Miracle-dz/UniFAR-FTUs huggingface dataset:
The Development, Characterization and Implementation of a Reactive Oxygen Species-Responsive Ratiometric Bioluminescent Reporter and Its Use As A Sensor for Programmed Cell Death

The process of programmed cell death (PCD) is a prevalent area of scientific research and is characterized by a highly complex proteolytic cascade. PCD is involved in development, homeostasis and the immune response. Further, unregulated PCD has been implicated in various, often, devastating pathologies including cancer, autoimmune diseases and neurodegenerative disorders. The importance of PCD in human health and disease has led to the widespread utilization of genetically encoded reporters for the non-invasive imaging of PCD in vitro and in vivo; however, it is currently not well understood whether the reporters themselves are susceptible to inactivation and/or degradation during PCD. Molecular reporters that do exhibit an unexpected sensitivity to their environment could lead to ambiguous findings and/or inaccurate conclusions. Interestingly, we have found that the commonly used bioluminescent reporter protein, Firefly Luciferase (f Luc), exhibits a rapid loss in activity in cells undergoing PCD. In contrast, a variant of Renilla Luciferase, RLuc8, demonstrated quite stable activity under the same conditions. Following extensive inhibition analyses, it was determined that reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2), play a large role in the disparity between f Luc and RLuc8 activity, in cells undergoing PCD. ROS are natural byproducts of oxygen metabolism that are normally regulated by antioxidants; if the balance between ROS and antioxidants becomes skewed, cells can enter a state of ‘oxidative stress. ’ It has been reported that many cases of PCD are associated with elevated levels of ROS. Consistent with these reports, when f Luc and RLuc8 were intracellularly coexpressed, it was found that the bioluminescence ratio, RLuc8:f Luc, served as a useful metric to report on caspase-dependent and –independent PCD in vitro and in vivo in an ROS-mediated manner. It is envisioned that this ratiometric reporter could have widespread impact on research endeavors involving the aforementioned maladies, including therapeutic development and evaluation. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Bioengineering First Advisor Andrew Tsourkas
Linkage Analysis of Retinitis Pigmentosa in Families of North Waziristan Agency

Retinitis Pigmentosa (RP) is a heterogeneous group of genetic diseases characterized by progressive loss of photoreceptor. In Pakistan, autosomal recessive RP is the most prevalent. We here address the issue of RP in families of very remote area of KPK, the North Waziristan Agency to molecularly characterize through linkage analysis for known loci in gene PDE6B. We collected blood samples of all the members the families having at least 2 affected individuals by RP. DNA was isolated by nonorganic method and master plate and replica plates were prepared accordingly. Amplification of microsatellite markers for reported loci was done through touch down PCR for any possible linkage analysis. Forward primer was labeled with one of the fluorescent dyes; FAM, VIC, HEX or NED. Only 4 families, PKRP398, PKRP399, PKRP400 and PKRP401 were included in this study. All the families belonged to Pashtun ethnic group. Family PKRP398 contained 4 affected individuals with their ages in the range of 12 to 27 years. No linkage was found in the family for the above-mentioned loci. Family PKRP399 consisted of 5 affected individuals and 6 normal individuals in three loops. All the affected and normal individuals were homozygous for markers D8S1110, D8S1737, D8S509, D8S2332 and D8S182, thus no linkage was seen in the family. Family PKRP401 comprised of 4 affected and 4 normal individuals but again no linkage was found. Family PKRP400 had two effected individuals in a loop and 4 normal individuals. The affected individuals had lost their vision in progressive fashion. Haplotype analysis of affected individuals showed linkage to PDE6B markers and their parents were heterozygous carriers of the diseased allele. Hence the knowledge of the disease causing genes seems to be the main element in better understanding of the disease, its diagnostics and novel therapies to combat the incidence of vision impairment.
The Necessity of Periodic Retesting of Virus-Free Regenerated Grapevine

Fanleaf virus (GFLV), arabis mosaic virus (ArMV), leafroll associated viruses 1+3 (GLRaV-1+3) and fleck virus (GFkV) are the most widespread and damaging grapevine viruses. The releasing in the culture of a high biological value propagation material requires the selection of healthy genotypes for both propagation and use in new clone/varieties production programs. Thus, virus elimination methods are often needed to regenerate healthy plants. In this study, virus-free grapevine genotypes regenerated by various methods (in vivo and in vitro thermotherapy, in vitro chemotherapy, electrotherapy in continuous electric field, direct stimulation with high frequency electrical currents, electrotherapy in horizontal electrophoresis tank) were several times ELISA retested to confirm the diagnostic. The virological tests revealed the recurrence of viral infection after 5 (GLRaV-1+3 and GFKV), respectively 6 years (GFLV, GVA, viral complexes) in plants regenerated by in vivo thermotherapy. GLRaV-1+3-free grapevine plants obtained by in vitro thermotherapy have maintained their acquired phytosanitary status for 4 years. From the electrotherapy methods, in the case of the stimulation with high frequency electric currents, the viral infection reappeared after 3 years. To date, in vitro chemotherapy offers increased safety, only GFLV infection re-emerging after 7 years. These results highlight the need of periodic viruses testing for the safe establishment of plants phytosanitary status. What is the number of sufficient vegetation periods to establish the viral diagnosis remains to be studied.
Butterfly Fauna of Mansa District of Punjab

Study revealed the presence of 36 species of butterflies related to 26 genera of 7 families during surveys conducted at various seasons. These species constituted 55.39 percent of total butterfly species found in Punjab. Seven families of Lepidoptera viz. Pieridae, Lycaenidae, Nymphalidae, Satgridae, Danaidae, Papilionidae and Acraeidae were most prevalent.
Amibes à potentiel pathogène dans les unités dentaires

It has been well documented that the various tubing of a dental unit are covered with a thick biofilm. This biofilm mostly consists of bacteria, but amoebae can be found within the biofilm as well. Some amoebae are potential pathogens and may cause serious infections. Two cases of amoebic infections that were possibly linked with dental units drew our attention and stimulated our researches. Morphologic identification of amoebae in order to determine their possible pathogenicity requires much expertise, and is even difficult for proficient protozoologists. Therefore, the use of PCR is essential to detect potentially pathogenic amoebae with subjectivity. We elaborated new primers for the detection of Acanthamoeba spp. and Naegleria spp. Samples of water and dirt were taken in the environment, and samples of water and biofilm were taken in dental units. A part of each samples was cultivated for morphological identification, when a second part was utilized for PCR identification. Acanthamoebae and/or Naegleriae were detected in 100% of our samples, but the species varied from one sample to another. Potentially pathogenic amoebae were detected in dental units and in the environment, which could represent a health risk for some individuals.
Genetic variation of Atlantic horse mackerel (Trachurus trachurus) in the Turkish waters.

Variation genetique du chinchard (Trachurus trachurus) dans les eaux turques. Les variations geographiques de Trachurus trachurus basees sur le gene mitochondrial 16S rDNA a 8 stations, incluant les Mer Noire, Marmara, Egee et le nord-est de la Mer Mediterranee ont ete recherchees. Les analyses RFLP revelent 14 haplotypes chez les 307 individus des differentes populations. La repartition des groupes haplotypiques suit la plupart du temps l'origine geographique des populations. La diversite haplotypique moyenne au sein des populations est elevee (0,7311) et la diversite nucleotidique faible (0,0071). La faible divergence nucleotidique moyenne entre les echantillons est de 0,00271. La plus forte valeur de divergence nucleotidique a ete detectee entre les echantillons de Mer Noire occidentale et orientale (0,01119) et la plus faible (-0,00018) entre les deux echantillons du nord-est de la Mediterranee. Des populations differant par leurs frequences haplotypiques ont ete detectees par la methode de Monte Carlo. La distribution des haplotypes et l'estimation de la divergence nucleotidique met en evidence une forte differenciation de la population de Mer Noire (BS2). Le test de Mantel montre que les differences genetiques entre ces populations ne sont pas correlees a leurs distances geographiques (r = 0,326; P > 0,05).
Histomorphology of the porcine oviduct.

Bu calisma; domuzlarda ovidukt epitelinin yapisini, isik ve elektron mikroskobik olarak incelemek, epitel hucreleri tarafindan salgilanan mukus iceriginin histokimyasal yapisini ortaya koymak ve ostrus siklusunun farkli donemlerindeki endotelyal nitrik oksit sentaz (eNOS) aktivitesinin, lokalizasyonu ve dagilimini belirlemek amaciyla yapildi. Calismada 5 adet saglikli, eriskin disi domuzdan alinan ovidukt, materyal olarak kullanildi. Histokimyasal olarak; ostral donemde artan glikozaminoglikan (GAG) salgisinin, ozellikle istmusdaki kriptlerde depolandigi goruldu. Elektron mikroskobik olarak; ostral donemde sekretorik hucrelerin sitoplazmalarinda artan salgi materyalinin, iki tip salgi granulunde toplandigi belirlendi. Immunohistokimyasal olarak; hem ostral hem de luteal donemde ampulla ve fimbriyada eNOS ekspresyonu gorulmez iken, istmusda ise yalnizca ostral donemde eNOS ekspresyonu saptanmistir
Investigation of neurobiological-genetic correlates and source-informants of attention deficit hyperactivity disorder (ADHD) in adolescents and adults

2 Statement of authorship . 3 Publications relevant to this thesis . 5 Acknowledgements . 6 Table of contents . 7 Table of figures . 13 Table of tables . 14 CHAPTER 1 – Introduction . 16 1.1 Abstract . 16 1.2 Introduction to ADHD . 16 1.2. 1 Diagnostic criteria of ADHD . 17 1.2. 2 Categorical and dimensional approaches . 19 1.2. 3 Epidemiology . 20 1.2. 4 Summary . 26 1.3 Informant sources in diagnosing ADHD . 27 1.3. 1 Evaluation of informant sources in adolescence and adulthood . 28 1.3. 2 Summary . 30 1.4 Aetiology of ADHD . 30 1.4. 1 Genetics . 30 1.4. 2 Environmental risk factors and gene-environment interplay . 33 1.4. 3 Summary . 35 1.5 Neurobiological impairments in ADHD . 35 1.5. 1 Studies of cognitive impairments . 36 1.5. 2 Studies of neurophysiological impairments . 38 1.5. 3 Studies of autonomic arousal . 44 1.5. 4 Summary . 46 1.6 Treatment and interventions for ADHD . 47 1.6. 1 Pharmacological and non-pharmacological treatments . 47 1.6. 2 Exercise as a protective factor and potential intervention . 49 1.6. 3 Summary . 51 1.7 Aims and objectives . 52 1.7. 1 Informant source validity of ADHD in adolescents and young adults (Chapters 2 and 3) . 52
Experimental validation of the Kronecker product Godard blind adaptive algorithms

To overcome the analytical challenge the nonconvex Godard criterion presents, the Kronecker product operator and higher order statistical moments have been proposed as a natural framework to obtain an exact and more tractable mathematical description of the behavior of the algorithm. The authors validate these findings by working out several examples in both notations. Particular attention is given to situations of standard constant modulus adaptive algorithm misbehavior. <<ETX>>
APPLICATION OF NANOTECHNOLOGY TO PATHOGEN DETECTION AND INACTIVATION

Listeria monocytogenes is a psychrotrophic, gram-positive pathogen frequently involved in outbreaks of food-borne disease in which milk, cheese, meat, and vegetables represent the incriminated foodstuffs. L. monocytogenes biofilms formed on food contact surfaces and processing environments are the major sources of contamination to ready-toeat food products. Nanotechnology as an emerging new technology has many biological applications. The objectives of this study were to apply immunonanoparticles, carboxyl modified nanoparticles covalently bound with anti-L. monocytogenes, for L. monocytogenes detection and inactivation. Immunonanopaticles and fluorescent immunonanoparticles were applied to indirect fluorescent immunoassay and direct fluorescent immunoassay, respectively, for sensitive detection of L. monocytogenes in biofilms. Immunonaoparticle-based immunoassay generated fluorescent intensity 16 times higher than antibody-based traditional immunoassay. In two-species biofilms, L. monocytogenes cells at different depths (0-3 μm) of biofilms were successfully detected by both immunonanoparticle-based indirect immunoassay and fluorescent immunonanoparticle-based direct immunoassay. Immuno-magnetic-nanoparticle (IMNP)-based immunomagnetic separation (IMS) in combination with real-time PCR (RT-PCR) was used for a rapid and quantitative detection of L. monocytogenes in artificially contaminated milk. Capture efficiencies (CEs) by plating for IMNP-based IMS were 1.4~26 times higher than those of Dynabeads-based IMS. When combined with RT-PCR, IMNP-based method, with a
Centrosomes in Cytokinesis, Cell Cycle Progression and Ciliogenesis: a Dissertation

The work presented here describes novel functions for centrosome proteins, specifically for pericentrn and centrolin. The first chapter describes the involvement of pericentrn in ciliogenesis. Cells with reduced pericentrn levels were unable to form primary cilia in response to serum staration. In addition we showed novel interactions between pericentrn, intrafagellar transport (1F) proteins and polycystin 2 (PC2). Pericentrn was co-localized with 1F proteins and PC2 to the base of priary cilia and motile cilia. Ciliar function defects have been shown to be involved in many human diseases and proteins and PC2 have been implicated in these diseases. We conclude that pericentrn is required for assembly of primary cilia possibly as an anchor for other proteins involved in primary cilia assembly. The second chapter describes identification of centrolin, a novel centrolar protein that localizes to subdista appendages and is involved in cytokinesis and cell cycle progression. Depletion of centrolin leads to defects in the fmal stages of cytokinesis , where cells remain connected by th intercellular bridges and are unable to complete abscission. The cytokinesis defects seemed to precede the GO/G 1 p53 dependant cell cycle arest. Finally, the third chapter is a continuation of the cytokinesis study and it identifies pericentrn as an interacting partner for centrolin. Like centrolin pericentrn knockdown induces defects in the final stages of cytokiesis and leads GO/G1 arest. Moreover, pericentrn and centrolin interact biochemically and show codependency in their centrosome localization. We conclude that pericentrn and centrolin are members of the same pathway and are necessar for the final stages of cytokinesis.
Variations of aquatic bryophyte assemblages in the Rhine Rift related to water quality. 2. The waterfalls of the Vosges and the Black Forest

Abstract The relationships between water quality and aquatic bryophyte assemblages were investigated in sixteen waterfalls in the Vosges Mountains and in the Black Forest. Species such as Marsupella emarginata and Scapania undulata tolerate neutral pH in oligomineral waters whereas species such as Chiloscyphus polyanthos can tolerate waters with low cation concentrations if the concentrations of protons is also low. The aquatic bryoflora of the waterfalls of the Black Forest and of the Vosges thus includes a combination of species characteristic for waters with low concentrations of dissolved minerals on the one hand and for waters with low concentrations of protons on the other. This combination relies on a fragile physico-chemical balance because the buffering capacity of the waters is very low. At such low concentrations, the chemical factors are limiting for the bryoflora, which may react rapidly to slight changes in ion concentration. Sewage effluent discharges coming from villages or trout hatcherie.
Phenotypic and functional characterization of mesenchymal stromal cells generated from human bone marrow CD271+ mononuclear cells

OBJECTIVE. In vitro proliferative and differentiation potential of mesenchymal stromal cells (MSCs) generated from CD271+ bone marrow mononuclear cells (CD271-MSCs) has been demonstrated in several earlier and recent reports. In the present study we focused, in addition to proliferative and differentiation potential, on in vitro and in vivo immunosuppressive and lymphohematopoietic engraftment-promoting potential of these mesenchymal stromal cells compared to bone marrow-derived mesenchymal stromal cells generated by plastic adherence (PA-MSCs). MATERIALS AND METHODS. We set up a series of experimental protocols in order to determine the phenotype of bone marrow-derived CD271-MSCs, their clonogenic, proliferative, differentiation and immunosuppressive potential. The potential of CD271-MSCs to improve the engraftment of CD133+ hematopoietic stem cells at co-transplantation was evaluated in immunodeficient NOD/SCID-IL2Rnull mice. RESULTS. In vitro studies demonstrated that CD271-mesenchymal stromal cells differentiate along adipogenic, osteogenic and chondrogenic lineages (trilineage potential), and significantly inhibit the proliferation of allogeneic T-lymphocytes in mixed lymphocyte reaction assays. Elevated levels of prostaglandin E2, but not nitric monoxide, IL-10 or soluble HLA-G, mediated the majority of this immunosuppressive effect. In vivo studies showed that CD271-mesenchymal stromal cells promoted significantly greater lymphoid engraftment than did PA-MSCs when co-transplanted with CD133+ hematopoietic stem cells at a ratio of 8:1 in immunodeficient NOD/SCID-IL2Rnull mice. They induced a 10.4-fold increase in the number of T cells, a 2.5-fold increase in the number of NK cells, and a 3.6-fold increase in the number of B cells, indicating a major qualitative difference between these two mesenchymal stromal cell populations. CONCLUSIONS. Our results indicate that CD271 antigen provides a versatile marker for prospective isolation and expansion of MSCs with immunosuppressive and lymphohematopoietic engraftment-promoting properties. The co-transplantation of such cells together with hematopoietic stem cells in patients with hematologic malignancies may prove valuable in the prevention of impaired/delayed T-cell recovery and graft-versus-host disease.
OPPOSING ROLES OF THE μ-OPIOID AND NOCICEPTIN/ORPHANIN FQ RECEPTORS IN OLIGODENDROCYTE DEVELOPMENT AND MYELINATION

x Introduction . 1 Myelin . 3 Structure . 3 Function . 9 Myelin Composition . 13 Myelin Basic Proteins . 13 Myelin Associated Disease States . 17 Oligodendrocytes . 19 Oligodendrocyte Differentiation and Myelination . 20 Opioid Receptors Present in Oligodendrocytes . 25 Opioids . 26 History . 26 Endogenous Opioid System . 27 Treatment and Abuse . 34 Opioid Abuse and Pregnancy . 36
Offspring performance is linked to parental identity and male breeding ornamentation in whitefish

The ‘good genes’ hypothesis predicts that males advertise their quality with different sexual ornaments and that females are able to recognize the genetic quality of males by evaluating these characteristics. In the present study, we investigated the parental effects on offspring performance (feeding and swimming ability of newly-hatched larvae) and examined whether male ornamentation indicates offspring success in performance trials of whitefish (Coregonus lavaretus Linnaeus). Offspring first-feeding success had a strong paternal effect and it was also positively correlated with the size of male breeding tubercles, indicating that breeding ornamentation of males can function as an honest indicator of their genetic quality. In addition, the observed positive correlation between male tubercle size and condition factor suggests that highly ornamented males are efficient foragers and that this trait may have a heritable basis. By contrast to feeding success, only a maternal effect was found in the swimming ability of the larvae. Clear family-specific differences observed in both measures of performance strongly suggest that parental identity may have important effects on larval survival in the wild. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 532–539.
The amphibious murines of New Guinea (Rodentia, Muridae): the generic status of Baiyankamys and description of a new species of Hydromys

The amphibious murine rodents of New Guinea have traditionally been classified in three genera: Hydromys E. Geoffroy, 1804, Parahydromys Poche, 1906, and Crossomys Thomas, 1907. Species currently classified in Hydromys can be further divided into two cladistic groups: species distributed in lowland habitats (below 2000 m) with glossy, dark brown dorsal pelage, and species restricted to upper montane rivers and lakes (generally above 2000 m) with soft, silvery grey dorsal pelage. These two groups differ not only in pelage traits and habitat association but also in craniodental and phallic anatomy. The generic-level name Baiyankamys Hinton, 1943, is resurrected for the latter cluster (which includes two species, B. shawmayeri of eastern New Guinea and B. habbema of west-central New Guinea). Additionally, a new species of Hydromys (H. ziegleri n. sp.) is described from the southern foothills of the Prince Alexander Range of Papua New Guinea. Mammalian zoogeography in the North Coast Ranges, an area of considerable geographicallyrestricted mammalian endemism, is reviewed.
Annotated key to weevils of the world. Part 3. Subfamily Conoderinae (Coleoptera, Curculionidae)

A new subtribe Parallelodemina Legalov, subtrib. n. (type genus Parallelodemas Faust, 1894) of the tribe Baridini is described. Zygobaridina Pierce, 1907, syn. n. is synonymized with Diorymerina Jekel, 1865, Anopsilini Bondar, 1942, syn. n. with Baridina Schoenherr, 1836, Leptoschoinides Lacordaire, 1865, syn. n. and Thaliabaridina Bondar, 1943, syn. n. with Madarina Jekel, 1865. The systematic positions of Eucalus Lacordaire, 1865, placem. n. , Diorymerina Jekel, 1865, placem. n. , Limnobarini Casey, 1922, placem. n. , Madopterina Lacordaire, 1865, placem. n. , Neosharpiina Hoffmann, 1956, placem. n. are changed. Changes of status for Nertinina Voss, 1954, stat. n. and Neosharpiina Hoffmann, 1956, stat. n. are made. A key to the supertribes of Conoderinae, keys to tribes and supertribes of Bariditae and Conoderitae, key to tribes of Ceutorhynchitae are provided. Systematic lists of tribes and subtribes of Bariditae, tribes of Conoderitae, Ceutorhynchitae and Orobitiditae are given.