Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards in vitro centrosome positioning in vesicles under physiologically relevant conditions

An ultrasonic color flow mapping system and a filtering method for filtering an ultrasonic Doppler signal are provided. The ultrasonic color flow mapping system includes a forward processing portion for excluding initial output data up to a predetermined number from outputs based on an ultrasonic Doppler signal input having a predetermined index sequence, a backward processing portion for excluding initial output data up to a predetermined number from outputs based on the ultrasonic Doppler signal input having a backward index sequence with respect to the input of the forward processing portion, and an operator for calculating a power and an average frequency of the ultrasonic Doppler signal based on the outputs of the forward and backward processing portions and providing the calculated result as an output for image regeneration. As a result, a transient response with respect to a low-frequency signal contained in the ultrasonic Doppler signal can be minimized and an image such as a blood stream velocity can be accurately regenerated in real time.
Discovery of miRNA-regulated processes in mammalian development

6 Acknowledgements . 7 CHAPTER 1: Introduction . 9 Introduction . 10 miRNA biogenesis . 10 pri-miRNA transcription and processing . 10 Pre-miRNA processing . 12 miRNA duplex unwinding and loading . 13 RISC/miRNP . 14 Modes of miRNA-mediated silencing. 16 Translational Repression . 17 mRNA destabilization. 18 Translational Activation. 19 miRNA binding sites in 5’UTRs and coding sequences. 20 Interface of the miRNA pathway with other post-transcriptional regulatory pathways 21 Discovery of miRNA biological functions . 21 Computational miRNA target prediction. 21 Biochemical miRNA target identification . 25 miRNA loss-of-function . 29 Introduction to miRNAs in murine Embryonic Stem cells. 32 ES cell biology . 32 Dicer loss in ES cells . 32 miRNA population in ES cells . 33 CHAPTER 2: Identification of Lefty1 as an Ago2-associated miRNA target in mouse embryonic stem cells. 37 Abstract. 38 Introduction . 39 Results . 41
Identification of elm yellows phytoplasma in plum trees in China.

Plum plants (Prunus cerasifera Ehrh) with small and rolled leaves resembling symptoms of phytoplasma infection were observed during 2008 and 2009 in the ornamental garden of Northwest A&F University (Republic of China). Nested polymerase chain reaction (PCR) using a combination of phytoplasma-specific universal primer pairs (R16F2m/R16R1m-R16F2 n/R16R2) amplified 16S rDNA with the expected size (1.2 kb) from all samples of symptomatic plum plants. Sequencing results and restriction fragment length polymorphism (RFLP) analysis of the 1248 bp R16F2n/R16R2 products showed that the phytoplasma belongs to group 16SrV. Phylogenetic analysis showed that the phytoplasma had a close relation to JWB phytoplasma. This is, we believe, the first report of elm yellows phytoplasma infecting plum plants in China.
Antioxidant and redox regulation of genes

Reactive Species as Intracellular Messengers: L. -O. Klotz, K. Briviba, and H. Sies, Signalling by Singlet Oxygen in Biological Systems. D.R. Crawford, T. Suzuki, and K.J.A. Davies, Oxidant-modulated Gene Expression. H.H. Hassanain and P.J. Goldschmidt-Clermont, RAC, Superoxide, and Signal Transduction. S.K. Koliwad, A.K. Brzezinska, and S.J. Elliott, Redox Regulation of Ion Channels. J. Giron-Calle and H.J. Forman, Cell Ca2+ in Signal Transduction: Modulation in Oxidative Stress. G.L. Schieven, Introduction of Protein Tyrosine Phosphorylation by Oxidative Stress and its Implications. A.A. Deora and H.M. Lander, Regulation of Signal Transduction and Gene Expression by Reactive Nitrogen Species. Redox Sensitive Molecular Processes and Cellular Responses: P.A. Baeuerle, Reactive Oxygen Species as Costimulatory Signals of Cytokine-Induced NFkappaB Activation Pathways. T. Okamoto, T. Tetsuka, and T. Kawabe, Redox Regulation of Nuclear Factor kappa B. C.K. Sen, Oxidants and Antioxidants in Aptosis: Role of Bcl-2. V. Goossens, K. De Vos, D. Vercammen, M. Steemans, K. Vancompernolle, W. Fiers, P. Vandenabeele, and J. Grooten, Role of Reactive Oxygen Species in TNF Toxicity. S. Roy, C.K. Sen, A. Gozin, V. Andrieu, and C. Pasquier, Redox Regulation of Cell Adhesion Processes. H. Masutani, M. Ueno, S. Ueda, and J. Yodoi, Role of Thioredoxin and Redox Regulation in Oxidative Stress Response and Signalling. A.H. Schonthal, S. Mueller, and E. Cadenas, Redox Regulation of p21, Role of Reactive Oxygen and Nitrogen Species in Cell Cycle Progression. Clinical Implications of Redox Signaling and Antioxidant Therapy: H. Viita and S. Yla-Hertuala, Effect of Lipoxygenases on Gene Expression in Mammalian Cells. A. Azzi, Tocopherol in the Pathogenesis of Atherosclerosis: One Molecule, Several Functions. D. -Y. Jin and K. -T. Jeang, Peroxiredoxins in Cell Signaling and HIV Infection. J.S. Bertram, T. King, L. Fukishima, and F. Khachik, Enhanced Activity of an Oxidation Product of Lycopene Found in Tomato Products and Human Serum Relevant to Cancer Prevention. C. Bladier, J.B. de Haan, and I. Kola, Antioxidant Genes and Reactive Oxygen Species in Down's Syndrome. B.S. Kristal and B.P. Yu, Oxidant-mediated Repression of mtDNA Transcription. Y. Kajimoto, Y. Yamasaki, T. Matsuoka, H. Kaneto, and M. Hori, Suppression of the Insulin Gene Promoter Activity by Oxidative Stress. N. Maulik and D.K. Das, Redox Regulation of Ischemic Adaptation. W.C. Orr and R.S. Sohal, Oxidative Stress as a Governing Factor in Physiological Aging. W. Droge, V. Hack, R. Breitkreutz, E. Holm, S. Holm, and R. Kinscherf, Antioxidants in Senescence and Wasting. Subject Index.
There and back again? Combining habitat suitability modelling and connectivity analyses to assess a potential return of the otter to Switzerland

After a steady decline in the early 20th century, several terrestrial carnivore species have recently recovered in Western Europe, either through reintroductions or natural recolonization. Because of the large space requirements of these species and potential conflicts with human activities, ensuring their recovery requires the implementation of conservation and management measures that address the environmental, landscape and social dimensions of the problem. Few examples exist of such integrated management.
Access Denied! Contrasting Data Access in the United States and Ireland

Abstract The ability of an Internet user to access data collected about himself as a result of his online activity is a key privacy safeguard. Online, data access has been overshadowed by other protections such as notice and choice. This paper describes attitudes about data access. 873 US and Irish Internet users participated in a survey designed to examine views on data access to information held by online companies and data brokers. We observed low levels of awareness of access mechanisms along with a high desire for access in both participant groups. We tested three proposed access systems in keeping with industry programs and regulatory proposals. User response was positive. We conclude that access remains an important privacy protection that is inadequately manifested in practice. Our study provides insight for lawmakers and policymakers, as well as computer scientists who implement these systems.
Growth Hormone Gene Polymorphism in Two Iranian Native Fowls (Short Communication)

Biochemical polymorphism study is a method of determination of genetic variation. This variability could be a basis for selection and subsequent genetic improvement in farm animals. The polymorphism in the intron 1 of chicken growth hormone (cGH) gene was investigated in the Iranian native fowls by using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method. The genomic DNA was extracted from 217 samples (129 samples from the native fowls of Isfahan province and 88 samples from the native fowls of Mazandaran province) by using modified salting out technique. The DNA fragment of the growth hormone gene with 776 bp was amplified by PCR using specific primers. Then the PCR products were digested with MspI restriction enzyme and analyzed on 2.5% agarose gel. The allelic frequency of intron 1 locus for A1, A2 and A3 alleles in Isfahan native fowls were 0.60, 0.21 and 0.19 and those in Mazandaran native fowls were 0.28, 0.05 and 0.67, respectively. The results of current study indicated that the intron 1 of cGH is polymorphic in Iranian native fowls and could be exploited as a candidate gene for marker-assisted selection for growth-related traits.
Variation in sexual and asexual reproduction among young and old populations of the perennial macrop

We examined how population age affects the relative importance of clonal propagation and sexual reproduction in the aquatic macrophyte Sparganium errectum. Plants were collected from two newly established populations and four successionally mature populations. The comparison of life history traits associated with sexual reproduction and clonal multiplication was carried out in a controlled environment experiment. We found that several physiological trade-offs occurred between sexual reproduction and clonal propagation. Moreover, we found a higher investment in sexual reproduction in newly established populations than in older populations. These results suggest that clonal propagation is favoured at the population level while, because seeds produced by sexual reproduction are the only means for long distance dispersal, selection will favour sexual reproduction at the metapopulation level. This discrepancy between selective pressures at different spatial scales could favour the maintenance of a mixed sexual-asexual reproductive system in Sparganium erectum.
Speciation and extinction asymmetries in paleontological phylogenies: evidence for evolutionary progress?

Abstract This paper concerns paleontological phylogenies that have a “budding” configuration, wherein “ancestral” species persist through branching events to coexist with their “descendants. ” Two principal tests are proposed for detecting patterns within such trees. The first test, called the “ancestor-descendant extinction test,” compares the number of cases in which, after a split, the ancestral species became extinct before its descendant with the number of cases in which the descendant became extinct before its ancestor. The second test, called the “ancestor-descendant speciation test,” compares the number of cases in which, after a split, the ancestral species gave rise to a further species with the number of cases in which the descendant species gave rise to a further species. The null hypothesis in each case is that the frequencies are equal, as predicted by a random Markovian branching model of evolution. Five stratophenetic species-level phylogenies of three taxonomic groups, planktonic foraminifera, nannofossils, and graptoloids, are examined using these tests, including one (Paleogene planktonic foraminifera) that is presented for the first time. In all cases, the phylogenetic trees are found to be strongly nonrandom. The general pattern, although by no means expressed perfectly in every case, corresponds to a Simpsonian “step-series,” in which ancestor taxa are simultaneously more likely to become extinct and less likely to speciate than their coexisting descendants. It is shown that this pattern cannot simply be the result of simple age-dependent factors such as an increasing extinction risk in older taxa. Instead, the very fact that a species has given rise to another appears to increase its future extinction risk and decrease its likelihood of further speciation. Many possible biases may affect the shape of paleontological phylogenies, which are as yet poorly understood and unquantified. One potentially important effect follows from the taxonomic subdivision of gradual chronoclines into artificial morphospecies, such as might conceivably induce a step-series pattern in the phylogeny. Even if this is the partial or entire reason for the observed patterns, it would appear to imply directional evolution in phyletic gradualism. Other possible artifacts are discussed, but they are regarded as probably too weak to produce the observed patterns. If the pattern is not artificial, the fact that three of the best known fossil groups exhibit substantial asymmetries in speciation and extinction argues against the currently popular “nonprogressive” view of evolution. Instead, the evolutionary step-series pattern is consistent with the classical Darwinian concept of the general competitive superiority of newly evolved species over their ancestors and supports the idea of evolutionary progress.
BEHAVIOR PATTERN AS THE INDICATOR OF REPRODUCTIVE SUCCESS OF ALPINE MUSK DEER

Summary To establish the behavioral indicator of reproductive success of female captive Alpine musk deer (Moschus sifanicus), the focal sampling was used to record the individual behaviors at Xinglongshan Musk Deer Farm (XMDF), Gansu province, China. Conducted between June 2008 and January 2009, 31 adult females were observed, of which 26 had successfully bred in the previous year, and five of which were barren. The frequencies of 12 behaviors were recorded and compared to explore variation in reproductive success and general behavior patterns. The results showed that there were differences in behavioral frequencies between females barren and fawned in the previous year. Compared to successful individuals, barren females expressed environment sniffing more frequently during non-mating season, but less frequently during mating season (P<0.05). Females which had previously fawned expressed ano-genital sniffing less frequently than barren females in non-mating season (P<0.05). Furthermore, both female groups elicited the male specific tail-pasting behavior, although the demonstration levels were not different significantly between both. The above behavioral differences have implications for musk deer farming practices, whereby females should be grouped and separated by their previous reproduction history, to maximize future reproductive success.
Phyllosoma larvae in the IIOE (1960-65) collections-systematics

The systematics of the phyllosoma larvae sorted out from the International Indian Ocean Expedition (1960-65) collections is dealt with. In a total of 84 specimens of larvae present in the collections, 51 are palinurids and the rest 33 scyllarids. The larval series contain phyllosoma stages of most of the commercially important spiny lobsters of the Indian Ocean region including the important species of the Indian coast, namely, Panulirus homarus (Linnaeus). The species with maximum number of larval specimens in the collection is P. versicolor (Latreille). The paucity of larvae in the samples from near the coastal areas of India and Ceylon is a strange feature noticed in the distribution of the larvae
DNA polymorphism at the BoLA-DRB3 gene of cattle in relation to resistance and susceptibility to leukemia

Polymorphism of exon 2 of the BoLA-DRB3 gene was investigated by the PCR-RFLP method in a sample of healthy and leukemia-afflicted Black Pied cattle. Allele variety was studied and allele frequencies were determined in a total sample and in the two groups. Alleles mediating resistance (BoLA-DRB3.2{sup *}11, {sup *}23, and {sup *}28) and susceptibility to leukemia (DRB3.2{sup *}22, {sup *}24, {sup *}16, and {sup *}8) were revealed in Black Pied cattle. The dominant type of inheritance of the disease resistance was confirmed. On the basis of original and published data obtained earlier for Holstein-Friesian cattle, a conclusion was made about the universal character of the spectrum of BoLA-DRB3 alleles providing resistance and susceptibility to leukemia. 18 refs., 1 fig., 3 tabs.
Two New Species of the Genus Gonydactylus (Sauria: Gekkonidae) from Eastern Nepal

Two new species of the naked-toed geckos of the genus Gonydactylus are described from Eastern Nepal. A comparison of the described species with another “himalayan” Gonydactylus ( G. khasiensis and occurring in the west of Nepal G. himalayanus ) is given.
Management practices and productivity status of cattle and buffaloes in Rajasthan

Livestock sector is an important source of livelihood in Rajasthan for rural masses and generates regular income to the farmer. Bovine farming is a process to convert available feed and fodder material (input) into milk and other byproducts (output). The present study assesses the management practices of cattle and buffalo in Rajasthan. Detailed information collected from farmers of all the nine agro-climatic sub-zones of Rajasthan were used for the study. The data were collected on various management practices including economic traits. Majority of farmers were relying on natural service for breeding their bovines. Adoption of AI was poor possibly due to poor awareness among the farmers or due to lack of confidence in AI or lack of accessibility to the facilities. Mid-heat detection and pregnancy diagnosis test were conducted by most of the farmers. Majority of farmers fed chaffed green and dry fodder roughages at stall. Lactating animals were offered concentrate and mineral mixture/common salt on individual basis. Majority of farmers washed the udders before milking the animals. Most of the farmers housed the animals in pens having pucca stall with kachcha floor. The average per day milk yield, peak milk yield and age at first calving were found significantly associated with each other and varied with the change in agro-climatic zones.
Generation of random states of electric power systems at assessment of their reliability by the Monte Carlo method

In this paper we deal with the problem related to effective assessment of reliability of electric power systems, particularly, the efficiency of pseudorandom number generators while using the Monte Carlo method for generation of random states of electric power systems. We consider the efficiency of four pseudorandom number generators: linear congruential generator, lagged Fibonacci generator, Mersenne Twister and Sobol sequence. The Kolmogorov-Smirnov test for analysis of randomness of sequences was used to analyze the above pseudorandom generators. Based on this analysis, it has been determined that the most random sequence may be obtained while using the Sobol sequences generator. Next, visual analysis of these pseudorandom number sequences was conducted. It showed that 2d points gained from the Sobol sequence filled the surface more evenly than other generators, where as the linear congruential generator and the lagged Fibonacci generator would form voids. In the final part of the research, the analyzed pseudo random generators were used in a model for reliability assessment using the Monte Carlo method. We modeled a three-node electric power system test scheme. As a result, the linear congruential generator and the lagged Fibonacci generator did not stabilize even after ten thousand random states of the system. These results correlate with the Kolmogorov-Smirnov test and show that these generators are barely random and unsuitable for reliability assessment using the Monte Carlo method. The Mersenne Twister and the Sobol sequence results were much better. The expected value of power shortage stabilized by the 4000th rando state with the Sobol sequence. In conclusion, we can say that the Sobol sequence is the most suitable pseudorandom generator for reliability assessment using the Monte-Carlo method than the other generators considered above.
Virulence Factor Production in PyrE Mutants of Pseudomonas Aeruginosa

It has been shown previously in our lab that mutations in the pyrimidine pathway reduced the ability of Pseudomonas aeruginosa to produce virulence factors. Knockout mutations in pyrB, pyrC and pyrD genes of the pyrimidine pathway showed that virulence factor production was decreased. Pyoverdin, pyocyanin, hemolysin, iron chelation, motility, and adherence are all considered virulence factors. Here I further investigate the effects of mutations in the pyrimidine pathway by studying a pyrE mutant. I studied the effect of the pyrE mutation on the production of the above virulence factors. Just like the effect of pyrB, pyrC and pyrD mutations,the pyrE mutation also showed that the bacteria were deficient in producing virulence factors when compared to the wild type. The broader impact of this research would be the possibility of finding drugs that could treat patients infected with P. aeruginosa and possibly extend the lives of chronically infected patients with cystic fibrosis.
Taxonomy, phylogeny and biogeography of Central European "Kybos" (Insecta: Hemiptera: Cicadellidae)

The Central European species of the taxonomically difficult Holarctic typhlocybine genus Kybos are revised with morphological, molecular and bioacoustic methods. Currently it is impossible to identify females and nymphs. In addition the otherwise diagnostic shape of the male genitalia is linked by intermediates in some morphologically similar nominal species. The second important diagnostic structure, the male sound apodemes, is not yet fully developped in teneral males, a fact which was not sufficiently taken into consideration by some authors. The present study evaluates the morphological variation of the male genitalia and sound apodemes. Females and nymphs are investigated for taxonomically relevant characters. For comparison molecular studies using sequences of the so called barcoding gene COI as well as 16S are performed and bioacoustic characters are investigated for some species. The morphological studies did not yield previously unknown characters particularly for the females and nymphs but suggested that the variation of the male genitalia has previously been overestimated. For this reason K. perplexus is synonymised with K. strigilifer (new synonymy). Similarly the small sound apodemes of K. volgensis are interpreted as not yet fully developped structures and the species is synonymised with K. virgator (new synonymy). The base of the female ovipositor is variable within Kybos and separates species groups but does not diagnose species. Nymphs vary in leg dimensions and colour forming the same species groups as the female genitalia but, again, do not diagnose species. In the molecular analyses neither COI nor 16S sequences could discriminated all the species defined by morphology. In particular K. butleri and K. rufescens were polyphyletic in both molecular analyses. These results clearly illustrate that the so called barcoding gene COI is not universally applicable for species definition. The few results from the bioacoustic studies indicate that this method may be helpful to solve some taxonomic problems of closely related sympatric species. Phylogenetic analyses are performed with morphological data and COI as well as 16S sequences. The three analyses strongly support the monophyly of Kybos. The consensus trees of the three analyses are poorly resolved and their topologies differ from each other. In the morphological tree the female genital characters make the most important contribution to tree structure whereas the male genitalia are of less importance, contrary to species diagnoses. It is interesting to note that the morphological tree comprises a monophyletic group of Betulaceae feeders not supported by the molecular trees.
Development of microsatellite markers for the Manila clam Ruditapes philippinarum

We isolated nine polymorphic microsatellites from the Manila clam Ruditapes philippinarum. These loci provide one class of highly variable genetic marker as the number of alleles ranged from six to 22, and the observed and expected heterozygosity ranged from 0.136 to 0.909 and from 0.553 to 0.954, respectively. We consider that these loci are potentially useful for detailing the genetic structure and gene flow among R. philippinarum populations.