Miracle-dz/UniFAR-FTUs huggingface dataset:
Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects

Abstract More than 190 plastid genomes have been completely sequenced during the past two decades due to advances in DNA sequencing technologies. Based on this unprecedented abundance of data, extensive genomic changes have been revealed in the plastid genomes. Inversion is the most common mechanism that leads to gene order changes. Several inversion events have been recognized as informative phylogenetic markers, such as a 30‐kb inversion found in all living vascular plants minus lycopsids and two short inversions putatively shared by all ferns. Gene loss is a common event throughout plastid genome evolution. Many genes were independently lost or transferred to the nuclear genome in multiple plant lineages. The trnR‐CCG gene was lost in some clades of lycophytes, ferns, and seed plants, and all the ndh genes were absent in parasitic plants, gnetophytes, Pinaceae, and the Taiwan moth orchid. Certain parasitic plants have, in particular, lost plastid genes related to photosynthesis because of the relaxation of functional constraint. The dramatic growth of plastid genome sequences has also promoted the use of whole plastid sequences and genomic features to solve phylogenetic problems. Chloroplast phylogenomics has provided additional evidence for deep‐level phylogenetic relationships as well as increased phylogenetic resolutions at low taxonomic levels. However, chloroplast phylogenomics is still in its infant stage and rigorous analysis methodology has yet to be developed.
Freshwater and brackish “oasis” fauna in the deep Black Sea

Received 03.08. 2012; accepted 03.09. 2012; printed 30.09. 2012 Present paper reports on the possible existence of recent freshwater fauna in the Black Sea. Based on information available from malacology, ecology, paleontology, stratigraphy, hydrogeology and observations in situ, the presence of freshwater biota on the shelf and continental slope is discussed, including the existence of aerobic life forms in the Black sea deep-water cavity.
Meiosis disturbances, aneuploidy and seed fertility in Raphanobrassica

Meiosis was studied in one F2- and one F7 population of the amphidiploid hybrid Raphanobrassica, the F7-population being the result of uninterrupted fertility selection. Univalents at M1 and laggards and bridges at A1 and AII are frequent, resulting in aneuploid gametes and plants. These disturbances are supposed to be caused by insufficient meiotic timing between the parental genomes, i.e. the same explanation as has been given for similar disturbances in triticale. There are no indications that repeated selection resulting in improved seed fertility has any influence on the rate of disturbances at meiosis. Meiosis appears to be only slightly influenced by external factors, while seed fertility is considerably influenced. The best seed fertility so far obtained from material grown in greenhouses in SvalOv is 31 %. A seed fertility of 43 % has been obtained from the same material when grown in the field in Spain. Raphanobrassica has potentials to become an interesting annual fodder crop if an economic seed production can be made possible through further improvements of seed fertility and by a proper choice of propagation sites. The population will, however, still be impaired by the same meiotic irregularities as the present material of Raphanobrassica.
Effects of dietary protein and energy levels on the reduction of nitrate and nitrite in the rumen and methemoglobin formation in sheep.

反芻家畜の第一胃内亜硝酸塩蓄積及び血中メトヘモグロビン形成に関与する飼料的要因を知る目的で,ルーメンフィステル装着コリデール種去勢メン羊4頭を用い,NRC飼養標準に基づいてTDN及びDCPについて異なる4種の飼料給与区分:R-1(TDN100%;DCP100%),R-2(TDN50%;DCP100%),R-3(TDN100%;DCP50%),R-4(TDN50%;DCP50%)を設定し,4×4のラテン方格法による硝酸塩投与試験を実施した. 硝酸塩は30gのNaNO3を30%(w/v)水溶液としてフィステルより第一胃内に投与した. 1) 第一胃内NO3-Nの消長には有意な処理間差は認められなかったが,第一胃内NO2-NはTDN給与量の低い区で高い蓄積の傾向がみられた. さらに,この傾向はDCP給与量の高いR-2区では顕著であった. 2) 血漿NO2-濃度はDCP給与量の高い区で比較的高い傾向を示した. また,血中メトヘモグロビン形成の程度はTDN給与量が低く,DCP給与量が高い条件下で高くなる傾向を認めた. 逆に,TDN給与量が高くDCP給与量が低い条件下では血中メトヘモグロビン形成の程度は相対的に低いもこと考えられた. 3) 赤血球GSH濃度の推移には有意な処理間差は認められなかったが,硝酸塩の投与により投与前の1. 5μmole/ml cellsの水準から24～60%減少の傾向を示した.
Simulations of Drop Impact on Hydrophobic Moving Walls

Numerical simulations of water drop impact onto a hydrophobic surface are carried out through usage of Eulerian multiphase model. Volume of uid (VOF) model is used to capture the deformation of the water drop interface. RANS equations were solved by realizable k − turbulence model. Two and three dimensional simulations are conducted. Results of the simulations are compared with the published experimental data. Results for maximum drop spreading have errors below 10% compared to their experimental counterparts. It is shown that 2D simulations augments splitting of droplets due to entrapped bubbles upon impact while 3D simulations reproduce deposition observed in experiments, but partial rebound and split deposition phenomena can not be reproduced. The discrepancy between the experiments and 2D as well as 3D simulations are analyzed.
Comparison of The Phagocytic Activity Of Gingival Crevicular Fluid (GCF) Neutrophils At Healthy Sites With Periodontally Diseased Sites

Aim and Objectives: The purpose of this study was to compare the GCF neutrophils function with the following objectives:1) To assess the total GCF neutrophils count in Healthy and Chronic Periodontitis patients. 2) To assess the percentage of phagocytic capacity of GCF neutrophils in Healthy and Chronic Periodontitis patients. Method and Materials:Total thirty subjects (17 females and 13 males) in the age range 20 to 57 years were recruited for the study. Two groups with 15 subjects each were designated as Group 1 (Clinically Healthy), and Group 2 (Chronic Periodontitis) respectively, according to the plaque index, Papillary Bleeding Index and diagnosis was based on their periodontal status assessed clinically and radiographically.2 μl of GCF samples was collected from Group 1 and Group 2 subjects. Total neutrophil count and the neutrophils with ingested bacteria was calculated in both the groups. Results:The mean total GCF neutrophil counts was significantly greater in Group 2 (9027.33 ± 404.16 per cu.mm) as compared to Group 1 (4046.66 ± 324.29 per cu.mm)with positive Pearson’s coerrelation coefficient test between neutrophil count and clinical parameters. However, the percentage of GCF Neutrophils phagocytosing the bacteria in Group 2 (59.66 ± 4.25) was significantly lower than the phagocytic activity of GCF Neutrophils from Group 1 (75.26 ± 4.11). Conclusion: Neutrophil count and its phagocytic activity is altered in chronic periodontitis as compared to healthy subjects, increasing the susceptibility of individual to disease. Therefore, GCF neutrophils count could be used to assess the disease activity as a simple chair-side diagnostic tool. Introduction Periodontitis is an inflammatory reaction to a microbial infection associated with dental plaque that results in tissue loss. It is classified as: Chronic periodontitis: An infectious disease resulting in inflammation within the supporting tissues of the teeth, progressive attachment loss and bone loss. Aggressive periodontitis: Comprises of group of rare, severe, rapidly progressive forms of periodontitis often characterized by an early loss of teeth. Periodontal diseases are best considered as the outcome of an imbalance in the host parasite interaction. The extent and severity of disease depends on the interaction between the pathogenic challenge and host response. The narrow balance between periodontal homeostasis and disease depends upon an GCF NEUTROPHIL ACTIVITY IN HEALTH AND DISEASE 3(1);2017 52 Journal Of Applied Dental and Medical Sciences 3(1);2017 Figure no. 1.Colour Coded Calibrated volumetric Micro capillary
Integrating Design of Experiments and Writing into a Manufacturing Processes Course

The manufacturing processes course taught at the University of Minnesota Duluth is an integration of traditional lecture, writing, and laboratory intensive. The laboratory component focuses on the use of writing and design of experiments to analyze and characterize manufacturing processes. Results and observations from the experiments are presented in a journal format. Plastic injection molding, green sand casting, extrusion, blank shearing, welding, and fiber reinforced composite processing have been taught and implemented in the laboratory using this approach. Students prepare detailed reports in a journal format on any four of the laboratory experiments conducted. In lecture, students learn theory of manufacturing processes, how to design and analyze experiments, and conduct literature review on manufacturing processes in professional journals. For each process, the instructor and students identify significant control process factors and quality characteristics to be investigated. The levels of the control factors are chosen in order not to obscure the influence of a control factor on the measured quality characteristics. This technique of teaching manufacturing processes course exposes students to critical thinking about the fundamental assumptions, discussing calculated results, analyzing plots of data, posing questions about the meaning of definitions, increasing interest in and connection with course material, and becoming familiar with engineering writing conventions. I. Background The College of Science and Engineering is a four-year ABET accredited engineering school offering engineering degrees in mechanical & industrial, chemical, computer science, and electrical & computer engineering. The curriculum emphasizes design, manufacture, and automation, while preparing students for careers in industry and continued education. A fourcredit manufacturing process course is designed for junior and senior level mechanical and industrial engineering students. The course consists of three hours of lecture and two hours of laboratory work each week. Department of Mechanical and Industrial Engineering has a material processing laboratory equipped with a wide range of traditional manufacturing processes equipment to support its practice oriented, hands-on, design-centered curriculum. The science of engineering involves understanding how things work in a mathematical fashion. Engineers build mathematical models of reality, but the models are always a simplification of reality. Hopefully, the model will give us greater understanding, but we must be careful that our model has some contact with the reality. We must verify model predictions with experiment and observation. Sometimes even the simplest situations are too difficult to describe with mathematical models. That is why the practice of engineering requires a combination of both art and science. To understand how things work, we must understand the underlying cause-
Effects of Vitamin A Restriction on Growth and Carcass Characteristics of Japanese Black Steers Measured by Ultrasonic Equipment

ビタミンA（VA）制限が産肉形質およびその経時的変化に及ぼす影響を，黒毛和種去勢牛10頭を用いて調査した．試験区はVAを10～21ヵ月齢まで無補給とし，22～27ヵ月齢まで補給した制限区と，10～27ヵ月齢まで補給した補給区を設定した．VA制限は増体には影響を及ぼさなかった．超音波診断装置により推定した脂肪交雑等級（BMS）の経時的変化は，18ヵ月齢から有意に高くなった（P＜0.05）．その時点の血中レチノール濃度は約30IU/dLであった．枝肉格付のBMSはVAを制限することで有意に高くなった（P＜0.05）．胸最長筋面積および皮下脂肪厚の経時的変化には影響を及ぼさなかった．VAを制限している期間の血中レチノール濃度の経時的変化はBMSの経時的変化に影響を及ぼしていることが生体画像情報として明らかとなった．
Tomas BALEŽENTIS,

This paper analyses the total factor productivity in the Lithuanian agricultural sector, namely family farms reporting to the Farm Accountancy Data Network. More specifically, the Malmquist productivity index and data envelopment analysis are employed to analyze productivity changes and thus define respective policy implications. The research covers the period of 2003–2009. The four output indicators were employed for DEA, namely land productivity, labour productivity, return on assets, and intermediate consumption productivity. The analysis showed that the total factor productivity in the Lithuanian family farms had been decreasing throughout 2004–2005, and has been recovering by 1.3–8.1 per cent annually. However, technical change contributed to the increase in the total factor productivity rather insignificantly.
11.3: Culture

Although the most visible elements of culture are dress, cuisine and architecture, culture is a highly psychological phenomenon. Culture is a pattern of meaning for understanding how the world works. This knowledge is shared among a group of people and passed from one generation to the next. This module defines culture, addresses methodological issues, and introduces the idea that culture is a process. Understanding cultural processes can help people get along better with others and be more socially responsible.
SELEKSI IN VITRO UNTUK MENDAPATKAN GALUR

In-vitro selection to produce drought tolerant and stem rot Sclerotium rolfsii resistant peanut. The main limiting factors of peanut cultivation in dry land are insufficient water and S. rolfsii infection. The effort of peanut cultivation management in upland is use of drought tolerant and disease resistant cultivar. Application of somaclonal variation induction and in vitro selection using selective agent is a reliable method to be developed to create new peanut line. For this reason, the objectives of this research was to obtain drought tolerant and stem rot disease resistant peanut line. The experiment was inisiated with induction of somaclonal variation in MS-P16. Medium of MS-P16 that added PEG 15% as selective agent for drought stress and MS-P16 medium with culture filtrate 30% as selective agent for disease resistance. Embriogenic calli were placed on PEG medium for three months per cycle. PEG insensitive somatic embryos (SE) were proliferated, and this SE named SE Pi. In vitro double selection was done with challenge SE Pi against culture filtrate medium, and insensitive SE named SE PiFi. All insensitive selected SEs were germinated to generate plantlets (R0 generation). These plants were harvested to obtain R0:1 seeds. The seeds were grown (R1 plant) to produce R1:2 seeds. These plants of R2 generation were used to somaclonal plant evaluation against water stress and pathogen infection. Result of this research showed somaclonal plants regenerated from in vitro selection against PEG and culture filtrate were more tolerance to water defisit and more resistance to S. rolfsii infection, and produced higher dry pod yield
MSFMT: MULTI-SPECTRAL FUSION SYSTEM BASED ON DEEP TRANSFER LEARNING AND DEMPSTER-SHAFER THEORY

This paper presents a multi-spectral fusion system for improving the object detection and classification results in military and terrorism domains that entitled MSFMT. It relies on a combination between deep transfer learning and Dempster-Shafer statistical method in decision level fusion. It improves the classification results through fusing multiple sensory data that are extracted from multiple sources into two data types, images and videos, in night modes. It fuses multiple spectrums for showing the best vision for each object or action. These spectrums are Visual Intensified images (VIS), Near-infrared spectroscopy (NIR) images, thermal images, long wave infrared images (LIWR), DHV, and RGB). The neural network structure is constructed based on six neural networks. Each neural network is based on AlexNet pre-trained transfer neural networks for classifying spectrums. Each neural includes two neural networks for classifying objects and actions. MSFMT system improves the classification results through creating a new algorithm for multi-spectral fusion that depends on integration between machine learning (transfer learning model) and statistics methods (Dempster-Shafer evidential reasoning technique). MSFMT uses a purified dataset that consists of tuned six datasets for multiple spectrums in variant type format. It applies the data augmentation for enlarging the dataset that includes 875,970 number of images and video's frames. The fusion accuracy results reach 96 % that increases the classification results by 21% for NIR and VIS spectrums, 7% for Thermal spectrum, and 4 to 6% for LIWR, DHV, RGB, spectrums.
Review of the Biological Oceanography of the Strait of Georgia: Pelagic Environment

Different components of the food web in the Strait of Georgia are reviewed. The phytoplankton are dominated by diatoms; however, flagellates may dominate in the winter. Chlorophyll a concentrations may range from 15 mg∙m−3 during blooms. The average annual primary productivity is about 280 g C∙m−2 for the strait, but it is higher in frontal areas at the north and south ends of the strait and near the Fraser River plume. Light limits primary productivity during the winter months, while nutrients (nitrogen) and grazing are the limiting factors during the late spring and summer. Turbidity and salinity effects occur near the Fraser River plume. The surface macrozooplankton community is composed chiefly of copepods. Mid- and deep-water communities consist of euphausiids, chaetognaths, and some deep-living copepods, which overwinter at depth. The standing stock of macrozooplankton (> 350 μm) to 400 m, ranges from 0.1 to 2.0 g wet wt∙m−3. Few estimates of secondary production and st.
Effect of injectable platelet rich fibrin (i-PRF) on thin gingival biotype: A clinical trial

Introduction and Aim: The term gingival biotype has been used to describe the thickness of the gingiva in the faciopalatal dimension. A gingival thickness of ≥2 mm is defined as thick biotype and a gingival thickness of <1.5 mm as thin biotype. A thin gingival biotype is considered as an important predisposing factor for gingival recessions. Gingival recession being common esthetic problem encountered in rountine dental practice, an attempt should be made to increase the gingival thickness inorder to prevent gingival recession. A liquid injectable-platelet-rich fibrin (i-PRF) is a rich source of autologous growth factor and is recently being used in regenerative dentistry. So, the aim of this study was to evaluate the effect of iPRF on thin gingival biotype. Methodology: Forty sites from systemically healthy patients having thin gingival biotype were included in this study. iPRF was injected at the selected site using microneedle at baseline, 1 week and 2 weeks. Plaque index (PI), gingival index (GI), gingival thickness (GT) and keratinized tissue width (KTW) were assessed before the treatment and one month and three months after the final injections. Results: At baseline mean PI, GI, GT and KTW were 0.63, 0.90, 0.55mm and 5.25mm respectively. At one month and three months follow up, there was statistically significant difference seen in PI, GI, GT and KTW. Mean GT increased from 0.55mm at baseline to 1.05mm and 1.03mm at 1month and 3months respectively. Conclusion: i-PRF using microneedle can be effective for increasing gingival thickness in subjects having thin gingival biotype. INTRODUCTION Marked transformation in the field of periodontics has led to the development of newer, less invasive therapeutic approaches along with improved diagnostic methods, which allows proper evaluation and management of surrounding tissues to provide best outcome of periodontal therapy. Minimally invasive treatment helps to achieve satisfactory therapeutic results with minimum trauma to tissues of any interventional process. The gingival biotype and different parts of the masticatory mucosa have become the subject of considerable interest in Periodontics, especially from an aesthetic and therapeutic perspective. The size of the alveolar bone, tooth morphology, events that occur during tooth eruption and the final position of the tooth when tooth is fully erupted determine the architecture of the gingival tissue. The term ‘gingival biotype’ has been used to describe the thickness of gingiva in the facio palatal dimension. According to Ochsenbien and Ross
A Review: Phylogeny Construction Methods

In bioinformatics, the phylogenetics is the study of evolutionary pathway that gives the relationship between various organisms. Phylogenetics act as an important tool of bioinformatics as it handle huge biological data in the form of evolutionary trees. This relationship can be inferred on the basis of the heritable traits such as nucleotide or protein sequences. The phylogenetic tree can be constructed using different methods: WPGMA, UPGMA, neighbor joining, maximum parsimony or etc. Phylogeny has become the central part of bioinformatics and can be used in different fields to solve their respective problems such as forensics, drug discovery, and vaccine development etc.
The Just-in-time Flipped Classroom: A New Way to Learn English in a Teacher Education Setting

This paper discusses the implementation of two pedagogical models: Just-in-time Teaching and Flipped Learning. The study was carried out in an English as a foreign language (EFL) setting. Participants were seventhsemester pre-service language teachers, so the context is a Teacher Education Program. Results have shown that the implementation has favored not only the student’s learning process, but also their own reflection towards learning.
Paternal care in rodents: Ultimate causation and proximate mechanisms

The evolution of paternal care in rodents has intrigued biologists for over decades. In this paper, both ultimate (adaptive significance, evolution) and proximate (ontogeny, mechanisms) questions related to the emergence and maintenance of male paternal care are reviewed. Paternal care is thought to be a consequence of social monogamy, but no definitive hypothesis adequately explains the evolution of paternal behavior in rodents. The onset, activation and maintenance of paternal care are shown to be governed by complex interactions in neuroendocrine systems that change during ontogeny. Depending on the species, different components of male experience as well as different exogenous cues are likely to be involved in the organization and activation of paternal behavior. Several hormones, including steroids (testosterone, estradiol, progesterone) and neuropeptides (prolactin, vasopressin, oxytocin), are involved in the onset, the maintenance, or both the onset and the maintenance of parental behavior, including direct paternal care. The effect of testosterone was found to be not universal and, moreover, species-specific. As for estrogens and neuropeptides, further investigations are needed to better understand the role of these hormones in activation and maintenance of rodent paternal behavior. Current research shows that male parental care in rodents is, to a great extent, an epigenetic phenomenon, and future studies will focus on the epigenetic modifications that can affect the paternal behavior in rodents. How to cite this article: Gromov V.S. 2020. Paternal care in rodents: ultimate causation and proximate mechanisms // Russian J. Theriol. Vol.19. No.1. P.1–20. doi: 10.15298/rusjtheriol.19. 1.01.