Miracle-dz/UniFAR-FTUs huggingface dataset:
Conditional RNA interference in vivo to study mutant p53 oncogenic gain of function on tumor malignancy

Mutant p53 proteins are thought to have acquired a "gain of function" (GOF) activity that mainly contributes to tumor aggressiveness. Previously we reported that constitutive downregulation of mutant p53 by RNA interference reduces the tumorigenicity of cancer cells in an animal model; however, effects of adaptation to long-term mutant p53 inhibition could not be excluded. To address this point, mimicking more physiological conditions, we now describe the establishment of a lentiviral-based system for conditional interference with mutant p53 expression. In vivo studies assessed the efficacy of conditional RNA interference in inhibiting gain of function activity of mutant p53 proteins by reducing tumor growth ability. Moreover by using this system, microarray data were validated in vitro and in vivo and putative mutant p53 target genes that may contribute to its gain of function effects in cancer were identified. Results are confirmatory that depletion of mutant p53 protein impacts on tumor malignancy and validated the inducible lentiviral-based system as an efficient tool to study the gain of function activity of human tumor derived p53 mutants.
Diversity of the Lactic Acid Bacterium and Yeast Microbiota in the Switch from Firm- to Liquid-Sourdough Fermentation

ABSTRACT Four traditional type I sourdoughs were comparatively propagated (28 days) under firm (dough yield, 160) and liquid (dough yield, 280) conditions to mimic the alternative technology options frequently used for making baked goods. After 28 days of propagation, liquid sourdoughs had the lowest pH and total titratable acidity (TTA), the lowest concentrations of lactic and acetic acids and free amino acids, and the most stable density of presumptive lactic acid bacteria. The cell density of yeasts was the highest in liquid sourdoughs. Liquid sourdoughs showed simplified microbial diversity and harbored a low number of strains, which were persistent. Lactobacillus plantarum dominated firm sourdoughs over time. Leuconostoc lactis and Lactobacillus brevis dominated only some firm sourdoughs, and Lactobacillus sanfranciscensis persisted for some time only in some firm sourdoughs. Leuconostoc citreum persisted in all firm and liquid sourdoughs, and it was the only species detected in liquid sourdoughs at all times; it was flanked by Leuconostoc mesenteroides in some sourdoughs. Saccharomyces cerevisiae, Candida humilis, Saccharomyces servazzii, Saccharomyces bayanus-Kazachstania sp. , and Torulaspora delbrueckii were variously identified in firm and liquid sourdoughs. A total of 197 volatile components were identified through purge and trap–/solid-phase microextraction–gas chromatography-mass spectrometry (PT–/SPME–GC-MS). Aldehydes, several alcohols, and some esters were at the highest levels in liquid sourdoughs. Firm sourdoughs mainly contained ethyl acetate, acetic acid, some sulfur compounds, and terpenes. The use of liquid fermentation would change the main microbial and biochemical features of traditional baked goods, which have been manufactured under firm conditions for a long time.
Heavy gluino as the lightest supersymmetric particle

We consider the possibility that the lightest supersymmetric particle is a heavy gluino. After discussing models in which this is the case, we demonstrate that the $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}\ensuremath{-}\mathrm{LSP}$ could evade cosmological and other constraints by virtue of having a very small relic density. We then consider how neutral and charged hadrons containing a gluino will behave in a detector, demonstrating that there is generally substantial apparent missing momentum associated with a produced $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}\ensuremath{-}\mathrm{LSP}. $ We next investigate limits on the $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}\ensuremath{-}\mathrm{LSP}$ deriving from CERN, LEP, LEP2 and run I Fermilab Tevatron experimental searches for excess events in the jets plus missing momentum channel and for stable heavily ionizing charged particles. The range of ${m}_{\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}}$ that can be excluded depends upon the path length of the $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}$ in the detector, the amount of energy it deposits in each hadronic collision, and the probability for the $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}$ to fragment to a pseudo-stable charged hadron after a given hadronic collision. We explore how the range of excluded ${m}_{\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}}$ depends upon these ingredients, concluding that for non-extreme cases the range $3\mathrm{GeV}\ensuremath{\lesssim}{m}_{\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}}\ensuremath{\lesssim}130\char21{}150\mathrm{GeV}$ can be excluded at 95% C.L. based on currently available OPAL and CDF analyses. We find that run II at the Tevatron can extend the excluded region (or discover the $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g})$ up to ${m}_{\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}}\ensuremath{\sim}160\char21{}180\mathrm{GeV}. $ For completeness, we also analyze the case where the $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}$ is the NLSP (as possible in gauge-mediated supersymmetry breaking) decaying via $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}\ensuremath{\rightarrow}g+\mathrm{gravitino}. $ We find that the Tevatron run I data exclude ${m}_{\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}}l~240\mathrm{GeV}. $ Finally, we discuss application of the procedures developed for the heavy $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{g}\ensuremath{-}\mathrm{LSP}$ to searches for other stable strongly interacting particles, such as a stable heavy quark.
Characterization of Methicillin-Resistant Staphylococcus aureus Isolated from Healthy Turkeys and Broilers Using DNA Microarrays

Methicillin-resistant Staphylococcus aureus (MRSA) is a major human health problem and recently, domestic animals are described as carriers and possible reservoirs. Twenty seven S. aureus isolates from five turkey farms (n = 18) and two broiler farms (n = 9) were obtained by culturing of choana and skin swabs from apparently healthy birds, identified by Taqman-based real-time duplex nuc-mecA-PCR and characterized by spa typing as well as by a DNA microarray based assay which covered, amongst others, a considerable number of antibiotic resistance genes, species controls, and virulence markers. The antimicrobial susceptibility profiles were tested by agar diffusion assays and genotypically confirmed by the microarray. Five different spa types (3 in turkeys and 2 in broilers) were detected. The majority of MRSA isolates (24/27) belonged to clonal complex 398-MRSA-V. The most frequently occurring spa types were accordingly t011, t034, and t899. A single CC5-MRSA-III isolated from turkey and CC398-MRSA with an unidentified/truncated SCCmec element in turkey and broiler were additionally detected. The phenotypic antimicrobial resistance profiles of S. aureus isolated from both turkeys and broilers against 14 different antimicrobials showed that all isolates were resistant to ampicillin, cefoxitin, oxacillin, doxycycline, and tetracycline. Moreover, all S. aureus isolated from broilers were resistant to erythromycin and azithromycin. All isolates were susceptible to gentamicin, chloramphenicol, sulphonamides, and fusidic acid. The resistance rate against ciprofloxacin was 55.6% in broiler isolates and 42.1% in turkey isolates. All tetracycline resistant isolates possessed genes tetK/M. All erythromycin-resistant broiler isolates carried ermA. Only one broiler isolate (11.1%) carried genes ermA, ermB, and ermC, while 55.6% of turkey isolates possessed ermA and ermB genes. Neither PVL genes (lukF/S-PV), animal-associated leukocidin (lukM and luk-P83) nor the gene encoding the toxic shock syndrome toxin (tst1) were found in turkey and broiler isolates. In conclusion, the detection of MRSA in healthy turkeys and broilers with even additional antibiotic resistance markers is of major public health concern. The difference in antibiotic resistance and virulence markers between MRSA isolates from turkeys and broilers was addressed.
THE KEEL – MORI THEOREM VIA STACKS

Let X be an Artin stack (always assumed to have quasi-compact and separated diagonal over SpecZ; cf. [2, §1.3]). A coarse moduli space for X is a map π : X → X to an algebraic space such that (i) π is initial among maps from X to algebraic spaces (note that the category of maps from X to an algebraic space is discrete), and (ii) for every algebraically closed field k the map [X (k)]→ X(k) is bijective (where [X (k)] denotes the set of isomorphism classes of objects in the small category X (k)). If X is equipped with a map to a scheme S then X has a unique compatible map to S, and so it is equivalent to require the universal property for algebraic spaces over S. In [5], Keel and Mori used a close study of groupoids to prove that if X is locally of finite type over a locally noetherian scheme S and its inertia stack IS(X ) = X ×X ×SX X is finite over X then there exists a coarse moduli space π : X → X with X locally of finite type over S (and separated over S when X is separated over S). They also proved that π is a proper universal homeomorphism, that for any flat (locally finite type) base change X ′ → X in the category of algebraic spaces the map π×X X ′ is a coarse moduli space, and that OX → π∗(OX ) is an isomorphism. The finiteness hypothesis on IS(X ) is weaker than finiteness of ∆X /S and is stronger than quasi-finiteness of ∆X /S . The purpose of this note is to explain how to systematically use stacks instead of groupoids to give a more transparent version of the Keel–Mori method and to eliminate noetherian assumptions. Since the formation of coarse spaces does not generally commute with (non-flat) base change, it does not seem possible to immediately reduce existence problems to the locally noetherian case. If we wish to avoid separatedness hypotheses on X over S but want π : X → X to be a universal homeomorphism then it is unreasonable to consider X for which ∆X /S is not quasi-finite (e.g., the non-separated stack Q = A/Gm that classifies line bundles equipped with a section has k-points specializing to other k-points and so it cannot admit a coarse moduli space Q → Q that is a universal homeomorphism).
Is population structure in the European white stork determined by flyway permeability rather than translocation history?

European white stork are long considered to diverge to eastern and western migration pools as a result of independent overwintering flyways. In relatively recent times, the western and northern distribution has been subject to dramatic population declines and country-specific extirpations. A number of independent reintroduction programs were started in the mid 1950s to bring storks back to historical ranges. Founder individuals were sourced opportunistically from the Eastern and Western European distributions and Algeria, leading to significant artificial mixing between eastern and western flyways. Here we use mitochondrial and microsatellite DNA to test the contention that prior to translocation, eastern and western flyways were genetically distinct. The data show a surprising lack of structure at any spatial or temporal scale suggesting that even though birds were moved between flyways, there is evidence of natural mixing prior to the onset of translocation activities. Overall a high retention of genetic diversity, high Nef, and an apparent absence of recent genetic bottleneck associated with early 20th century declines suggest that the species is well equipped to respond to future environmental pressures.
The Open University ’ s repository of research publications and other research outputs A generic shape descriptor using Bezier curves Conference Item

Bezier curves are robust tool for a wide array of applications ranging from computer-aided design to calligraphic character outlining and object shape description. In terms of the control point generation process, existing shape descriptor techniques that employ Bezier curves do not distinguish between regions where an object’s shape changes rapidly and those where the change is more gradual or flat. This can lead to an erroneous shape description, particularly where there are significantly sharp changes in shape, such as at sharp corners. This paper presents a novel shape description algorithm called a generic shape descriptor using Bezier curves (SDBC) which defines a new strategy for Bezier control point generation by integrating domain specific information about the shape of an object in a particular region. The strategy also includes an improved dynamic fixed length coding scheme for control points. The SDBC framework has been rigorously tested upon a number of arbitrary shapes, and both quantitative and qualitative analyses have confirmed its superior performance in comparison with existing algorithms.
Enhanced Chemosensory Detection of Negative Emotions in Congenital Blindness

It is generally acknowledged that congenitally blind individuals develop superior sensory abilities in order to compensate for their lack of vision. Substantial research has been done on somatosensory and auditory sensory information processing of the blind. However, relatively little information is available about compensatory plasticity in the olfactory domain. Although previous studies indicate that blind individuals have superior olfactory abilities, no studies so far have investigated their sense of smell in relation to social and affective communication. The current study compares congenitally blind and normal sighted individuals in their ability to discriminate and identify emotions from body odours. A group of 14 congenitally blind and 14 age- and sex-matched sighted control subjects participated in the study. We compared participants' abilities to detect and identify by smelling sweat from donors who had been watching excerpts from emotional movies showing amusement, fear, disgust, or sexual arousal. Our results show that congenitally blind subjects outperformed sighted controls in identifying fear from male donors. In addition, there was a strong tendency that blind individuals were also better in detecting disgust. Our findings reveal that congenitally blind individuals are better at identifying ecologically important emotions and provide new insights into the mechanisms of social and affective communication in blindness.
Pathology of subclinical paratuberculosis (Johne's Disease) in Awassi sheep with reference to its occurrence in Jordan.

In this study, the pathological lesions and occurrence of subclinical Johne's disease in Awassi sheep is investigated using histopathological (HP) and immunohistochemical (IHC) examinations, Acid Fast Staining (AFS) of tissue sections, direct smears from tissues and culture. Histopathological examination of 202 ilea and the corresponding mesenteric lymph nodes (179) was conducted. In addition, IHC examination, using rabbit poly - clonal antiserum, of 134 ilea and 123 mesenteric lymph nodes was also conducted. The occurrence of the disease was observed in 50% and 93% of the ilea examined using histopathology and IHC techniques, respectively. Fifty nine percent of lymph nodes were positive by IHC. The histopathological lesions were graded from І-IV, I being the least severe, based on the type of cellular infiltrate (lymphocytes, macrophages and epithelioid cells) and the severity of the lesions. Grades III and IV (SP) were considered positive while I and II were considered suspected. Analysis of the results also revealed that the majority of suspected cases (grades I and II) reacted positive with the IHC. Furthermore, the IHC reactions were classified into three categories depending on the number of stained cells and the intensity of the staining (I-mild, II-moderate and III-strong). Direct smears, and tissue sections obtained from the ilea and stained with AFS revealed that out of 202 tissue samples, 53 (26%) and 22 (11%) were positive, respectively. Results of the culture revealed that 22 (11%) out of 202 were positive. These results showed that the occurrence of paratuberculosis (Johne's disease) in Awassi sheep is very high in Jordan and needs further study in order to develop rational methods of control effective for the Jordanian sheep population.
A Deep Multicolor Survey I. Imaging Observations and Catalog of Stellar Objects

We have used the KPNO 4-meter Mayall telescope to image 0.83 square degrees of sky in six fields at high galactic latitude in six filters spanning 3000-10000\AA\ to magnitude limits ranging from 22.1 to 23.8. We have assembled a catalog of 21,375 stellar objects detected in the fields for use primarily in conducting a multicolor search for quasars. This paper describes the data reduction techniques used on the CCD data, the methods used to construct the stellar object catalog, and the simulations performed to understand its completeness and contamination.
Impact of Male Obesity on Semen Quality and Serum Sex Hormones

Introduction. To investigate the association of high Body Mass Index (BMI) with semen parameters and reproductive hormones in men of reproductive age. Setting. The Saudi Center for Assisted Reproduction. Method. This study was conducted during the period from February 2009 to February 2011. Subjects were exposed through medical history evaluation as well as physical examination. BMI was calculated. Two semen samples about 1 week apart were taken from each participant by masturbation after 2–5 days of abstinence. The samples were assessed according to the WHO Criteria. Blood samples (5 ml) were withdrawn; centrifuged and the resulting sera were preserved at −4 degrees Centigrade. Serum FSH, LH, PRL, and Testosterone levels were estimated by the ELISA method. Results. There was no significant correlation between BMI and any of semen and hormonal parameters. There was significant negative correlation between age and total motility. Only the advanced paternal age has shown significant association with low motility (P = 0.007). Conclusion. Our study showed a significant effect of aging on sperm motility and concentration.
AN ENHANCED SELF-ADAPTIVE MAPREDUCE SCHEDULING ALGORITHM

Map-Reduce [6] is " a programming model and an associated implementation for processing and generating large data sets. " Hadoop is an open-source implementation of MapReduce, enjoying wide adoption, and is used not only for batch jobs but also for short jobs where low response time is critical. However, Hadoop's performance is currently limited by its default task scheduler, which implicitly assumes that cluster nodes are homogeneous and tasks make progress linearly, and uses these assumptions to decide when to speculatively re-execute tasks that appear to be stragglers. In practice , the homogeneity assumptions do not always hold. Longest Approximate Time to End (LATE) [27] is a scheduling algorithm that takes a heterogeneous environment into consideration. However, its problem is that it still depends on a static method to compute the progress of tasks. As a result neither Hadoop default nor LATE schedulers perform well in a heterogeneous environment. Self-adaptive MapReduce Scheduling Algorithm (SAMR) [4] is more advantageous than LATE. It uses historical information to adjust the stage weights of map and reduce tasks when estimating task execution times. However, SAMR does not consider the fact that for different types of jobs their map and reduce stages' weights may be different. Even for the same type of jobs, different datasets may lead to different weights. To this end, we propose ESAMR: an Enhanced Self-Adaptive MapReduce scheduling algorithm to improve the speculative re-execution of slow tasks in MapReduce. In ESAMR, in order to identify slow tasks accurately, we differentiate historical stage weights information on each node and divide them into K clusters using a K-means clustering algorithm; and when executing a job's tasks on a node, ESAMR classifies the tasks into one of the clusters and uses the clusters weights to estimate the execution time of the job's tasks on the node. Experimental results show that among the aforementioned algorithms, ESAMR leads to the smallest error in task execution time estimation and identifies slow tasks most accurately. iv ACKNOWLEDGMENTS The value of the master thesis goes beyond its scientific content since it summarizes the work of three years of education. In my particular case, this thesis symbolically represents all the years spent in UNL with all the gained amount of experience and personal development. I have been working on this thesis for more than one year. This document reports only the final outcome, leaving out everything that is behind it. My …
Tolerance analysis of model-based camera tracking by modeling errors

Accuracy of 3-D models is important in model-based camera tracking. However, their precise modeling requires delicate procedures. On the other hand, end-users are difficult to perceive tracking errors, which are caused by a certain level of modeling errors. Therefore, human perceptual errors can be different from real tracking errors. In this paper, we analyze the tolerance of modeling errors by comparing computational matching errors of model-based camera tracking with its human perceptual matching errors through user evaluations. We also discuss permissible ranges of modeling errors for reliable tracking without precise modeling.
Matter’s Electromagnetic Signature Reproduction by Graded-Dielectric Multilayer Assembly

A lot of effort has been devoted in the last decades by technology research to realizing materials with a priori defined electromagnetic (EM) properties. One of the challenges at present is to configure the reflection coefficient (RC) of a structure so that any shape of a fixed microwave response is followed. A method for realizing microwave absorbers made by carbon nanocomposite layers assembly able to mimic a given reflection profile is described and experimentally validated. The multilayer design (layer sequence, material, and thickness) is pursued by means of a customized numerical optimization algorithm, which allows to get the required microwave behavior. The novelty of the research is the possibility of tuning the EM field propagation through the combination of different materials in a specific layered compound, in order to imitate the response of any “real” object (i.e., with known EM properties). For the experimental validation of the process, three multilayered structures were designed and manufactured, and their microwave RC was measured in the frequency range of 2–18 GHz. The comparison with the related targets (an ideal frequency selective pattern and the defined profiles of dry soil and salt water as retrieved from literature survey) highlights the effective simulating capability of the realized structures. The preliminary results suggest to exploit the graded-dielectric properties provided by carbon-based nanocomposites for EM mimicking purposes: this would be an ideal approach to tackle still unsolved issues in EM compatibility, remote sensing, communication, and safety fields, as well as for low-cost and time-saving metrology applications.
Current Status of Left Ventricular Assist Devices and Cell Sheet Engineering for Treatment of Severe Heart Disease in Japan.

In Japan, heart disease is the second most common cause of death after cancer. About 1.6 million people in Japan are cardiac patients (as of October 2011). Advanced treatments and research have been conducted to reduce the number of patients and number of deaths. The current status of left ventricular assist devices (LVADs) and cell sheet engineering for treatment of severe heart disease in Japan is introduced in this article.