Miracle-dz/UniFAR-FTUs huggingface dataset:
Methyl‐CpG binding proteins identify novel sites of epigenetic inactivation in human cancer

Methyl‐CpG binding proteins (MBDs) mediate histone deacetylase‐dependent transcriptional silencing at methylated CpG islands. Using chromatin immunoprecitation (ChIP) we have found that gene‐specific profiles of MBDs exist for hypermethylated promoters of breast cancer cells, whilst a common pattern of histone modifications is shared. This unique distribution of MBDs is also characterized in chromosomes by comparative genomic hybridization of immunoprecipitated DNA and immunolocalization. Most importantly, we demonstrate that MBD association to methylated DNA serves to identify novel targets of epigenetic inactivation in human cancer. We combined the ChIP assay of MBDs with a CpG island microarray (ChIP on chip). The scenario revealed shows that, while many genes are regulated by multiple MBDs, others are associated with a single MBD. These target genes displayed methylation‐ associated transcriptional silencing in breast cancer cells and primary tumours. The candidates include the homeobox gene PAX6, the prolactin hormone receptor, and dipeptidylpeptidase IV among others. Our results support an essential role for MBDs in gene silencing and, when combined with genomic strategies, their potential to ‘catch’ new hypermethylated genes in cancer.
Neogene Paratethyan croakers (Teleostei, Sciaenidae)

The fossil record of sciaenid fishes (based on both otoliths and osteological finds) from the Neogene of the Paratethys is reviewed. The species Labrax (=Morone) multipinnatus Gorjanovic-Kramberger, 1882 from the Sarmatian of Croatia (Sv. Nedelja) that was originally described as a sea bass of the family Moronidae is re-assigned to the extant croaker genus Argyrosomus. Two new genera and species of sciaenid fishes are described based on a single skeleton each, namely Landinisciaena popovi gen. et sp. nov. from the Tarkhanian (Lower/Middle Miocene) North Shirvanskaya Formation exposed along the Pshekha River, North Caucasus, Russia, and Croatosciaena krambergeri gen. et sp. nov. from the Sarmatian s.s. (Middle Miocene) deposits of Dolje in the nearby of the city of Zagreb, Croatia. The holotype of the former taxon possesses a well-preserved saccular otolith in situ (first record of in situ croacker otolith in Europe) similar to the otoliths of the extant genus Atractoscion. The otolith-based Ottnangian species Atractoscion elongatissimus Schwarzhans, 1993 is transferred to the genus Landinisciaena gen. nov. A comprehensive revision of the Neogene otholith-based sciaenid record from Paratethys resulted in the recognition of three new genera (Chaoia gen. nov., Pontosciaena gen. nov. and Leptosciaena gen. nov.) as well as in the description of a new species L. caputoi sp. nov. from the uppermost Messinian (Lago-mare phase) of Italy. A number of known otholith-based species were either synonymized or assigned to a new generic affiliation. The complex biogeographic history of the Neogene Paratethyan sciaenids (based on both otoliths and skeletal records) is discussed, resulting in the recognition of a vanished “sciaenid bioprovince”.
Increase in p202 Expression during Skeletal Muscle Differentiation: Inhibition of MyoD Protein Expression and Activity by p202

ABSTRACT p202 is a primarily nuclear, interferon-inducible murine protein that is encoded by the Ifi 202 gene. Overexpression of p202 in transfected cells retards cell proliferation. p202 modulates the pattern of gene expression by inhibiting the activity of various transcription factors including NF-κB, c-Fos, c-Jun, E2F-1, and p53. Here we report that p202 was constitutively expressed in mouse skeletal muscle and that the levels of 202 RNA and p202 greatly increased during the differentiation of cultured C2C12 myoblasts to myotubes. When overexpressed in transfected myoblasts, p202 inhibited the expression of one muscle protein (MyoD) without affecting the expression of a second one (myogenin). Thus, the decrease in the level of MyoD (but not of myogenin) during muscle differentiation may be the consequence of the increase in p202 level. Overexpressed p202 also inhibited the transcriptional activity of both MyoD and myogenin. This inhibition was correlated with an interaction of p202 with both proteins, as well as the inhibition by p202 of the sequence-specific binding of both proteins to DNA. This inhibition of the expression of MyoD and of the transcriptional activity of MyoD and myogenin may account for the inhibition of the induction of myoblast differentiation by premature overexpression of p202.
Exercise as cardiovascular therapy.

To the Editor: Drs Shephard and Balady1 discuss the potential dangers of excessive exercise and the appropriate dose of physical activity. They cite 2 reports showing that in healthy persons, prolonged exercise can cause myocardial fatigue with a temporary depression of myocardial function.2 3 In addition, recent research demonstrates that prolonged aerobic exercise may cause subclinical myocardial necrosis in individuals with no risk factors for cardiovascular disease.4 5 Evidence also exists that apparently healthy individuals who are not active enough to meet a traditional exercise prescription (structured vigorous activity) are at a high risk for subclinical myocardial damage caused by prolonged strenuous exercise.6 These findings may be of some importance: a recent well-conducted, randomized trial demonstrated that a lifestyle approach to …
Shredding Your Garbage: Reducing Data Lifetime Through Secure Deallocation

Today's operating systems, word processors, web browsers, and other common software take no measures to promptly remove data from memory. Consequently, sensitive data, such as passwords, social security numbers, and confidential documents, often remains in memory indefinitely, significantly increasing the risk of exposure. We present a strategy for reducing the lifetime of data in memory called secure deallocation. With secure deal-location we zero data either at deallocation or within a short, predictable period afterward in general system allocators (e.g. user heap, user stack, kernel heap). This substantially reduces data lifetime with minimal implementation effort, negligible overhead, and without modifying existing applications. We demonstrate that secure deallocation generally clears data immediately after its last use, and that without such measures, data can remain in memory for days or weeks, even persisting across reboots. We further show that secure deallocation promptly eliminates sensitive data in a variety of important real world applications.
Sevoflurane Inhibits Angiotensin II–induced, Protein Kinase C–mediated but Not Ca2+-elicited Contraction of Rat Aortic Smooth Muscle

BackgroundWhether volatile anesthetics attenuate angiotensin II–mediated vascular tone has not been determined. The current study was designed to investigate the effects of sevoflurane on the angiotensin II–stimulated, Ca2+- and protein kinase C (PKC)–mediated contraction of rat aortic smooth muscle. MethodsThe dose-dependent effects of sevoflurane on angiotensin II (10−7 m)–induced contraction, the increase in intracellular Ca2+ concentration, and PKC phosphorylation of rat aortic smooth muscle were measured using an isometric force transducer, a fluorometer, and Western blotting, respectively. ResultsAngiotensin II induced a transient increase in intracellular Ca2+ concentration, phosphorylation of Ca2+-dependent PKC (cPKC)-&agr;, and consequently, a transient contraction of rat aortic smooth muscle. Phosphorylation of the Ca2+-independent PKC-&egr; was not detected. The angiotensin II–induced contraction was almost completely abolished by removing extracellular Ca2+ and was significantly inhibited by the selective cPKC inhibitor Gö 6976 (10−5 m) but was not inhibited by the nonselective PKC inhibitor Ro 31-8425 (10−5 m). Sevoflurane dose-dependently inhibited the angiotensin II–induced contraction, with reductions of 14.2 ± 5.2% (P > 0.05), 26.7 ± 8.9% (P < 0.05), and 38.5 ± 12.8% (P < 0.01) (n = 10) in response to 1.7, 3.4, and 5.1% sevoflurane, respectively. The angiotensin II–elicited increase in intracellular Ca2+ concentration was not significantly influenced by 3.4, 5.1, or 8.5% sevoflurane. However, cPKC-&agr; phosphorylation induced by angiotensin II was inhibited dose dependently by 1.7, 3.4, and 5.1% sevoflurane, with depressions of 20.5 ± 14.2% (P > 0.05), 37.0 ± 17.8% (P < 0.05), and 62.5 ± 12.2% (P < 0.01) (n = 4), respectively. ConclusionThe current study indicates that Ca2+ and cPKC-&agr; are involved in angiotensin II–induced vascular contraction. Sevoflurane dose-dependently inhibited the angiotensin II–stimulated, cPKC-mediated but not Ca2+-elicited contraction of rat aortic smooth muscle.
Geometric tachyon to universal open string tachyon

A system of k Neveu-Schwarz (NS) 5-branes of type II string theory with one transverse direction compactified on a circle admits various unstable D-brane systems, some with geometric instability arising out of being placed at a point of unstable equilibrium in space and some with the usual open string tachyonic instability but no geometric instability. We discuss the effect of NS 5-branes on the descent relations among these branes and their physical interpretation in the T-dual ALF spaces. We argue that if the tachyon potential controlling these descent relations obeys certain conditions, then in certain region in the parameter space labelling the background the two types of unstable branes become identical via a second order phase transition, with the geometric tachyon in one system getting mapped to the usual open string tachyon of the other system. This would provide a geometric description of the tachyonic instability of the usual non-BPS Dp-brane in ten dimensional flat space-time.
Multiplatform Mobile Laser Scanning: Usability and Performance

Mobile laser scanning is an emerging technology capable of capturing three-dimensional data from surrounding objects. With state-of-the-art sensors, the achieved point clouds capture object details with good accuracy and precision. Many of the applications involve civil engineering in urban areas, as well as traffic and other urban planning, all of which serve to make 3D city modeling probably the fastest growing market segment in this field. This article outlines multiplatform mobile laser scanning solutions such as vehicle- and trolley-operated urban area data acquisition, and boat-mounted equipment for fluvial environments. Moreover, we introduce a novel backpack version of mobile laser scanning equipment for surveying applications in the field of natural sciences where the requirements include precision and mobility in variable terrain conditions. In addition to presenting a technical description of the systems, we discuss the performance of the solutions in the light of various applications in the fields of urban mapping and modeling, fluvial geomorphology, snow-cover characterization, precision agriculture, and in monitoring the effects of climate change on permafrost landforms. The data performance of the mobile laser scanning approach is described by the results of an evaluation of the ROAMER on a permanent MLS test field. Furthermore, an in situ accuracy assessment using a field of spherical 3D targets for the newly-introduced Akhka backpack system is conducted and reported on.
Nonablative radiofrequency treatment of facial laxity.

OBJECTIVE To share our current experience and review the current literature concerning the use of radiofrequency for the treatment of facial laxity. METHODS We discuss our experience and review the current literature. RESULTS Radiofrequency can impart mild tightening of mid- and lower facial laxity as well as periorbital laxity. In addition, it may help acne scars and acne. CONCLUSIONS Radiofrequency appears to impart mild improvement to facial laxity and is a viable nonsurgical option for patients with mild facial laxity. There is, however, a need for blinded, randomized controlled studies to further validate these claims.
Radon Risk and Remediation: A Psychological Perspective

Although radon exposure in the home increases the risk of lung cancer, this risk can be managed. However, evidence indicates that testing for radon and subsequent home remediation rates are generally low in many countries. The present perspective outlines some key insights from psychological science that might account for sub-optimal radon protection. Psychological aspects of how the health risks posed by radon are perceived and managed are outlined. There is need to consider radon risk perception in terms of the (a) cognitive and emotional responses to radon and (b) social context in which the radon threat occurs. In addition, the nature of the threat itself is integral to the failure for people to act in response to a radon threat. Finally, the challenges arising from defensive processing of radon threat information are outlined.
A Computational Analysis of Linear Price Iterative Combinatorial Auction Formats

Iterative combinatorial auctions (ICAs) are IT-based economic mechanisms where bidders submit bundle bids in a sequence and an auctioneer computes allocations and ask prices in each auction round. The literature in this field provides equilibrium analysis for ICAs with nonlinear personalized prices under strong assumptions on bidders' strategies. Linear pricing has performed very well in the lab and in the field. In this paper, we compare three selected linear price ICA formats based on allocative efficiency and revenue distribution using different bidding strategies and bidder valuations. The goal of this research is to benchmark different ICA formats and design and analyze new auction rules for auctions with pseudodual linear prices. The multi-item and discrete nature of linear price iterative combinatorial auctions and the complex price calculation schemes defy much of the traditional game theoretical analysis in this field. Computational methods can be of great help in exploring potential auction designs and analyzing the virtues of various design options. In our simulations, we found that ICA designs with linear prices performed very well for different valuation models even in cases of high synergies among the valuations. There were, however, significant differences in efficiency and in the revenue distributions of the three ICA formats. Heuristic bidding strategies using only a few of the best bundles also led to high levels of efficiency. We have also identified a number of auction rules for ask price calculation and auction termination that have shown to perform very well in the simulations.
Hadronic B decays at BABAR

The BABAR collaboration has performed a number of measurements on hadronic B decays to charmonium and open charm mesons. Preliminary results based on a sample of nearly 23 million BB pairs, collected between October 1999 and October 2000, are reviewed. These include measurements of exclusive branching fractions and ratios of branching fractions, as well as angular distributions.
Three‐dimensional Born inversion with an arbitrary reference

Recent work of G. Beylkin helped set the stage for very general seismic inversions. We have combined these broad concepts for inversion with classical high‐frequency asymptotics and perturbation methods to bring them closer to practically implementable algorithms. Applications include inversion schemes for both stacked and unstacked seismic data. Basic assumptions are that the data have relative true amplitude, and that a reasonably accurate background velocity c(x, y, z) is available. The perturbation from this background is then sought. Since high‐frequency approximations are used throughout, the resulting algorithms essentially locate discontinuities in velocity. An expression for a full 3-D velocity inversion can be derived for a general data surface. In this degree of generality the formula does not represent a computationally feasible algorithm, primarily because a key Jacobian determinant is not expressed in practical terms. In several important cases, however, this shortcoming can be overcome and .
Operating systems and network protocols for wireless sensor networks

Sensor network protocols exist to satisfy the communication needs of diverse applications, including data collection, event detection, target tracking and control. Network protocols to enable these services are constrained by the extreme resource scarcity of sensor nodes—including energy, computing, communications and storage—which must be carefully managed and multiplexed by the operating system. These challenges have led to new protocols and operating systems that are efficient in their energy consumption, careful in their computational needs and miserly in their memory footprints, all while discovering neighbours, forming networks, delivering data and correcting failures.
An Emerging Tick-Borne Disease of Humans Is Caused by a Subset of Strains with Conserved Genome Structure

The prevalence of tick-borne diseases is increasing worldwide. One such emerging disease is human anaplasmosis. The causative organism, Anaplasma phagocytophilum, is known to infect multiple animal species and cause human fatalities in the U.S., Europe and Asia. Although long known to infect ruminants, it is unclear why there are increasing numbers of human infections. We analyzed the genome sequences of strains infecting humans, animals and ticks from diverse geographic locations. Despite extensive variability amongst these strains, those infecting humans had conserved genome structure including the pfam01617 superfamily that encodes the major, neutralization-sensitive, surface antigen. These data provide potential targets to identify human-infective strains and have significance for understanding the selective pressures that lead to emergence of disease in new species.
elding methods for joining thermoplastic polymers for the hermetic nclosure of medical devices

New high performance polymers have been developed that challenge traditional encapsulation materials for permanent active medical implants. The gold standard for hermetic encapsulation for implants is a titanium enclosure which is sealed using laser welding. Polymers may be an alternative encapsulation material. Although many polymers are biocompatible, and permeability of polymers may be reduced
A novel Fuzzy approach to speech recognition

This paper presents a novel approach to speech recognition using fuzzy modeling. The task begins with conversion of speech spectrogram into a linguistic description based on arbitrary colors and lengths. While phonemes are also described using these fuzzy measures, and recognition is done by normal fuzzy reasoning, a genetic algorithm optimizes phoneme definitions so that to classify samples into correct phonemes. The method is tested over a standard speech data base and the results are presented.
Cornulitids from the Upper Devonian of the Central Devonian Field, Russia

ABSTRACT Two species of cornulitids, Cornulites devonicus and C. sokiranae sp. nov., commonly occur on Upper Devonian (Upper Frasnian and Lower Famennian) brachiopod shells in the area of the Central Devonian Field in Russia. Previously, C. devonicus was assigned to the serpulid species Serpula devonica. However, the present study shows that it is not a serpulid polychaete but a cornulitid with a microlamellar shell microstructure. Both Upper Devonian cornulitids are devoid of pseudopunctae and vesicular wall structures; the absence of the former in these species presumably does not constitute a useful adaptation. The greatest number of cornulitid species occurs in the Lower Devonian; their numbers seem to be lower in the Middle and Upper Devonian than in the Ordovician and Silurian. There are very few similarities between cornulitid faunas found in different palaeogeographical areas in the Devonian.
Novel brain‐penetrating oximes for reactivation of cholinesterase inhibited by sarin and VX surrogates

Current oxime reactivators for organophosphate‐inhibited cholinesterase (ChE) do not effectively cross the blood–brain barrier and therefore cannot restore brain ChE activity in vivo. Our laboratories have studied highly relevant sarin and VX surrogates, which differ from their respective nerve agents only in the leaving group and thereby leave ChE phosphylated with the same chemical moiety as sarin and VX. Our laboratories have developed novel substituted phenoxyalkyl pyridinium oximes that lead to reduced ChE inhibition in the brains of rats challenged with a high sublethal dosage of the sarin surrogate, whereas 2‐PAM did not, using a paradigm designed to demonstrate brain penetration. In addition, treatment of rats with these novel oximes is associated with attenuation of seizure‐like behavior compared to rats treated with 2‐PAM, providing additional evidence that the oximes penetrate the blood–brain barrier. Further, some of the oximes provided 24‐h survival superior to 2‐PAM, and shortened the duration of seizure‐like behavior when rats were challenged with lethal dosages of the sarin and VX surrogates, providing additional support for the conclusion that these oximes penetrate the brain.
Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated antiviral signal transduction

The caspase recruitment domain (CARD) of intracellular adaptors and sensors plays a critical role in the assembly of signaling complexes involved in innate host defense against pathogens and in the regulation of inflammatory responses. The cytosolic receptor retinoic acid-inducible gene-I (RIG-I) recognizes viral RNA in a 5′-triphosphate-dependent manner and initiates an antiviral signaling cascade. Upon viral infection, the N-terminal CARDs of RIG-I undergo the K63-linked ubiquitination induced by tripartite motif protein 25 (TRIM25), critical for the interaction of RIG-I with its downstream signaling partner MAVS/VISA/IPS-1/Cardif. Here, we demonstrate the distinct roles of RIG-I first and second CARD in TRIM25-mediated RIG-I ubiquitination: TRIM25 binds the RIG-I first CARD and subsequently ubiquitinates its second CARD. The T55I mutation in RIG-I first CARD abolishes TRIM25 interaction, whereas the K172R mutation in the second CARD eliminates polyubiquitin attachment. The necessity of the intact tandem CARD for RIG-I function is further evidenced by a RIG-I splice variant (SV) whose expression is robustly up-regulated upon viral infection. The RIG-I SV carries a short deletion (amino acids 36–80) within the first CARD and thereby loses TRIM25 binding, CARD ubiquitination, and downstream signaling ability. Furthermore, because of its robust inhibition of virus-induced RIG-I multimerization and RIG-I-MAVS signaling complex formation, this SV effectively suppresses the RIG-I-mediated IFN-β production. This study not only elucidates the vital role of the intact tandem CARD for TRIM25-mediated RIG-I activation but also identifies the RIG-I SV as an off-switch regulator of its own signaling pathway.