Miracle-dz/UniFAR-FTUs huggingface dataset:
Generation and characterization of heavy chain antibodies derived from Camelids

Antibodies and antibody fragments are essential tools in basic research, diagnostics and therapy. Conventional antibodies consist of two heavy and two light chains with both chains contributing to the antigen-binding site. In addition to these conventional antibodies, camelids (llamas, alpacas, dromedaries and camels) possess so-called heavy chain antibodies (hcAbs) that lack the light chains. The antigen binding site of these unusual antibodies is formed by one single domain only, the so called VHH domain. The VHH domain represents the smallest intact antigen binding fragment (~ 15 kDa) and is characterized by very high stability, solubility and specificity. These unique features render VHHs a promising alternative to conventional antibodies and antibody fragments with a multitude of possible applications. In the course of this thesis, we aimed to generate and characterize VHHs suitable for different applications ranging from biochemical studies to immunofluorescence assays and live cell imaging. In order to meet the diverse requirements of the intended downstream applications, a new selection method differing from traditional phage display, called native panning, was developed and established. In combination with the protein-protein interaction fluorescent two-hybrid (F2H) assay, a new process to identify antigen specific VHHs functional inside living cells was developed. We used the immune system of alpacas to generate VHH libraries against various antigens, ranging from small peptides to large proteins. The libraries were screened by phage display and antigen specific VHHs were identified by phage ELISA. We were able to identify antigen specific VHHs against different antigens which were characterized and their functionality was tested in various applications. Furthermore, we could demonstrate that the selection method influences which VHHs are identified and therefore needs to be chosen very carefully with regard to the intended biochemical and cell biological application. In summary, we developed and established an efficient and versatile process to screen and identify antigen specific VHHs suitable for different downstream applications.
Stress-induced genomic responses in Arabidopsis thaliana and Saccharomyces cerevisiae

La comprehension des differents mecanismes moleculaires responsables du maintien de la stabilite genomique a ete un interet central des biologistes moleculaires depuis plusieurs decennies. En particulier, par le fait que de nombreuses cellules cancereuses contiennent des rearrangements chromosomiques. L'instabilite genomique cree des mutations, qui dans le cas des cellules cancereuses se produisent, par exemple, au sein de genes regulateurs de croissance. D'une maniere generale, le controle de la replication et de la reparation de l'ADN, l'exacte distribution des chromosomes dans chacunes des cellules filles ainsi que le maintien des elements silencieux sont necessaires pour garantir l'integrite du genome. L'objectif principal de ce projet de these visait a etudier les mechanismes moleculaires du maintien de la stabilite genomique en reponse aux stress. Les deux chapitres de cette these sont presentes de manieres independentes.
A Machine Learning Approach to Detect the Dog's Behavior using Wearable Sensors

In recent years welfare of animals is the biggest challenge because animals, especially dogs are widely recognized as pet as well as they are using as service animals. So, for the wellbeing of the dog it is necessary to perform objective assessment to track their behavior in everyday life. In this paper, we have proposed an automatic behavior assessment system for dogs based on a neck worn and tail worn accelerometer and gyroscope platform, and data analysis techniques that recognize typical dog activities. We evaluate the system based on the analysis of 8 behavior traits in 3 dogs, incorporating 2 breeds of various sizes. Our proposed framework able to reproduce the manual assessment that is based on the video recording which is treated as gold standard that exhibits the real-life use case of automated dog behavior analysis.
EFFECTS OF LACTIC ACID BACTERIA INOCULATION ON MOUNTAIN GRASS AND ALFALFA SILAGE FERMENTATION CHARACTERISTICS

The objective of this work was to evaluate the effects of six lactic acid bacterial strains originated from different natural habitats of fermented food and feedstuff on pasture grass and alfalfa laboratory scale silages. The prepared mini silos were inoculated with the following bacterial strains alone or in combination: Lactobacillus brevis LbB (2x107 cfu/mL), Enterococcus faecalis EF (3.6x108 cfu/mL), Lactobacillus plantarum subsp. plantarum LbP (2.8x108 cfu/mL), Weissella paramesenteroides WP (3.6x107 cfu/mL), Leuconostoc lactis LL (3.5x108 cfu/mL), Lactobacillus paracasei subsp. tolerans LbPT (8.1x108 cfu/mL). The inoculation of the grass and alfalfa laboratory silos improved the chemical composition and fermentation patterns of the silages. Significant difference was detected (P <0.05) in crude protein content, lactic acid production and acid detergent fibre and neutral detergent fiber content in some of the treated samples compared to the control. The best performing treatment in the case of grass silage was the Lactobacillus brevis LbB inoculant, for alfalfa silage the most effective was the Enterococcus faecalis EF inoculant. Also considerably good results were achived with the inoculant Lactobacillus paracasei subsp. tolerans LbPT. Our results indicate that a bacterial consortium containing Lactobacillus brevis LbB, Enterococcus faecalis EF and Lactobacillus paracasei subsp. tolerans LbPT could be a strategy for silage inoculant with fermentation acceleration and prevention of nutritive value loss for the achievement of high quality silages.
Analyzing Virus Genomic Variability To Design And Test Genetic Constructs For Resistance

Grapevines can be affected by many viruses and viral diseases. However, despite their long history of cultivation and breeding efforts, little useable resistance to viral diseases has been identified in Vitis species. As a result, management of viral diseases has largely relied upon prevention/exclusion or on the use of economically and/or environmentally consequential methods to manage vector populations. Resistance to dagger nematode vectors has been identified and successfully transferred to rootstock genotypes that are commercially available, but these resistant materials do not prevent virus translocation into the scion – although a significant delay in infection can allow for suitable production. In this review, we critically evaluate the literature regarding resistance against viruses and vectors in Vitis and Muscadinia species. We examine the challenges of breeding grapevines for virus resistance and the methodologies used to test for resistance. The availability of useful sources of resistance and tolerance toward both viruses and their vectors, or lack thereof, is evaluated and discussed in terms of disease management. 1 Oliver, J.E. and Fuchs, M. 2011. Tolerance and resistance to viruses and their vectors in Vitis sp. : A virologist‘s perspective of the literature. Am. J. Enol. Vitic. (in revision).
Role of the nuclear pore in transcription regulation of inducible genes in Saccharomyces cerevisiae

This study provides evidence for a new role for the NPC and the NPC-associated SUMO-protease Ulp1 in transcription regulation of two inducible genes, GAL1 and HXK1. Interestingly, thanks to the complexity of GAL1 activation, we could show that Ulp1 is involved in the initial derepression step of GAL1 and not in its transcription activation, suggesting an early role of Ulp1 upon GAL1 induction. Furthermore, we showed that Ssn6 is a target of Ulp1. Ssn6 is sumoylated and acts as a repressor of GAL1. Our current model is that Ssn6 bound to the GAL1 promoter is relocalized to the NPC at an early stage of galactose induction. This allows the desumoylation of Ssn6, and probably other gene bound factors, by Ulp1 leading to the full derepression and activation of GAL1. Interestingly, we also found that Ulp1 is required for GAL1 localization at the NPC.
The regulation of RNA polymerase III transcription by protein kinase CK2

In order for cells to proliferate, a certain size has to be reached, which depends primarily on the rate of translation. RNA polymerase (pol) III plays a key role in protein synthesis by catalysing the production of small, untranslated RNA molecules such as transfer (tRNA) and 5S ribosomal RNA (5S rRNA). Indeed, recent evidence suggests that tRNAiMet production is limiting for translation and proliferation in some cell types. Therefore, the rate of pol III transcription plays a fundamental role in cellular growth and proliferation. Regulation of pol III output is mediated via a number of different mechanisms that can alter the activities of the transcription factors which are responsible for directing pol III transcription. Work presented in this thesis aimed at investigating the mechanisms behind the regulation of pol III transcription by the protein kinase CK2.
PENGARUH PERSEPSI MANFAAT, PERSEPSI KEMUDAHAN DAN PERSEPSI KEPERCAYAAN TERHADAP KEPUTUSAN PENGGUNAAN GO-PAY PADA MAHASISWA STIE AUB SURAKARTA

Go-Pay merupakan metode pembayaran transportasi Go-Jek. Riset IDC (2017) menyebutkan Go-Pay menduduki posisi ke 6 layanan fintech dengan pertumbuhan tercepat di Indonesia. Penelitian ini bertujuan untuk menganalisis prinsip manfaat, kemudahan dan kepercayaan terhadap keputusan penggunaan Go-Pay mahasiswa STIE AUB Surakarta. Teori Swastha (2002:25), Davis (1989) Moorman (1993) dan Sugiyono (2011) menyatakan bahwa pengambilan keputusan dipengaruhi oleh prinsip manfaat, kemudahan, kepercayaan pengguna produk serta latar belakang ilmu pengetahuan. Penelitian ini bersifat kuantitatif dengan sample 100 responden. Instrumen pengumpulan data adalah kuesioner. Data yang diperoleh dianalisis melalui uji regresi linier berganda, uji linieritas, uji t, uji F, serta uji R2. Uji linieritas dan uji regresi linier berganda menunjukkan semua variabel terbebas dari multikolinieritas dan berpengaruh positif. Secara parsial Uji t menunjukkan variabel manfaat dan kepercayaan berpengaruh signifikan, dimana persepsi manfaat menjadi variabel dominan. Sedangkan variabel kemudahan dan ilmu pengetahuan tidak signifikan. Hasil uji F menujukkan secara bersama-sama semua variabel berpengaruh signifikan. Uji Koefisien Determinasi diperoloeh angka 0,850 atau 85% keputusan penggunaan Go-Pay mahasiswa STIE AUB Surakarta dipengaruhi oleh variabel penelitian sedangkan sisanya 15% dipengaruhi faktor lain yang tidak diteliti. Hasil Penelitian ini bermanfaat sebagai rekomendasi dan referensi bagi praktisi manajemen, pelaku bisnis, maupun peneliti yang berhubungan dengan kajian pemasaran khususnya dengan keputusan penggunaan jasa.
ASSESSING SIZE AND CONFORMATION OF THE BODY OF NIGERIAN INDIGENOUS TURKEY

Body measurements, wing length, neck length, shank length, thigh length, body length, beak length, head length, keel length and chest circumference of 110 twenty weeks old Nigerian indigenous turkeys reared under semi intensive system were subjected to principal component analysis. The objectives of the study were to assess variability among body shape characteristics, deduce components that describe these traits, quantify the sex difference in size and shape, and predict live weight at that age from both original and orthogonal traits. Variation was noted between male and female turkey, in favour of the male as an expression of sexual dimorphism for all traits. Pair wise correlation between body weight and body measurements in both sexes ranged from 0.41 - 0.97 in males and 0.34 - 0.99 in females, respectively. Eigen values and share of total variance of the principal component analysis for the first 3 PCs were 80.25, 9.85 and 3.11% for males, and 78.03, 11.61 and 7.77% for females, respectively. The first factor in both sexes accounted for the greatest percentage of the total variation and was representative of general size. Independent body shape characters derived from factor scores accounted for 97% and 96% of the variation in the live weight in male and female turkeys, respectively.
Effects of ratoon harvesting on the root systems of processing spinach

: The mechanical harvesting of processing spinach (spinach used in production of processed food) is potentially becoming a common practice in Japan. Root distribution affects water and nutrient absorption, but how the roots spread in the soil profile during the regrowth period of spinach remains unknown. In this study, we investigate the root systems of processing spinach in topsoil (5 and 15 cm deep) and deeper soil layers (25, 35, 45, and 55 cm deep) cultivated using ratoon harvesting system. The total root length densities (calculated using the average of the densities at 0 and 15 cm horizontal distance from the row for each depth) in the second harvest were more than two-fold greater than those in the first harvest. The root length percentage in the topsoil and root depth indexes indicate that root systems are in shallower soil layers at the second harvest than at first har -vest.
In vitro propagation of Campanula polymorpha Witas. - an endemic plant of Carpathian Mountains.

Campanula polymorpha is an endemic plant of Carpathian Mountains, included in the Carpathian List of Endangered Species. An efficient micropropagation system was developed for regeneration and in vitro conservation of C. polymorpha. Single-node aerial stem segments from mature flowering plants collected from natural growing populations was sterile inoculated on regeneration media. For an efficient regeneration a range of 12 variant of basal MS (Murashige - Skoog) media formulation was tested, with different growth regulators combinations. Histological investigation shows that axillary bud dormancy was broken after 5 days of culture. The best rate of shoot production (average 14.8 shoot/explant) was achieved after 5 weeks of culture on media supplemented with 0.1 mg/l NAA (1-naphthylacetic acid) and 1 mg/l BAP (6-benzylaminopurine). Shoots of about 4-5 cm high, developed roots after 3-4 weeks on media without growth regulators. The established protocols offer a valuable micropropagation method that could be useful as a starting point for in vitro conservation of this endemic plant, or for mass propagation of other Campanula species of horticultural importance.
SeDAR: Reading floorplans like a human

The use of human-level semantic information to aid robotic tasks has recently become an important area for both Computer Vision and Robotics. This has been enabled by advances in Deep Learning that allow consistent and robust semantic understanding. Leveraging this semantic vision of the world has allowed human-level understanding to naturally emerge from many different approaches. Particularly, the use of semantic information to aid in localisation and reconstruction has been at the forefront of both fields. Like robots, humans also require the ability to localise within a structure. To aid this, humans have designed highlevel semantic maps of our structures called floorplans. We are extremely good at localising in them, even with limited access to the depth information used by robots. This is because we focus on the distribution of semantic elements, rather than geometric ones. Evidence of this is that humans are normally able to localise in a floorplan that has not been scaled properly. In order to grant this ability to robots, it is necessary to use localisation approaches that leverage the same semantic information humans use. In this paper, we present a novel method for semantically enabled global localisation. Our approach relies on the semantic labels present in the floorplan. Deep Learning is leveraged to extract semantic labels from RGB images, which are compared to the floorplan for localisation. While our approach is able to use range measurements if available, we demonstrate that they are unnecessary as we can achieve results comparable to state-of-the-art without them.
Two new species of Lentidium (Myida: Corbulidae) from tropical northern Australia: remarkable fresh/fluviatile to brackish-water bivalves

Lentidium, sole genus in the subfamily Lentidiinae of the Corbulidae, is remarkable because of its active lifestyle, strong foot and thin shell, as well as being far more equivalve and equilateral than the majority of species within the family. Lentidium is presently known by the extant Euasian species Lentidium mediterraneum (O.G. Costa, 1823) in addition to four fossil species. Two new extant species from tropical northern Australia are described, of which L. origolacus n. sp. has an extensive fossil record, particularly in non-marine phases of the Gulf of Carpentaria basin through most of the last Interglacial period (from approx. 130,000 years) to the present time. The other, L. dalyfluvialis n. sp. , appears to be restricted to the Daly River in the Northern Territory. Both species are extremely abundant in certain fluviatile/lacustrine habitats. Aspects of the ecology of each species are discussed. L. dalyfluvialis, though normally infaunal and endobyssate, is capable of rapid movement and active burrowing. Such behaviour, while highly unusual for the family, is presumably necessary for survival in major rivers prone to sudden flooding during the monsoon season.
Computed Tomography and 3D Reconstruction of the Respiratory Organs of the Egyptian Tortoise (Testudo kleinmanni)

This study is designed to identify, describe and illustrate the topography of the respiratory organs of the Egyptian tortoise (Testudo kleinmanni) using a digital camera and computed tomography. This may aid in obtaining complete data on dissection procedures, the topography and the initial section outlines and the safety of access during surgical procedures. The core of the present study is a series of photographs showing stages of the dissection. A detailed description of the dissection method and anatomy of the exposed organs are also given. Thirteen wild adult live tortoises, Testudo kleinmanni, (three males and ten females) were collected from Marsa Matroh and Cairo governorates with an age ranging from 15-19 years, weight between 430–450 gm, and carapace, and plastron lengths 10.5-11cm and 9.5-9.8 cm respectively. Computed tomography provides detailed information on the respiratory system, the location of the coelomic structures with respect to the carapace (the upper shell) and the vertebrae, and allows a comparison of cross-sectional anatomic views obtained with the digital camera with images obtained via computed tomography sections of the coelomic structures.
Biochimie et histologie de la dégradation enzymatique du son de blé par une endoxylanase

Les co-produits agricoles representent une matiere premiere renouvelable disponible en quantite importante pouvant etre valorisee par bioconversion enzymatique. La valorisation des substrats lignocellulosiques par voie enzymatique represente une alternative aux procedes chimiques polluants et non specifiques, generalement employes. Le son de ble, co-produit issu de la production du ble, est particulierement riche en hemicelluloses (40 % de sa matiere seche). L’hydrolyse du son de ble par une β (1,4) endoxylanase thermostable de 20 KDa permet la liberation de 50 % des arabinoxylanes. Ce taux maximal d’hydrolyse est observe meme lorsque le rapport [E]/[S] est tres faible (de l’ordre de 8 µg de proteine/g de substrat). La determination de la composition en monosaccharide des produits de reactions montre que la xylanase permet la solubilisation de structures arabinoxylanes de type faiblement substituees. En plus de la liberation d’oligosaccharides dans le surnageant, l’action de la xylanase s’accompagne de la solubilisation de proteines et de β-glucanes. Les structures hemicellulosiques non degradees par l’enzyme sont fortement (X/A = 1). Nos travaux mettent en evidence que le degre de substitution eleve des arabinoxylanes residuels represente un facteur limitant l’action de l’enoxylanase. Cependant, en plus de la structure des arabinoxylanes, d’autres polymeres parietaux sont responsables de la limitation de la degradation enzymatique des hemicelluloses in situ. Les parois vegetales sont composees de microfibrilles de cellulose englobees dans une matrice composee de differents polysaccharides (arabinoxylane et pectine), proteines, et de lignine. Ces differents polymeres s’associent entre eux par differents types de liaisons pour former un reseau compact qui limite l’acces aux hydrolases. En particulier, les acides feruliques peuvent former des liaisons covalentes entre les polysaccharides, ou entre les lignines et les polysaccharides, pouvant empecher l’action enzymatique. Dans l’optique de mieux identifier les limitations structurales (structure des arabinoxylanes) et histologiques impliquees lors de l’hydrolyse enzymatique du son de ble, une partie de notre etude a ete menee sur des fractions de son de ble obtenues par microdissection. L’hydrolyse de trois sous-enveloppes, la couche de cellules aleurones (AL), la couche moyenne (CM, composee du nucelle, la testa, les cellules tubullaires et croisees) et la couche externe (CE, composee de l’epiderme et de l’hypoderme) a ete etudiee. La xylanase degrade 80 % des arabinoxylanes constitutifs de la couche aleurone ; ainsi que 50 % des arabinoxylanes de la couche moyenne. En revanche, la couche externe est insensible a l’hydrolyse enzymatique.