Miracle-dz/UniFAR-FTUs huggingface dataset:
CONSERVATION OF GENETIC RESOURCES IN HORSE BREEDING AND MAJOR STRUCTURAL DAMAGES OF SPERM DURING SEMEN CRYOPRESERVATION IN STALLIONS

Assisted reproductive technologies have been used in zoos and breeding centres to preserve rare and endangered species of wild animals over the past three decades. The most common way to preserve the genetic material of farm and wildlife animals is to create cryobanks of semen producers and embryos. Studies of domestic species under controlled conditions provide an excellent opportunity to develop effective semen handling techniques for application to wild species of the genus Equus. The All-Russian Research Institute for Horse Breeding (ARRIH) began studies on the cryopreservation of genetic resources in the early 1950s. In 1954 the ARRIH got the world’s first foal from the artificial insemination by cryopreserved sperm. The collection of genetic resources of ARRIH has been successfully working since 1972 and contains nowadays cryopreserved sperm from 56 stallions of 16 breeds of domestic and foreign selections. Freezing and subsequent thawing of stallion sperm leads to a decrease in progressive sperm motility and an increase in the number of sperm with structural pathologies. Electron microscopy is one of the most accurate methods used to assess the structural integrity of sperm. We conducted an electron microscopic study of native and cryopreserved sperm of 35 stallions of riding and trotting breeds, aged 4 to 22 years (mean age 11.3 ± 0.9 years). We found that organoids with a denser structure are more resistant to freezing and subsequent thawing of sperm. The use of stallion sperm cryopreservation according to the standard technology of ARRIH leads to a decrease in the number of sperms with intact heads by an average of 19.7%, and the share of sperm with intact heads in cryopreserved sperm is 49.1 ± 2.7% (p < 0.001). The most negatively cryopreservation of semen affects an acrosome of sperms. The main pathologies of acrosomes in sperm cryopreservation are acrosome hypoplasia and its degradation (secondary absence of acrosome). The number of spermatozoa with acrosome hypoplasia and the absence of internal content after cryopreservation increases by 20.9%, and the share of such sperms is 31.7% in thawed sperm (p < 0.001). The number of sperm with acrosome degradation during sperm freezing and thawing increases by 10.4%, and is 18.6 ± 2.4% in average. The share of spermatozoa with normal mitochondrial structure in native sperm is 89.3 ± 2.0% in average, in cryopreserved sperm – decreases by 6.5%. The share of spermatozoa with normal axoneme after cryopreservation decreases slowly, averaging by 4.4% and is 81.4 ± 2.0%. Some of the available assisted reproduction technologies will need to be further optimised in domestic horses before they can be applied to the endangered Przewalski’s horse Equus ferus przewalskii.
Using Unsupervised Artificial Neural Networks to Detect Sibling Species: A case in Myxomycetes

Species distribution modelling (SDM) --i.e. the prediction of species potential geographic distributions based on correlations between known presence records and the environmental conditions at occurrence localities-- is one of the most freqently cited developments in recent years in the realm of biodiversity studies (Web of Science 2019). The reasons for the explosion in SDM studies reside in: a) the pressure to know species distributions (under both present and future climate change scenarios) with precision to satisfy scientific as well as societal objectives; b) the impossibility of knowing every occurrence of all but the most conspicuous and/or special interest species; c) the availability of primary occurrence and environmental data in unprecedented amounts, thanks to initiatives like the Global Biodiversity Information Facility (GBIF); and d) the development of algorithms and software, along with the computing power, which allow inference of species distribution models from the available data. The standard methods to produce such models are based on environmental feature vectors, and some well-established algorithms such as distance-based machine learning, regression or a combination of these (Tsoar et al. 2007). In this presentation, we explore deep learning techniques (LeCun et al. 2015), particularly how those developed in recent years could contribute to the study of species distribution (see also Botella et al. 2018; Deneu et al. 2018). In this contribution we aim to identify sibling species on the basis of their ecological preferences. In this exercise, we prepare an image-based environmental representation space using an unsupervised classification approach, instead of a set of environmental feature vectors. For our case study, we chose a well-known cosmopolitan myxomycete (i.e., mycetozoan) species: Hemitrichia serpula (Scop.) Rostaf. , whose ecological preferences --involving several biomes-- may suggest that it could comprise several sibling species.
KCH kinesin drives nuclear transport and cytoskeletal coalescence for tip cell growth

Long-distance transport along microtubules (MTs) is critical for intracellular organisation. In animals, antagonistic motor proteins kinesin (plus end-directed) and dynein (minus end-directed) drive cargo transport. In land plants, however, the identity of motors responsible for transport is poorly understood, as genes encoding cytoplasmic dynein are missing. How other functions of dynein are brought about in plants also remains unknown. Here, we show that a subclass of the kinesin-14 family, KCH—which can also bind actin—drives MT minus end-directed nuclear transport in the moss Physcomitrella patens. When all four KCH genes were deleted, the nucleus was not maintained in the cell centre but was translocated to the apical end of protonemal cells. In the knockout (KO) line, apical cell tip growth was also severely suppressed. KCH was localised on MTs, including at the MT focal point near the tip where MT plus ends coalesced with actin filaments. MT focus was not persistent in KCH KO lines, whereas actin destabilisation also disrupted the focus despite KCH remaining on unfocused MTs. Functions of nuclear transport and tip growth were distinct, as a truncated KCH construct restored nuclear transport activity but not tip growth retardation of the KO line. Thus, our study identified KCH as a long-distance retrograde transporter as well as a cytoskeletal crosslinker, reminiscent of the versatile animal dynein.
Cyclin binding Cy motifs have multiple activities in the initiation of DNA replication

The initiation of DNA replication involves the cell cycle-dependent assembly and disassembly of protein complexes, including the Origin Recognition Complex (ORC) and CDC6 AAA+ ATPases. We report that multiple short, linear protein motifs (SLiMs) within intrinsically disordered regions in ORC1 and CDC6, including Cyclin-binding (Cy) motifs, mediate Cyclin-CDK dependent and independent protein-protein interactions, conditional on cell cycle phase. The ORC1 Cy motif mediates an auto-regulatory self-interaction, and the same Cy motif prevents CDC6 binding to ORC1 in mitosis, but then facilitates the destruction of ORC1 in S phase. In contrast, in G1, the CDC6 Cy motif promotes ORC1-CDC6 interaction independent of Cyclin-CDK protein phosphorylation. CDC6 interaction with ORC also requires a basic region of ORC1 that in yeast mediates ORC-DNA interactions. We also demonstrate that protein phosphatase 1 binds directly to a SLiM in ORC1, causing de-phosphorylation upon mitotic exit. Thus, Cy-motifs have wider roles, functioning as a ligand and as a degron.
Genotypic variations in salinity tolerance among Bt cotton

Salinity stress is one of the most serious environmental problem that negatively affects the growth of plants, especially in arid and semi-arid regions. Scientists have been struggling to address this problem through land reclamation methods and by adding various organic manures into the soil. However, the most cost effective method is to develop salt tolerant varieties. Keeping this in view, fifty cotton genotypes were collected from different areas and were subjected to evaluation. Plants were irrigated with nutrient solution with an electrical conductivity of 10dSm and 15dSm from 10 day seedlings stage to 40 day. Plants were harvested when they were 40 days old and the data was compared at absolute value and relative values from the seedlings. Analysis of variance indicated that there were significant differences among genotypes at control and both salinity levels. Results showed that salinity adversely affected the root length, shoot length, fresh root weight, fresh shoot weight, dry shoot weight, dry root weight in comparison to chlorophyll contents. Magnitude of Sodium under NaCl stress increased many folds and reduction in potassium was also witnessed in the leaves. Broad sense heritability was high whereas phenotypic variance is equal or less than genotypic variances. The genotypes that perform better for the trait that had high broad sense heritability were selected as salt tolerant genotypes such as KEHKSHAN, S-3, NIAB-824 and MNH-988 whereas C-26, FH-114 and FH-173 were conceived as salt sensitive genotypes. The results indicate that selection for cotton will be problematic due to masking effects of environment, and imply rigorous and careful selection of salt tolerant genotypes.
Similar Searching, Unsimilar Clicking

In the study, a search engine log is partitioned into IP classes that differently present audiences of free and busy searchers. It is shown that searching behavior of users from different classes is practically identical in all characteristics except their click behavior. Differences in click behavior between classes are great. Free users click more frequently than busy users while search in the same manner on other counts.
How do fruit productivity, fruit traits and dietary specialization affect the role of birds in a mutualistic network?

Abstract Many plant traits might explain the different ecological and network roles of fruit-eating birds. We assessed the relationship of plant productivity, fruit traits (colour, seed size and nutritional quality) and dietary specialization, with the network roles of fruit-eating birds (number of partners, centrality and selectivity) in the Atlantic Forest, Brazil. We classified bird species according to their dietary specialization into three categories: obligate, partial and opportunistic fruit-eating birds. To test if network roles changed according to dietary specialization, fruit productivity and traits, we used a generalized linear model analysis. The selected 14 species of plant interacted with 52 bird species, which consumed 2199 fruits. The most central and generalist fruit-eating bird, Turdus albicolis, interacted with plants that produced more fruits, such as Miconia cinerascens, and had, on average, larger seeds, such as Myrcia splendens. The most selective birds interacted with fruits with a higher concentration of lipids and less intense colour, and plants that produced fewer fruits. Obligate fruit-eating birds, such as Patagioenas plumbea, were more selective than partial and opportunistic birds. Different plant traits are therefore related to the different network roles of fruit-eating birds in the Atlantic Forest, which are also dependent on bird dietary specialization.
Improving process mining with trace clustering [in Korean]

Process mining aims at mining valuable information from process execution results (called "event logs"). Even though process mining techniques have proven to be a valuable tool, the mining results from real process logs are usually too complex to interpret. The main cause that leads to complex models is the diversity of process logs. To address this issue, this paper proposes a trace clustering approach that splits a process log into homogeneous subsets and applies existing process mining techniques to each subset. Based on log profiles from a process log, the approach uses existing clustering techniques to derive clusters. Our approach are implemented in ProM framework. To illustrate this, a real-life case study is also presented.
Tressel: Semantic mark-up of RSS feeds

The recent explosion in the popularity of RSS and other syndication technologies has led to a wealth of information being published from an increasingly diverse range of sources. However this popularity makes it dicult for users to find interesting documents, and this challenge is compounded by the fact that most RSS clients oer very modest personalization capabilities. We propose Tressel, a collaborative RSS aggregator that extracts semantically meaningful passages of text from RSS feeds. Tressel employs a semi-supervised machine learning algorithm to identify semantic information. The algorithm learns from a small amount of training data provided by the user. Tressel is collaborative in that the input of each user is used to benefit all of the users. One challenge with such an open system is the danger that users could (intentionally or accidentally) introduce noisy training data. In this paper, we describe Tressel’s architecture and adaptive information extraction algorithm, and then report on experiments which demonstrate that we can reliably detect noisy training data.
Dynamics of proteins in solution

Abstract The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
Similar efficacies of selection shape mitochondrial and nuclear genes in Drosophila melanogaster and Homo sapiens

Deleterious mutations contribute to polymorphism even when selection effectively prevents their fixation. The efficacy of selection in removing deleterious mitochondrial mutations from populations depends on the effective population size (Ne) of the mtDNA, and the degree to which a lack of recombination magnifies the effects of linked selection. Using complete mitochondrial genomes from Drosophila melanogaster and nuclear data available from the same samples, we re-examine the hypothesis that non-recombining animal mtDNA harbor an excess of deleterious polymorphisms relative to the nuclear genome. We find no evidence of recombination in the mitochondrial genome, and the much-reduced level of mitochondrial synonymous polymorphism relative to nuclear genes is consistent with a reduction in Ne. Nevertheless, we find that the neutrality index (NI), a measure of the excess of nonsynonymous polymorphism relative to the neutral expectation, is not significantly different between mitochondrial and nuclear loci. Reanalysis of published data from Homo sapiens reveals the same lack of a difference between the two genomes, though small samples in previous studies had suggested a strong difference in both species. Thus, despite a smaller Ne, mitochondrial loci of both flies and humans appear to experience similar efficacies of selection as do loci in the recombining nuclear genome.
Micropipeline DSP-ASIC for a DS-SS receiver

This paper presents a fully asynchronous DSP for a Direct-Sequence Spread Spectrum (DS-SS) radio receiver. Issues relevant to micropipeline VLSI implementation and performance are discussed. The circuit has been designed using a standard cell library in 0.8 /spl mu/m CMOS and contains 100,000 transistors. The receiver handles up to 48 million samples per second and the power consumption is 600 mW.
The sponge fauna of the Seno Magdalena and Puyuhuapi Fjord (Chile), with a description of two new species.

The presence of fjords, islands and channels originating from glacial erosion and ice cap retreat, makes the Chilean benthic biodiversity difficult to explore and study. Our survey of this region allowed the identification of 29 Demospongiae species in total. Two of them are new to science and here described: Biemna lutea sp. nov., and Hamigera cleistochela sp. nov. Two species (Clathria (Clathria) microxa and Lissodendoryx (Ectyodoryx) patagonica,) are new for the region and the Chilean fjords. Lissodendoryx (Ectyodoryx) patagonica was found for the second time after the original description by Ridley Dendy, 132 years ago. These results - considering the small number of species identified on the whole - are promising and confirm that the marine biodiversity of Chilean fjords is remarkable but not well known yet.
Functional characterization of wheat ALMT1 transporter and its involvement in extreme pH stress tolerance

4 Declaration . 7 Acknowledgments . 8 Dedication . 10 List of Publications from this Thesis . 11 List of Abbreviations . 12 Chapter 1: Introduction and Literature Review Role of ALMT1 transporter during alkaline pH stress . 14 1.
Heterogeneous Exposure and Hotspots for Malaria Vectors at Three Study Sites in Uganda

Heterogeneity in malaria transmission has household, temporal, and spatial components. These factors are relevant for improving the efficiency of malaria control by targeting heterogeneity. To quantify variation, we analyzed mosquito counts from entomological surveillance conducted at three study sites in Uganda that varied in malaria transmission intensity. Using a Bayesian zero-inflated negative binomial model, validated via a comprehensive simulation study, we quantified household differences in malaria exposure and examined its spatial distribution. We found that housing quality explained large variation among households in mosquito counts. In each site, there was evidence for hot and cold spots, spatial patterns associated with urbanicity, elevation, or other environmental covariates. We also found some differences in the hotspots in rainy vs. dry seasons or before vs. after control. This work identified methods for quantifying heterogeneity in malaria exposure and offered a critical evaluation of spatially targeting interventions at malaria hotspots.
Identification and Introgression of Novel Genes for Stem Rust Ug99 Resistance from Relative Species of Wheat

iii ACKNOWLEDGMENTS . v LIST OF TABLES . viii LIST OF FIGURES . x CHAPTER 1. GENERAL INTRODUCTION . 1 Literature cited . 2 CHAPTER 2. LITERATURE REVIEW . 5 Wheat and its genetic improvement . 5 Wheat stem rust. 14 Detection, evolution, and movement of Ug99 . 20 Types of host resistances . 21 Molecular markers in breeding . 31 Usage of Ug99 resistance genes in wheat breeding . 35 Literature cited . 36 CHAPTER 3. INTROGRESSION OF A NOVEL STEM RUST RESISTANCE GENE FROM THINOPYRUM JUNCEUM INTO WHEAT . 53 Abstract . 53 Introduction . 54 Materials and methods . 57 Results . 62 Discussion . 65 Literature cited . 77 CHAPTER 4. IDENTIFICATION AND MAPPING OF STEM RUST RESISTANCE GENES FROM TETRAPLOID PERSIAN WHEAT (T. TURGIDUM SUBSP. CARTHLICUM) . 83
Investigating TPACK: Knowledge Growth in Teaching with Technology

Technological pedagogical and content knowledge (TPACK) presents a dynamic framework for describing teachers' knowledge required for designing, implementing, and evaluating curriculum and instruction with technology. TPACK strategic thinking includes knowing when, where, and how to use domain-specific knowledge and strategies for guiding students' learning with appropriate information and communication technologies. Multiple visual and verbal descriptions reflect evolving recognitions of teacher educators and educational researchers as they have struggled to respond to the challenges in describing and developing teachers' TPACK. This extensive reflection maps the historical acceptance of pedagogical content knowledge (PCK) with the emerging views of and challenges with TPACK. A review of empirical progress in the investigation of TPACK serves to illuminate potential insights, values, and challenges for directing future educational implementations designed to identify a teacher's learning trajectory in the development of a more robust and mature TPACK for supporting them in teaching with current and emerging technologies.
De novo Transcriptome Characterization of Iris atropurpurea (the Royal Iris, Iris section Oncocyclus) and Phylogenetic Analysis of MADS-box and R2R3-MYB Gene Families

The Royal Irises, Iris section Oncocyclus, are a Middle-Eastern group of irises, characterized by extremely large flowers with a huge range of flower colors and a unique pollination system. The Royal Irises are considered to be in the course of speciation and serve as a model for evolutionary processes of speciation and pollination ecology. However, no transcriptomic and genomic data for molecular characterization are available for these plants. Transcriptome sequencing is a valuable resource for determining the genetic basis of ecological-meaningful traits, especially in non-model organisms. Here we describe the de novo transcriptome sequencing and assembly of Iris atropurpurea, an endangered species, endemic to Israel’s coastal plain. We employed RNA sequencing to analyze the transcriptomes of roots, leaves, and three stages of developing flower buds. To identify genes involved in developmental processes we generated phylogenetic gene trees for two major gene families, the MADS-box and MYB transcription factors, which play an important role in plant development. In addition, we identified 1,503 short sequence repeats that can be developed for molecular markers for population genetics in irises. In the era of large genetic datasets, the Iris transcriptome sequencing provides a valuable resource for studying adaptation-associated traits in this non-model plant. This first reported transcriptome for the Royal Irises, and the data generated from this study, will facilitate gene discovery, functional genomic studies, and development of molecular markers in irises, to complete the intensive eco-evolutionary studies of this group.
Fluctuating fitness shapes the clone size distribution of immune repertoires

The adaptive immune system relies on the diversity of receptors expressed on the surface of B and T-cells to protect the organism from a vast amount of pathogenic threats. The proliferation and degradation dynamics of different cell types (B cells, T cells, naive, memory) is governed by a variety of antigenic and environmental signals, yet the observed clone sizes follow a universal power law distribution. Guided by this reproducibility we propose effective models of somatic evolution where cell fate depends on an effective fitness. This fitness is determined by growth factors acting either on clones of cells with the same receptor responding to specific antigens, or directly on single cells with no regards for clones. We identify fluctuations in the fitness acting specifically on clones as the essential ingredient leading to the observed distributions. Combining our models with experiments we characterize the scale of fluctuations in antigenic environments and we provide tools to identify the relevant growth signals in different tissues and organisms. Our results generalize to any evolving population in a fluctuating environment.