Miracle-dz/UniFAR-FTUs huggingface dataset:
De novo-generated small palindromes are characteristic of amplicon boundary junction of double minutes

Double minutes (DMs) are hallmarks of gene amplification. However, their molecular structure and the mechanisms of formation are largely unknown. To elucidate the structure and underlying molecular mechanism of DMs, we obtained and cloned DMs using microdissection; and degenerated oligonucleotide primed polymerase chain reaction (DOP‐PCR) from the ovarian cancer cell line UACC‐1598. Two large amplicons, the 284 kb AmpMYCN, originating from locus 2p24.3 and the 391 kb AmpEIF5A2, from locus 3q26.2, were found co‐amplified on the same DMs. The two amplicons are joined through a complex 7 kb junction DNA sequence. Analysis of the junction has revealed three de novo created small palindromes surrounding the six breakpoints. Consistent with these observations, we further found that 70% of the 57 reported DM junction sequences have de novo creation of small palindromic sequences surrounding the breakpoints. Together, our findings indicate that de novo‐generated small palindromic sequences are characteristic of amplicon boundary junctions on DMs. It is possible that the de novo‐generated small palindromic sequences, which may be generated through non‐homologous end joining in concert with a novel DNA repair machinery, play a common role in amplicon rejoining and gene amplification.
Expression-Invariant Age Estimation Using Structured Learning

In this paper, we investigate and exploit the influence of facial expressions on automatic age estimation. Different from existing approaches, our method jointly learns the age and expression by introducing a new graphical model with a latent layer between the age/expression labels and the features. This layer aims to learn the relationship between the age and expression and captures the face changes which induce the aging and expression appearance, and thus obtaining expression-invariant age estimation. Conducted on three age-expression datasets (FACES [1] , Lifespan [2] and NEMO [3] ), our experiments illustrate the improvement in performance when the age is jointly learnt with expression in comparison to expression-independent age estimation. The age estimation error is reduced by 14.43, 37.75 and 9.30 percent for the FACES, Lifespan and NEMO datasets respectively. The results obtained by our graphical model, without prior-knowledge of the expressions of the tested faces, are better than the best reported ones for all datasets. The flexibility of the proposed model to include more cues is explored by incorporating gender together with age and expression. The results show performance improvements for all cues.
Parametric Approaches for Eigenstructure Assignment in High-order Descriptor Linear Systems

This paper considers eigenstructure assignment in high-order descriptor linear systems via proportional plus derivative state feedback. It is shown that the problem is closely related with a type of so-called high-order Sylvester matrix equations. Through establishing two general parametric solutions to this type of matrix equations, two complete parametric methods for the proposed eigenstructure assignment problem are presented. Both methods give simple complete parametric expressions for the feedback gains and the closed-loop eigenvector matrices. The first one mainly depends on a series of singular value decompositions, and is thus numerically simple and reliable; the second one utilizes the right factorization of the system, and allows the closed-loop eigenvalues to be set undetermined and sought via certain optimization procedures. An example shows the effect of the proposed approaches
Microdosimetry of proton and carbon ions.

PURPOSE To investigate microdosimetry properties of 160 MeV/u protons and 290 MeV/u(12)C ion beams in small volumes of diameters 10-100 nm. METHODS Energy distributions of primary particles and nuclear fragments in the beams were calculated from simulations with the general purpose code SHIELD-HIT, while energy depositions by monoenergetic ions in nanometer volumes were obtained from the event-by-event Monte Carlo track structure ion code PITS99 coupled with the electron track structure code KURBUC. RESULTS The results are presented for frequencies of energy depositions in cylindrical targets of diameters 10-100 nm, dose distributions yd(y) in lineal energy y, and dose-mean lineal energies yD. For monoenergetic ions, the yD was found to increase with an increasing target size for high-linear energy transfer (LET) ions, but decrease with an increasing target size for low-LET ions. Compared to the depth dose profile of the ion beams, the maximum of the yD depth profile for the 160 MeV proton beam was located at ∼ 0.5 cm behind the Bragg peak maximum, while the yD peak of the 290 MeV/u (12)C beam coincided well with the peak of the absorbed dose profile. Differences between the yD and dose-averaged linear energy transfer (LETD) were large in the proton beam for both target volumes studied, and in the (12)C beam for the 10 nm diameter cylindrical volumes. The yD determined for 100 nm diameter cylindrical volumes in the (12)C beam was approximately equal to the LETD. The contributions from secondary particles to the yD of the beams are presented, including the contributions from secondary protons in the proton beam and from fragments with atomic number Z = 1-6 in the (12)C beam. CONCLUSIONS The present investigation provides an insight into differences in energy depositions in subcellular-size volumes when irradiated by proton and carbon ion beams. The results are useful for characterizing ion beams of practical importance for biophysical modeling of radiation-induced DNA damage response and repair in the depth profiles of protons and carbon ions used in radiotherapy.
Mouse nerve growth factor gene: structure and expression

The organization and biologically significant sequences of the entire mouse nerve growth factor (NGF) gene have been determined. The gene spans 45 kilobases and contains several small 5' exons. Transcription of the gene results in four different mRNA species, which can be accounted for by alternative splicing and independent initiation from two promoters. These transcripts encode proteins which have divergent N termini and the NGF moiety at their C termini. The levels of the various NGF transcripts have been determined in different tissues and throughout postnatal development. We have also examined the expression of these transcripts in the brain in response to specific early sensory deprivation. The results suggest that the expression of NGF mRNA during postnatal development is regulated independently of the formation of complex neural networks.
WEESA: Web engineering for semantic Web applications

The success of the Semantic Web crucially depends on the existence of Web pages that provide machine-understandable meta-data. This meta-data is typically added in the semantic annotation process which is currently not part of the Web engineering process. Web engineering, however, proposes methodologies to design, implement and maintain Web applications but lack the generation of meta-data. In this paper we introduce a technique to extend existing Web engineering methodologies to develop semantically annotated Web pages. The novelty of this approach is the definition of a mapping from XML Schema to ontologies, called WEESA, that can be used to automatically generate RDF meta-data from XML content documents. We further show how we integrated the WEESA mapping into an Apache Cocoon transformer to easily extend XML based Web applications to semantically annotated Web application.
Growth Factor–dependent Activation of αvβ3 Integrin in Normal Epithelial Cells: Implications for Tumor Invasion

Integrin activation is a multifaceted phenomenon leading to increased affinity and avidity for matrix ligands. To investigate whether cytokines produced during stromal infiltration of carcinoma cells activate nonfunctional epithelial integrins, a cellular system of human thyroid clones derived from normal glands (HTU-5) and papillary carcinomas (HTU-34) was employed. In HTU-5 cells, αvβ3 integrin was diffused all over the membrane, disconnected from the cytoskeleton, and unable to mediate adhesion. Conversely, in HTU-34 cells, αvβ3 was clustered at focal contacts (FCs) and mediated firm attachment and spreading. αvβ3 recruitment at FCs and ligand-binding activity, essentially identical to those of HTU-34, occurred in HTU-5 cells upon treatment with hepatocyte growth factor/scatter factor (HGF/SF). The HTU-34 clone secreted HGF/SF and its receptor was constitutively tyrosine phosphorylated suggesting an autocrine loop responsible for αvβ3 activated state. Antibody-mediated inhibition of HGF/SF function in HTU-34 cells disrupted αvβ3 enrichment at FCs and impaired adhesion. Accordingly, activation of αvβ3 in normal cells was produced by HTU-34 conditioned medium on the basis of its content of HGF/SF. These results provide the first example of a growth factor–driven integrin activation mechanism in normal epithelial cells and uncover the importance of cytokine-based autocrine loops for the physiological control of integrin activation.
The Escherichia coli O157:H7 cattle immunoproteome includes outer membrane protein A (OmpA), a modulator of adherence to bovine rectoanal junction squamous epithelial (RSE) cells

Building on previous studies, we defined the repertoire of proteins comprising the immunoproteome (IP) of Escherichia coli O157:H7 (O157) cultured in DMEM supplemented with norepinephrine (O157 IP), a β‐adrenergic hormone that regulates E. coli O157 gene expression in the gastrointestinal tract, using a variation of a novel proteomics‐based platform proteome mining tool for antigen discovery, called “proteomics‐based expression library screening” (PELS; Kudva et al., 2006). The E. coli O157 IP (O157‐IP) comprised 91 proteins, and included those identified previously using proteomics‐based expression library screening, and also proteins comprising DMEM and bovine rumen fluid proteomes. Outer membrane protein A (OmpA), a common component of the above proteomes, and reportedly a contributor to E. coli O157 adherence to cultured HEp‐2 epithelial cells, was interestingly found to be a modulator rather than a contributor to E. coli O157 adherence to bovine rectoanal junction squamous epithelial cells. Our results point to a role for yet to be identified members of the O157‐IP in E. coli O157 adherence to rectoanal junction squamous epithelial cells, and additionally implicate a possible role for the outer membrane protein A regulator, TdcA, in the expression of such adhesins. Our observations have implications for the development of efficacious vaccines for preventing E. coli O157 colonization of the bovine gastrointestinal tract.
Computer support for distributed asynchronous software design teams: experimental results on creativity and quality

Previous research has indicated that the creative task of deciding upon the initial specifications for a software system can benefit from a structured process to guide group interaction in face-to-face meetings, and can benefit from computer support. This 2/spl times/2 experiment is the first to look at the joint effects of a distributed asynchronous computer conferencing mode of communication (CC, as compared to face to face), and a structured process on software design outcomes. Subjects were teams of graduate students in computer science and business, who designed an automated post office as a course assignment. Though the quality of solution produced by the CC groups was judged to be higher, it was not significantly so. However, the CC groups were considerably more creative. There were no main effects for the structured/unstructured factor, nor any significant interactions. <<ETX>>
A guide to knowledge translation theory

&NA; Despite calls over several decades for theory development, there remains no overarching knowledge‐translation theory. However, a range of models and theoretical perspectives focused on narrower and related areas have been available for some time. We provide an overview of selected perspectives that we believe are particularly useful for developing testable and useful knowledge‐translation interventions. In addition, we discuss adjuvant theories necessary to complement these perspectives. We draw from organizational innovation, health, and social sciences literature to illustrate the similarities and differences of various theoretical perspectives related to the knowledge‐translation field. A variety of theoretical perspectives useful to knowledge translation exist. They are often spread across disciplinary boundaries, making them difficult to locate and use. Poor definitional clarity, discipline‐specific terminology, and implicit assumptions often hinder the use of complementary perspectives. Health care environments are complex, and assessing the setting prior to selecting a theory should be the first step in knowledge‐translation initiatives. Finding a fit between setting (context) and theory is important for knowledge‐translation initiatives to succeed. Because one theory will not fit all contexts, it is helpful to understand and use several different theories. Although there are often barriers associated with combining theories from different disciplines, such obstacles can be overcome, and to do so will increase the likelihood that knowledge‐translation initiatives will succeed.
Robust place recognition with stereo cameras

Place recognition is a challenging task in any SLAM system. Algorithms based on visual appearance are becoming popular to detect locations already visited, also known as loop closures, because cameras are easily available and provide rich scene detail. These algorithms typically result in pairs of images considered depicting the same location. To avoid mismatches, most of them rely on epipolar geometry to check spatial consistency. In this paper we present an alternative system that makes use of stereo vision and combines two complementary techniques: bag-of-words to detect loop closing candidate images, and conditional random fields to discard those which are not geometrically consistent. We evaluate this system in public indoor and outdoor datasets from the Rawseeds project, with hundred-metre long trajectories. Our system achieves more robust results than using spatial consistency based on epipolar geometry.
HUBBLE SPACE TELESCOPE FAR ULTRAVIOLET SPECTROSCOPY OF THE RECURRENT NOVA T PYXIDIS

With six recorded nova outbursts, the prototypical recurrent nova T Pyxidis (T Pyx) is the ideal cataclysmic variable system to assess the net change of the white dwarf mass within a nova cycle. Recent estimates of the mass ejected in the 2011 outburst ranged from a few ∼10−5 M☉ to 3.3 × 10−4 M☉, and assuming a mass accretion rate of 10−8–10−7 M☉ yr−1 for 44 yr, it has been concluded that the white dwarf in T Pyx is actually losing mass. Using NLTE disk modeling spectra to fit our recently obtained Hubble Space Telescope COS and STIS spectra, we find a mass accretion rate of up to two orders of magnitude larger than previously estimated. Our larger mass accretion rate is due mainly to the newly derived distance of T Pyx (4.8 kpc, larger than the previous 3.5 kpc estimate), our derived reddening of E(B − V) = 0.35 (based on combined IUE and GALEX spectra), and NLTE disk modeling (compared to blackbody and raw flux estimates in earlier works). We find that for most values of the reddening (0.25 ⩽ E(B − V) ⩽ 0.50) and white dwarf mass (0.70 M☉ ⩽ Mwd ⩽ 1.35 M☉) the accreted mass is larger than the ejected mass. Only for a low reddening (∼0.25 and smaller) combined with a large white dwarf mass (0.9 M☉ and larger) is the ejected mass larger than the accreted one. However, the best results are obtained for a larger value of reddening.
Assessment of hand bone loss in rheumatoid arthritis by high-resolution peripheral quantitative CT

Objectives A new high-resolution peripheral quantitative CT (HR-pQCT) system allows for in vivo assessment of bone microarchitecture and volumetric bone mineral density (vBMD) with an 82 µm isotropic resolution. With this device, the microarchitecture impairment was evaluated in patients with rheumatoid arthritis (RA) in comparison with healthy controls and measured the erosion volume at metacarpal heads (MCPs). Methods In this cross-sectional study, the reproducibility was first assessed by 3 HR-pQCT exams with repositioning in 14 patients with late RA and 14 healthy subjects. Then, HR-pQCT parameters were measured in a group of 93 patients with RA and 31 healthy controls. Two RA subgroups were distinguished: early RA (disease duration ≤2 years) (n=36) and late RA (n=57) and compared them to healthy controls. Results The precision of the HR-pQCT volumetric measurements as assessed with coefficient of variation ranged from 0.7% to 1.8% in patients with late RA and from 0.6% to 1.4% in healthy subjects at MCPs. Total and trabecular vBMD and trabecular thickness were significantly decreased in patients with RA compared to healthy subjects and were significantly correlated to disease activity. The erosion volume was highly correlated to a semiquantitative assessment using the Outcome Measures in Rheumatoid Arthritis Clinical Trials (OMERACT) scoring system applied to the HR-pQCT slices. Conclusions This study demonstrated the good reproducibility of the HR-pQCT volumetric measurements at MCPs and confirmed the involvement of trabecular compartment in periarticular osteopoenia. Thus, HR-pQCT appears interesting to simultaneously assess differences in bone volumetric density, microarchitecture and erosions.
A categorification of Morelli's theorem and homological mirror symmetry for toric varieties

An equivariant, ample line bundle on a toric variety XΣ defines a polytope in a vector space MR. We extend this simple correspondence to a functor from the derived category of coherent sheaves on XΣ to a category of constructible sheaves on MR. We prove this functor is an equivalence, thus categorifying Morelli’s description of the equivariant K-theory of a toric variety. We connect this construction to mirror symmetry by two processes: T-duality and microlocalization. T-duality relates coherent sheaves on XΣ to a Fukaya category on the cotangent bundle of the vector space, T ∗MR. Microlocalization relates this Fukaya category to constructible sheaves on MR. These results generalize work of the first author on projective spaces.
In Vivo Potential Anti-Inflammatory Activity of Melissa officinalis L. Essential Oil

Melissa officinalis L. (Lamiaceae) had been reported in traditional Moroccan medicine to exhibit calming, antispasmodic, and strengthening heart effects. Therefore, this study is aimed at determining the anti-inflammatory activities of M. officinalis L. leaves. The effect of the essential oil of the leaves of this plant was investigated for anti-inflammatory properties by using carrageenan and experimental trauma-induced hind paw edema in rats. The essential oil extracted from leaves by hydrodistillation was characterized by means of gas chromatography-mass spectrometry (GC-MS). M. officinalis contained Nerol (30.44%), Citral (27.03%), Isopulegol (22.02%), Caryophyllene (2.29%), Caryophyllene oxide (1.24%), and Citronella (1.06%). Anti-inflammatory properties of oral administration of essential oil at the doses of 200, 400 mg/kg p.o. , respectively, showed significant reduction and inhibition of edema with 61.76% and 70.58%, respectively, (P < 0.001) induced by carrageenan at 6 h when compared with control and standard drug (Indomethacin). On experimental trauma, M. officinalis L. essential oil showed pronounced reduction and inhibition of edema induced by carrageenan at 6 h at 200 and 400 mg/kg with 91.66% and 94.44%, respectively (P < 0.001). We can conclude that the essential oil of M. officinalis L. possesses potential anti-inflammatory activities, supporting the traditional application of this plant in treating various diseases associated with inflammation and pain.
An Arnoldi code for computing selected eigenvalues of sparse, real, unsymmetric matrices

Arnoldi methods can be more effective than subspace iterationmethods for computing the dominant eigenvalues of a large, sparse, real,unsymmetric matrix. A code, <? Pub Fmt bold>EB12<? Pub Fmt /bold>, for thesparse, unsymmetric eigenvalue problem based on a subspace iterationalgorithm, optionally combined with Chebychev acceleration, has recentlybeen described by Duff and Scott and is included in the HarwellSubroutine Library. In this article we consider variants of the methodof Arnoldi and discuss the design and development of a code to implementthese methods. The new code, which is called<? Pub Fmt bold>EB13<? Pub Fmt /bold>, offers the user the choice of abasic Arnoldi algorithm, an Arnoldi algorithm with Chebychevacceleration, and a Chebychev preconditioned Arnoldi algorithm. Eachmethod is available in blocked and unblocked form. The code may be usedto compute either the rightmost eigenvalues, the eigenvalues of largestabsolute value, or the eigenvalues of largest imaginary part. Theperformance of each option in the <? Pub Fmt bold>EB13<? Pub Fmt /bold>package is compared with that of subspace iteration on a range of testproblems, and on the basis of the results, advice is offered to the useron the appropriate choice of method. <abstrbyl>—<? Pub Fmt italic>Author's Abstract<? Pub Fmt /italic></abstrbyl>
Adalimumab for induction of clinical remission in moderately to severely active ulcerative colitis: results of a randomised controlled trial

Objective The aim of this study was to assess the efficacy and safety of adalimumab (ADA), a recombinant human monoclonal antibody against tumour necrosis factor α (TNF), for the induction of clinical remission in anti-TNF naïve patients with moderately to severely active ulcerative colitis. Methods This 8-week, multicentre, randomised, double-blind, placebo-controlled study (NCT00385736), conducted at 94 centres in North America and Europe, enrolled ambulatory adult patients with Mayo score of ≥6 points and endoscopic subscore of ≥2 points despite treatment with corticosteroids and/or immunosuppressants. Under the original study protocol, 186 patients were randomised (1:1) to subcutaneous treatment with ADA160/80 (160 mg at week 0, 80 mg at week 2, 40 mg at weeks 4 and 6) or placebo. Subsequently, at the request of European regulatory authorities, the protocol was amended to include a second induction group (ADA80/40: 80 mg at week 0, 40 mg at weeks 2, 4 and 6). The primary efficacy endpoint was clinical remission (Mayo score ≤2 with no individual subscore >1) at week 8, assessed in 390 patients randomised (1:1:1) to ADA160/80, ADA80/40, or placebo. Safety was assessed in all enrolled patients. Patients, study site personnel, investigators, and the sponsor were blinded to treatment assignment. Results At week 8, 18.5% of patients in the ADA160/80 group (p=0.031 vs placebo) and 10.0% in the ADA80/40 group (p=0.833 vs placebo) were in remission, compared with 9.2% in the placebo group. Serious adverse events occurred in 7.6%, 3.8% and 4.0% of patients in the placebo, ADA80/40, and ADA160/80 groups, respectively. There were two malignancies in the placebo group, none in the ADA groups. There were no cases of tuberculosis and no deaths. Conclusions ADA160/80 was safe and effective for induction of clinical remission in patients with moderately to severely active ulcerative colitis failing treatment with corticosteroids and/or immunosuppressants. Clinical trial NCT00385736.