatively.
Study on differentiation of chicken spermatogonial stem cells into osteoblasts in vitro

The current project is conducted to investigate the capability of spermatogonial stem cells(SSCs) differentiating into osteoblasts in vitro.SSCs were isolated from chicken embryo testis on 18th~20th hatching days,then cultured and subcultured in vitro.SSCs were induced into osteoblasts by desamethason,glycerol 2-phosphate disodium salt hydrate and vitamin C and examined by Von Kossa's stain,cytochemistry staining and immunohistochemistry staining.The results showed that osteoblasts were differentiated from SSCs after 15~21 days of induction and with 75%~80% of positive cells efficiency.Black granules were distributed in the differentiated cells by Von Kossa's staining,suggesting mineral cumulation in the cells.Our results were also confirmed by ALP and immunohistochemistry staining.Together,our results indicated that the chicken SSCs could be differentiated into osteoblasts,suggesting SSCs have the capability of multipotential differentiation in vitro.
The Genetic Diversity and Phylogenetic Relationships among Pig Breeds of Shandong Province Based on Partial Sequence of mtDNA D-loop Region

In order to study the genetic diversity and phylogenetic relationships among pig breeds of Shandong Province,the mtDNA D-loop regions of 165 samples representing the pig breeds of Shandong Province(Laiwu Black pigs,Dapulian Black pigs,Licha Black pigs,Yantai Black pigs,Yimeng Black pigs,Wulian Black pigs,Changwei White pigs and Luyan White pigs) and the exotic pig breeds(Duroc,Yorkshire,Landrace) were determined using the PCR amplification,sequencing for partial sequence of mtDNA D-loop region(1 102 bp) and data was analyzed using bioinformatics software.The result indicated that the mean distances among pig breeds of Shandong Province(0.000 5-0.004 6) were smaller than that between Duroc,Landrance and pig breeds of Shandong Province(0.14). But Yorkshire had rather small mean distances(0.005) with pig breeds of Shandong Province.The NJ phylogenetic tree classified the above samples into 2 clusters.One was composed of pig breeds of Shandong Province and partial Yorkshire,and the other was composed wholly of exotic pig breeds.In the cluster of Shandong Province pig breeds,Laiwu and Dapulian Black pigs were clustered in the NJ trees,and the others were rather dispersive.It indicated that Laiwu and Dapulian Black pigs had simple maternal bloods,and the other breeds had complex maternal bloods,and ever had large gene flow with each other.
The Mechanism of Interference with Fish Viral Infection in the RTG-2 Cell Line

The influence of cell density on viral infectivity titers and interferon production were studied by a plaque and end-point dilution method. The RTG-2 cell line was infected with eel virus European (EVE), infectious pancreatic necrosis virus (IPNV) and infectious hematopoietic necrosis virus (IHNV). The confluent condition of RTG-2 cells was classified into two phases according to the cell density, viz. loosely confluent (6.0 × 104 cells/cm2) and tightly confluent cell sheets (1.2 × 105 cells/cm2). Viral infectivity titers were highest in loosely confluent cell sheets. Virus titers decreased by 50-70% in a plaque method and 90-99% by end-point dilution in tightly confluent cell sheets. Conversely more interferon was produced in tightly rather than loosely confluent cell sheets. We may, therefore, conclude that interferon seems to be a factor contributing to the significant reduction of viral infectivity titers in tightly confluent cell sheets.
Tolerance to Fusarium Root Rot and Changes in Antioxidative Ability in Mycorrhizal Asparagus Plants

Tolerance to fusarium root rot caused by Fusarium oxysporum f. sp. asparagi (Foa, MAFF305556 and N9-31) and the changes in antioxidative abilities in mycorrhizal asparagus (Asparagus officinalis L., cv. Welcome) plants were investigated. Asparagus plants were inoculated with arbuscular mycorrhizal fungus (AMF, Glomus sp. R10) and Foa was inoculated 10 weeks after AMF inoculation. AMF plants accumulated higher dry weight of ferns and roots than non-AMF plants before and after Foa inoculation. AMF colonization level reached more than 70% and no difference noted among the treatments. Asfordiseasetolerance,non-AMFplantsshowed100%inincidenceofrootrotandhighest severityinbothFoaisolates;theseverityofsymptomwasrelativelyhigherinMAFF305556 compared with N9-31. However, AMF plants showed lower severity than non-AMF plants in both Foa isolates. Before and after Foa inoculation, antioxidative abilities increased in most of the AMF plants than non-AMF in the following items: activity of superoxide dismutase (SOD) and ascorbate peroxidase (APX), 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, and total contents of polyphenol and ascorbic acids. These resultssuggestthatplantgrowthenhancementandtolerancetofusariumrootrotappeared inmycorrhizalasparagusplants.Inthiscase,thediseasetolerancemightbeassociatedwith the increase in antioxidative ability.
Spectrophotometry

light as a beam of light passes through sample solution. The basic principle is that each compound absorbs or transmits light over a certain range of wavelength. This measurement can also be used to measure the amount of a known chemical substance. Spectrophotometry is one of the most useful methods of quantitative analysis in various fields such as chemistry, physics, biochemistry, material and chemical engineering and clinical applications.
In Situ Hybridization: Fruit Fly Embryos and Tissues

It is well known that transcript localization controls important biological processes, including cell fate determination, cell polarity, cell migration, morphogenesis, neuronal function, and embryonic axis specification. Thus, the sub‐cellular visualization of transcripts in ‘their original place’ (in situ) is an important tool to infer and understand their trafficking, stability, translation, and biological functions. This has been made possible through the use of labeled ‘anti‐sense’ probes that can be readily detected after hybridization to their ‘sense’ counterparts. The following is a series of protocols for conducting in situ hybridization in Drosophila (fruit fly) embryos or tissues. Probe‐detection methods include a relatively simple alkaline phosphatase reaction, as well as higher‐resolution and higher‐throughput versions using fluorescence‐conjugated tyramide labeling. New modifications that enhance probe penetration and detection in various tissues are also provided. © 2017 by John Wiley & Sons, Inc.
Visual Analysis of the Finite‐Time Lyapunov Exponent

In this paper, we present an integrated visual analytics approach to support the parametrization and exploration of flow visualization based on the finite‐time Lyapunov exponent. Such visualization of time‐dependent flow faces various challenges, including the choice of appropriate advection times, temporal regions of interest, and spatial resolution. Our approach eases these challenges by providing the user with context by means of parametric aggregations, with support and guidance for a more directed exploration, and with a set of derived measures for better qualitative assessment. We demonstrate the utility of our approach with examples from computation fluid dynamics and time‐dependent dynamical systems.
A Comparative Study on the Fruit and Nut Characters of 12 Pecan(Carya illinoemis) Clones and Their Yield

Fruit characters,nut traits and yield of 12 pecan(Carya illinoensis) clones were compared and the correlation between them was analyzed.The result showed highly significant difference among the clones in the 12 indexes studied.The CV(coefficient of variance) of the fruit characters appeared in the order of fresh fruit yield per tree fruit weight peel thickness fruit height fruit shape index fruit diameter,being 61.06%,30.18%,25.60%,16.48%,13.77% and 10.54%,respectively.A similar order was observed for the nut traits,i.e.nut yield per tree nut weight nut weight in fruit nut height nut shape index nut diameter.Fruit weight was in a significant positive correlation with nut weight in various clones,and fruit height was in a highly significant positive correlation with nut height.It is,therefore,postulated that nut size and shape of C.illinoensis can be predicted based on its fruit size and shape.
A Visual Analytics Approach to Facilitate Crime Hotspot Analysis

Computer‐based technology has played a significant role in crime prevention over the past 30 years, especially with the popularization of spatial databases and crime mapping systems. Police departments frequently use hotspot analysis to identify regions that should be a priority in receiving preventive resources. Practitioners and researchers agree that tracking crime over time and identifying its geographic patterns are vital information for planning efficiently. Frequently, police departments have access to systems that are too complicated and excessively technical, leading to modest usage. By working closely together with domain experts from police agencies of two different countries, we identified and characterized five domain tasks inherent to the hotspot analysis problem and developed SHOC, a visualization tool that strives for simplicity and ease of use in helping users to perform all the domain tasks. SHOC is included in a visual analytics system that allows users without technical expertise to annotate, save, and share analyses. We also demonstrate that our system effectively supports the completion of the domain tasks in two different real‐world case studies.
Survey on the Analysis of User Interactions and Visualization Provenance

There is fast‐growing literature on provenance‐related research, covering aspects such as its theoretical framework, use cases, and techniques for capturing, visualizing, and analyzing provenance data. As a result, there is an increasing need to identify and taxonomize the existing scholarship. Such an organization of the research landscape will provide a complete picture of the current state of inquiry and identify knowledge gaps or possible avenues for further investigation. In this STAR, we aim to produce a comprehensive survey of work in the data visualization and visual analytics field that focus on the analysis of user interaction and provenance data. We structure our survey around three primary questions: (1) WHY analyze provenance data, (2) WHAT provenance data to encode and how to encode it, and (3) HOW to analyze provenance data. A concluding discussion provides evidence‐based guidelines and highlights concrete opportunities for future development in this emerging area. The survey and papers discussed can be explored online interactively at https://provenance-survey.caleydo. org.
Simulation of Dendritic Painting

We present a new system for interactive dendritic painting. Dendritic painting is characterized by the unique and intricate branching patterns that grow from the interaction of inks, solvents and medium. Painting sessions thus become very dynamic and experimental. To achieve a compelling simulation of this painting technique we introduce a new Reaction‐Diffusion model with carefully designed terms to allow natural interactions in a painting context. We include additional user control not possible in the real world to guide and constrain the growth of the patterns in expressive ways. Our multi‐field model is able to capture and simulate all these complex phenomena efficiently in real time, expanding the tools available to the digital artist, while producing compelling animations for motion graphics.