Miracle-dz/UniFAR-FTUs huggingface dataset:
A cell-free replication system for human polyomavirus JC DNA

The human polyomavirus JC virus (JCV) establishes persistent infections in most individuals and is the etiologic agent of progressive multifocal leukoencephalopathy. In this report, we describe the establishment of a soluble cell-free system that is capable of replicating exogenous plasmid DNA containing the JCV origin of replication. Replication in this system is completely dependent on the addition of JCV large T antigen (TAg). To prepare JCV TAg for replication analysis, a recombinant baculovirus containing the JCV TAg-coding sequence was generated. TAg expressed in insect cells was purified by metal chelate chromatography. JCV TAg supported initiation of JCV DNA replication in the presence of DNA polymerase alpha-primase, replication protein A, and topoisomerase I in a dose-dependent manner and was also capable of supporting DNA replication in crude human cell extracts. Point mutation of TAg-binding site I strongly diminished TAg binding and concomitantly reduced JCV DNA replication in vivo and in vitro by approximately 50%. Point mutation of TAg-binding site II or deletion of the early palindrome completely abolished replication of JCV origin-containing plasmid DNA in vivo and in vitro, marking these sequences as essential components of the JCV core origin. A comparison of several TAgs showed that simian virus 40 TAg, but not mouse polyomavirus (PyV) TAg, supported replication of a plasmid containing a JCV origin. These findings provide evidence that replication in the cell-free system faithfully mimics JCV DNA replication in vivo. Therefore, it may be a useful tool for future analysis of interactions between JCV and its host cell.
RELATION OF CYCLIC AMP TO THE RELEASE AND ACTIONS OF PROSTAGLANDINS *

In studying the biological effects of the prostaglandins, one is impressed by the ubiquity of their distribution and their unparalleled ability to modify hormone action, an effect now known to correlate with changes in cyclic AMP levels in many different cell types. Prostaglandins themselves are known to stimulate accumulation of cyclic AMP in many different tissues, while in other tissues inhibitory effects of prostaglandins on certain hormone-induced cyclic AMP-mediated responses have been 24 A regulatory role for endogenous prostaglandins has been postulated since, in general, both quantitative and qualitative changes in the cellular efflux of prostaglandins have been detected following hormonal stimulation of tissues.
Congenital Granuloprival Hypoplasia of Cerebellar and Hippocampal Cortex

Two siblings with congenital granule cell hypoplasia of the cerebellum and hippocampus are reported. The patients, both male, showed severe psychomotor retardation, microcephaly, hypotonia, athetosis, and seizures; they died at the ages of 37/12 years and 510/12 years, respectively. Postmortem examinations in both cases revealed nearly complete absence of the granule cells of the cerebellum with relative preservation of the Purkinje cells. Also absent were the granule cells of the fascia dentata of the Ammon's horns of the hippocampus, without any detectable gliosis; this has not previously been reported. Twenty-three autopsy cases of granuloprival cerebellar hypoplasia are reviewed. The present cases illustrate a singularly unique disease process, comparable to the classical cerebellar hypoplasia experimentally induced by parvoviruses, and suggest a granule cell specific insult to the brain during the late second trimester. (J Child Neurol 1987;2:279-286).
Localization of d- and l-methadone after intraventricular injection into rat brains.

Stereotaxic injections of 10 µg of either d - or l -methadone, into a lateral cerebral ventricle of rats, produced analgesia only in those animals injected with the pharmacologically active l -isomer of methadone. The intraventricular injection of C 14 -labeled d - or l -methadone with H 3 -mannitol as an inert marker resulted in the accumulation of both d - and l -methadone in the region of the anterior hypothalamus before and during the period of maximal analgesia. There was no significant difference in the accumulation of the two isomers. Sagittal sectioning of the anterior hypothalamus showed no significant difference in the rates of diffusion of the two isomers of methadone, although the greater diffusabiity of mannitol laterally from the third ventricle compared to methadone could be demonstrated.
Protein kinase C-dependent coupling of alpha(2A/D)-adrenergic receptors to phospholipase D.

To clarify the role of protein kinase C (PKC) in regulating the coupling pathway of alpha(2)-adrenergic receptors, we examined receptor activation of phospholipase D (PLD) in PC12 cells overexpressing alpha(2A/D) receptors, using [(3)H]phosphatidylbutanol formation as an index of PLD activity. In intact PC12/alpha(2A/D) cells, the ability of either epinephrine or the alpha(2)-receptor-selective agonist UK14304 to stimulate PLD was completely dependent on concomitant PKC activation. Pretreatment with the PKC activator phorbol dibutyrate revealed an agonist-stimulated PLD activity which was blocked by the alpha(2)-receptor-selective antagonist rauwolscine and by pertussis toxin treatment. Removal of extracellular calcium or tyrosine kinase inhibition by genistein pretreatment also eliminated the ability of epinephrine to stimulate PLD. These results indicate that alpha(2A/D)-adrenergic receptors couple via pertussis toxin-sensitive G proteins to PLD in a PKC-requiring and tyrosine kinase regulated manner.
Transposition Cipher with Pseudo-Random Shuffling: the Dynamic Transposition Combiner

Extensions are made to a class of transposition cipher based on continued shuffling. These ciphers permute plaintext into ciphertext by swapping every message element with some message element selected at pseudo-random; elements can be characters (e.g., bytes) or bits. Extensions include operation on very large data blocks, cryptographic shuffling variations, and the efficient extraction of plaintext from ciphertext. In addition, selected extra data can be adjoined to the plaintext to eliminate the data-dependent weak encipherings otherwise inherent in transposition. This bit-balancing data is supposed to completely eliminate all normal usage-frequency statistics from bit-transposition ciphertext. The same mechanism can also be viewed as a cryptographic combiner, and, with sequence-to-block and block-to-sequence conversions, can generally replace the exclusive-OR combining function used in Vernam stream ciphers.
A Dispensable Yeast Ribosomal Protein Optimizes Peptidyltransferase Activity and Affects Translocation*

Yeast ribosomal protein L41 is dispensable in the yeast. Its absence had no effect on polyphenylalanine synthesis activity, and a limited effect on growth, translational accuracy, or the resistance toward the antibiotic paromomycin. Removal of L41 did not affect the 60:40 S ratio, but it reduced the amount of 80 S, suggesting that L41 is involved in ribosomal subunit association. However, the two most important effects of L41 were on peptidyltransferase activity and translocation. Peptidyltransferase activity was measured as a second-order rate constant (k cat/K s ) corresponding to the rate of peptide bond formation; thisk cat/K s was lowered 3-fold to 1.15 min−1 mm −1 in the L41 mutant compared with 3.46 min−1mm −1 in the wild type. Translocation was also affected by L41. Elongation factor 2 (EF2)-dependent (enzymatic) translocation of Ac-Phe-tRNA from the A- to P-site was more efficient in the absence of L41, because 50% translocation was achieved at only 0.004 μm EF2 compared with 0.02 μm for the wild type. Furthermore, the EF2-dependent translocation was inhibited by 50% at 2.5 μm of the translocation inhibitor cycloheximide in the L41 mutant compared with 1.2 μm in the wild type. Finally, the rate of EF2-independent (spontaneous) translocation was increased in the absence of L41.
An improved fuzzy C-means clustering algorithm based on simulated annealing

Fuzzy C-means clustering algorithm (FCM) is a widely used clustering algorithm, however it has its drawbacks: the initial number of clusters needs to be determined by the manual control according to the prior knowledge; the objective function ignores the disequilibrium problems among the sample attribute data. In view of these problems, this paper proposes a sample weighted FCM algorithm based on simulated annealing algorithm. It uses the simulated annealing algorithm which has an excellent ability of seeking global optimal solution to calculate the initial value of the number of clusters and makes certain weighting process on the clustering center function and the objective function. The experiment results show that this proposed algorithm has better classification accuracy and classification accuracy rate compared with FCM algorithm and the common sample weighted FCM clustering algorithms. Meanwhile, this algorithm needs not to be determined the initial value of clusters manually. The improved algorithm possesses the superiority and the actual application value.
Relationship of neonatologists’ end-of-life decisions to their personal fear of death

Objective: To study the relationship of Australian and New Zealand (ANZ) neonatologists’ personal fear of death to their forgoing life-sustaining treatment and hastening death in newborns destined for severe disability and newborns for whom further treatment is considered non-beneficial or overly burdensome. Design: A self-report questionnaire survey of ANZ neonatologists. Setting: Neonatologists registered in the 2004 ANZ Directory of Neonatal Intensive Care Units. Participants: 78 of 138 (56%) neonatologists who responded to the study questionnaire. Main outcome measures: Between-group differences in the Multidimensional Fear of Death Scale. Results: In newborns for whom further treatment was deemed futile, 73 neonatologists reported their attitude to hastening death as follows: 23 preferred to hasten death by withdrawing minimal treatment, 35 preferred to hasten death with analgesia-sedation, and 15 reported that hastening death was unacceptable. Analysis of variance showed a statistically significant difference between the three groups regarding fear of the dying process (F = 3.78, p = 0.028), fear of premature death (F = 3.28, p = 0.044) and fear of being destroyed (F = 3.20, p = 0.047). Post hoc comparisons showed that neonatologists who reported that hastening death was unacceptable compared with neonatologists who preferred to hasten death with analgesia-sedation had significantly less fear of the dying process and fear of premature death, and significantly more fear of being destroyed. Conclusions: ANZ neonatologists’ personal fear of death and their attitude to hastening death when further treatment is considered futile are significantly related. Neonatologists’ fear of death may influence their end-of-life decisions.
Transport of NCL Applications over the Digital Radio Mondiale Broadcasting System for Ginga-enabled receivers: Signaling and Definitions

ISDB-T International standard is currently adopted by most Latin America countries and is already installed in most TV sets sold in recent years in the region. To support interactive applications in Digital TV receivers, ISDBT defines the middleware Ginga and its declarative language NCL (Nested Context Language). Similar to Digital TV, Digital Radio standards also provide the means to carry interactive applications; however, their specifications for interactive applications are usually more restricted than the ones used in Digital TV. Also, interactive applications for Digital TV and Digital Radio are usually incompatible. Motivated by such observations, this report considers the importance of interactive applications for both TV and Radio Broadcasting and the advantages of using the same middleware and language specification for Digital TV and Radio. More specifically, it establishes the signaling and definitions on how to transport and execute NCL (Nested Context Language) applications over DRM (Digital Radio Mondiale) transmission. Brazil is carrying trials with Digital Radio Mondiale standard in order to evaluate the best system to be used as reference for the Brazilian Digital Radio System.
Design at the end of the silicon roadmap

Scaling of silicon integrated technology into the deep sub-100 nm space brings with it a number of formidable challenges to the designer. Issues such as design complexity, power dissipation, process variability and reliability are challenging the traditional design methodologies. In this presentation, it is conjectured that the only viable long-term solution to these challenges is to drastically revise the way we do design, and a roadmap of potential solutions is presented. Ultimately, these innovative design solutions will help to pave the way to the post-silicon era.
Combining type-checking with model-checking for system verification

We present ATS/PML, a modeling language with an expressive type system (supporting both dependent types and linear types), and argue that the types in ATS/PML can be of great help in detecting modeling errors at compile-time. On one hand, we introduce modeling primitives with well-designed types into ATS/PML to facilitate a synergic combination of type-checking with model-checking. On the other hand, we compile ATS/PML into Promela so that the SPIN modelchecker can be readily employed to perform checking on models constructed in ATS/PML.
ΔNp73α inhibits PTEN expression in thyroid cancer cells

ΔNp73 is a N‐terminally truncated p53 family member with a dominant negative function, which is upregulated in cancer. PTEN is a lipid phosphatase, which is involved in the attenuation of tyrosine kinase signaling. PTEN expression is increased by p53, and its function is blunted in several malignancies. Because in most of the thyroid carcinomas, ΔNp73α is upregulated, whereas PTEN expression down regulated, we investigated whether ΔNp73α may influence PTEN expression in this cell model. We found that ΔNp73α overexpression in thyroid cancer cells reduces PTEN expression, whereas ΔNp73α down‐regulation by siRNA increases PTEN expression. Real‐time PCR indicated that overexpression of ΔNp73α is able to reduce PTEN mRNA levels. Moreover, chromatin immunoprecipitation (ChIP) and luciferase assays indicated that ΔNp73α binds to −1031‐779 region of the PTEN promoter, which is a different site than that for p53, thereby inhibiting promoter activity. Interestingly, also the transcriptionally active p73 isoforms (TAp73α and TAp73β) bound to this DNA sequence and, at variance with ΔNp73α, stimulated PTEN promoter activity to an extent similar to that of p53. In accordance with its effect on PTEN protein levels, ΔNp73α increased phospho‐Akt protein content and, as a consequence, Mdm2‐mediated p53 degradation. This effect of ΔNp73α resulted in increased thyroid cancer cell proliferation and reduced apoptosis and was reverted by the PI3‐kinase inhibitor LY294002, indicating the role of Akt pathway in this effect. Taken together, these results indicate a novel p73 regulated mechanism for PTEN expression in thyroid cancer cells, and that, also through this mechanism, ΔNp73α exerts its protumorigenic effect. © 2008 Wiley‐Liss, Inc.
Late Vascular Responses From 2 to 4 Years After Implantation of Sirolimus-Eluting Stents: Serial Observations by Intracoronary Optical Coherence Tomography

Background—Late vascular responses after implantation of drug-eluting stents may play a key role in steadily increasing occurrence of very late stent thrombosis have not yet been fully investigated in human beings. Methods and Results—Serial optical coherence tomography observations at 2 and 4 years were collected for 17 patients treated with 21 sirolimus-eluting stents. Corresponding 376 cross sections within single-stent segments at intervals of 1 mm were selected for analyses, and neointimal thickness on each strut was measured. Extrastent lumen (ESL) was defined as an external lumen of the stent. Area and angle of ESL were measured. A total of 3369 and 3221 struts were identified at 2 and 4 years, respectively. From 2 to 4 years, mean neointimal thickness increased (76.8±75.6 &mgr;m versus 123.0±102.5 &mgr;m; P<0.0001), whereas frequency of patients with uncovered struts decreased (88% versus 29%; P=0.002). Although prevalence of patients that had ESL was similar (59% of 2 years versus 65% of 4 years; P=1.0), the cross sections with ESL increased (9.6% versus 15.2%; P=0.02). Moreover, area and angle of ESL increased from 2 to 4 years (0.28±0.27 mm2 versus 0.62±0.68 mm2 and 16.6±5.4° versus 65.1±38.4°; P<0.01, respectively). The incidence of subclinical thrombus did not decrease (24% at 2 years versus 29% at 4 years; P=1.0). All thrombi were identified in patients who had cross sections with ESL. Conclusions—The current serial optical coherence tomography study showed an augmentation of neointimal growth at the late phase of sirolimus-eluting stent implantation. ESL may contribute to thrombus formation and ESL of sirolimus-eluting stents expanded from 2 to 4 years.
Catechol-O-Methyltransferase ( COMT )-mediated Metabolism of Catechol Estrogens : Comparison of Wild-Type and Variant COMT Isoforms 1

The oxidative metabolism of 17 -estradiol (E2) and estrone (E1) to catechol estrogens (2-OHE2, 4-OHE2, 2-OHE1, and 4-OHE1) and estrogen quinones has been postulated to be a factor in mammary carcinogenesis. Catechol-O-methyltransferase (COMT) catalyzes the methylation of catechol estrogens to methoxy estrogens, which simultaneously lowers the potential for DNA damage and increases the concentration of 2methoxyestradiol (2-MeOE2), an antiproliferative metabolite. We expressed two recombinant forms of COMT, the wild-type (108Val) and a common variant (108Met), to determine whether their catalytic efficiencies differ with respect to catechol estrogen inactivation. The His-tagged proteins were purified by nickel-nitrilo-triacetic acid chromatography and analyzed by electrophoresis and Western immunoblot. COMT activity was assessed by determining the methylation of 2-OHE2, 4-OHE2, 2-OHE1, and 4-OHE1, using gas chromatography/mass spectrometry for quantitation of the respective methoxy products. In the case of 2-OHE2 and 2-OHE1, methylation occurred at 2-OH and 3-OH groups, resulting in the formation of 2-MeOE2 and 2-OH-3-MeOE2, and 2-MeOE1 and 2-OH-3-MeOE1, respectively. In contrast, in the case of 4-OHE2 and 4-OHE1, methylation occurred only at the 4-OH group, yielding 4-MeOE2 and 4-MeOE1, respectively. Individual and competition experiments revealed the following order of product formation: 4-MeOE2 > 4-MeOE1 2-MeOE2 > 2-MeOE1 > 2-OH-3-MeOE1 > 2-OH-3-MeOE2. The variant isoform differed from wild-type COMT by being thermolabile, leading to 2–3-fold lower levels of product formation. MCF-7 breast cancer cells with the variant COMT 108Met/Met genotype also displayed 2–3-fold lower catalytic activity than ZR-75 breast cancer cells with the wild-type COMT 108Val/Val genotype. Thus, inherited alterations in COMT catalytic activity are associated with significant differences in catechol estrogen and methoxy estrogen levels and, thereby, may contribute to interindividual differences in breast cancer risk associated with estrogen-mediated carcinogenicity.
Rapid development of colitis in NSAID-treated IL-10-deficient mice.

BACKGROUND & AIMS Interleukin (IL)-10 is an anti-inflammatory and immune regulatory cytokine. IL-10-deficient mice (IL-10(-/-)) develop chronic inflammatory bowel disease (IBD), indicating that endogenous IL-10 is a central regulator of the mucosal immune response. Prostaglandins are lipid mediators that may be important mediators of intestinal inflammation. In this study we assessed the role of prostaglandins in the regulation of mucosal inflammation in the IL-10(-/-) mouse model of IBD. METHODS Prostaglandin (PG) synthesis was inhibited with nonselective or cyclooxygenase (COX)-isoform selective inhibitors. Severity of inflammation was assessed histologically. Cytokine production was assessed by ribonuclease protection analysis and enzyme-linked immunosorbent assay. PGE(2) levels were assessed by enzyme immunoassay. COX-1 and COX-2 expression was assessed by Western blot analysis. RESULTS Nonsteroidal anti-inflammatory drug (NSAID) treatment of wild-type mice had minimal effect on the colon. In contrast, NSAID treatment of 4-week-old IL-10(-/-) mice resulted in rapid development of colitis characterized by infiltration of the lamina propria with macrophages and interferon gamma-producing CD4(+) T cells. Colitis persisted after withdrawal of the NSAID. NSAID treatment decreased colonic PGE(2) levels by 75%. Treatment of IL-10(-/-) mice with sulindac sulfone (which does not inhibit PG production) did not induce colitis whereas the NSAID sulindac induced severe colitis. COX-1- or COX-2-selective inhibitors used alone did not induce IBD in IL-10(-/-) mice. However, the combination of COX-1- and COX-2-selective inhibitors did induce colitis. CONCLUSIONS NSAID treatment of IL-10(-/-) mice results in the rapid development of severe, chronic IBD. Endogenous PGs are important inhibitors of the development of intestinal inflammation in IL-10(-/-) mice.
Recognition of local features for camera-based sign language recognition system

A sign language recognition system is required to use information from both global features, such as hand movement and location, and local features, such as hand shape and orientation. We present an adequate local feature recognizer for a sign language recognition system. Our basic approach is to represent the hand images extracted from sign-language images as symbols which correspond to clusters by a clustering technique. The clusters are created from a training set of extracted hand images so that a similar appearance can be classified into the same cluster on an eigenspace. The experimental results indicate that our system can recognize a sign language word even in two-handed and hand-to-hand contact cases.
Diagrams for contact 5‐manifolds

According to Giroux, contact manifolds can be described as open books whose pages are Stein manifolds. For 5‐dimensional contact manifolds the pages are Stein surfaces, which permit a description via Kirby diagrams. We introduce handle moves on such diagrams that do not change the corresponding contact manifold. As an application, we derive classification results for subcritically Stein fillable contact 5‐manifolds and characterize the standard contact structure on the 5‐sphere in terms of such fillings. This characterization is discussed in the context of the Andrews–Curtis conjecture concerning presentations of the trivial group. We further illustrate the use of such diagrams by a covering theorem for simply connected spin 5‐manifolds and a new existence proof for contact structures on simply connected 5‐manifolds.
Classification of Melodic Motifs in Raga Music with Time-series Matching

Abstract Ragas are characterized by their melodic motifs or catch phrases that constitute strong cues to the raga identity for both the performer and the listener, and therefore are of great interest in music retrieval and automatic transcription. While the characteristic phrases, or pakads, appear in written notation as a sequence of notes, musicological rules for interpretation of the phrase in performance in a manner that allows considerable creative expression, while not transgressing raga grammar, are not explicitly defined. In this work, machine learning methods are used on labelled databases of Hindustani and Carnatic vocal audio concerts to obtain phrase classification on manually segmented audio. Dynamic time warping and HMM based classification are applied on time series of detected pitch values used for the melodic representation of a phrase. Retrieval experiments on raga-characteristic phrases show promising results while providing interesting insights on the nature of variation in the surface realization of raga-characteristic motifs within and across concerts.