Miracle-dz/UniFAR-FTUs huggingface dataset:
BET proteins promote efficient murine leukemia virus integration at transcription start sites

The selection of chromosomal targets for retroviral integration varies markedly, tracking with the genus of the retrovirus, suggestive of targeting by binding to cellular factors. γ-Retroviral murine leukemia virus (MLV) DNA integration into the host genome is favored at transcription start sites, but the underlying mechanism for this preference is unknown. Here, we have identified bromodomain and extraterminal domain (BET) proteins (Brd2, -3, -4) as cellular-binding partners of MLV integrase. We show that purified recombinant Brd4(1-720) binds with high affinity to MLV integrase and stimulates correct concerted integration in vitro. JQ-1, a small molecule that selectively inhibits interactions of BET proteins with modified histone sites impaired MLV but not HIV-1 integration in infected cells. Comparison of the distribution of BET protein-binding sites analyzed using ChIP-Seq data and MLV-integration sites revealed significant positive correlations. Antagonism of BET proteins, via JQ-1 treatment or RNA interference, reduced MLV-integration frequencies at transcription start sites. These findings elucidate the importance of BET proteins for MLV integration efficiency and targeting and provide a route to developing safer MLV-based vectors for human gene therapy.
Validation of emulated omnidirectional antenna output using directive antenna data

In this paper, we present validation of a method for constructing a virtual omnidirectional antenna in the azimuth plane. The virtual omnidirectional antenna utilizes a combination of data from directive horn antennas. The aim is to utilize the high gain of the horn antenna to improve the dynamic range of channel sounding measurements conducted in the centimeter and millimeter wave bands. The resulting complex impulse response from the virtual omnidirectional antenna is used to find the power-delay-profile (PDP). This is then compared to measurements conducted at the same time using a real omnidirectional antenna. The validation shows that the synthesized omnidirectional is capable of predicting main components and the slope of the PDF. Further, it is shown that by choosing angular sampling steps corresponding to the half power beam width (HPBW) of the used antenna similar power levels can be achieved.
Specifying a positive threshold function via extremal points

An extremal point of a positive threshold Boolean function $f$ is either a maximal zero or a minimal one. It is known that if $f$ depends on all its variables, then the set of its extremal points completely specifies $f$ within the universe of threshold functions. However, in some cases, $f$ can be specified by a smaller set. The minimum number of points in such a set is the specification number of $f$. It was shown in [S. -T. Hu. Threshold Logic, 1965] that the specification number of a threshold function of $n$ variables is at least $n+1$. In [M. Anthony, G. Brightwell, and J. Shawe-Taylor. On specifying Boolean functions by labelled examples. Discrete Applied Mathematics, 1995] it was proved that this bound is attained for nested functions and conjectured that for all other threshold functions the specification number is strictly greater than $n+1$. In the present paper, we resolve this conjecture negatively by exhibiting threshold Boolean functions of $n$ variables, which are non-nested and for which the specification number is $n+1$. On the other hand, we show that the set of extremal points satisfies the statement of the conjecture, i.e., a positive threshold Boolean function depending on all its $n$ variables has $n+1$ extremal points if and only if it is nested. To prove this, we reveal an underlying structure of the set of extremal points.
CtrlCloud: Performance-Aware Adaptive Control for Shared Resources in Clouds

Consolidating applications of conflicting service level objectives (SLOs) to share virtualized resources in cloud datacenters requires efficient resource management to ensure overall high Quality-of-Service (QoS). Applications of different performance targets often exhibit different resource demands. Thus, it is not trivial to translate individual application SLOs to corresponding resource shares in a shared virtualized environment to meet performance targets. In this paper, we present CtrlCloud, a performance-aware resource controlling system, that adaptively allocates resources, with a resource-share controller and an allocation optimization model. The controller automatically adapts resource demands based on performance deviations, while the optimization model resolves conflicts in resource demands from multiple co-located applications based on their ongoing performance achieved. We implement a proof-of-concept prototype of CtrlCloud in Python on top of Xen hypervisor. Our experimental results indicate that CtrlCloud can optimize allocations of CPU resources across multiple applications to maintain the 95th percentile latency within predefined SLO targets. CtrlCloud also provides QoS differentiation and yet fulfilling of CPU share demands from applications is maximized given resource availability. We further compare CtrlCloud against two other resource allocation methods commonly used in current clouds. CtrlCloud improves resource utilization by allocating resource shares optimal to 'actual needs' as it employs share-performance online modeling.
The effect on human sex ratio at birth by assisted reproductive technology (ART) procedures – an assessment of babies born following single embryo transfers, Australia and New Zealand, 2002–2006

Please cite this paper as: Dean J, Chapman M, Sullivan E. The effect on human sex ratio at birth by assisted reproductive technology (ART) procedures – an assessment of babies born following single embryo transfers, Australia and New Zealand, 2002–2006. BJOG 2010;117:1628–1634.
Análisis observacional de las relaciones interlíneas de la Selección Española de Fútbol, mediante coordenadas polares.

El objetivo del presente estudio fue determinar el grado de relacion (activacion e inhibicion) inter-lineas y respecto a su rival que presenta la Seleccion Espanola de futbol cuando se encuentra en posesion del balon. Para ello se analizaron los partidos de Espana durante la UEFA Euro 2012 (6861 multieventos han sido codificados). Se ha utilizado un instrumento de observacion ad hoc, formado por 8 criterios y 96 categorias, que permitieron registrar cuatro lineas o niveles de organizacion: POR (portero), DEF (defensas), CEN (centrocampistas) y DEL (delanteros), asi como tambien su relacion con el rival (JR). Los datos fueron sometidos a un analisis de coordenadas polares, utilizando cada linea como conducta focal. Los resultados muestran la relacion y cohesion inter-lineas que presenta el equipo, asi como la activacion de jugadores rivales. Esto nos permite conocer el componente tactico de la seleccion espanola y su relacion con los jugadores rivales. Tambien se ha destacado la eficacia de la metodologia observacional como un filtro metodologico optimo para el estudio del comportamiento espontaneo de los jugadores, incluyendo poderosos tecnicas como el analisis de coordenadas polares. Los estudios futuros pasan por profundizar en la realidad del jugador en particular, para a continuacion construir la compleja estructura que conforman las interrelaciones entre los diferentes integrantes de un equipo. Sin duda esto redundara en un mejor desempeno de la realidad del futbol en los campos de juego.
Extragastrointestinal stromal tumors (EGIST): a series of case reports.

BACKGROUND/AIM Gastrointestinal stromal tumors (EGIST) are mesenchymal tumors which may originate in sites outside the gastrointestinal tract with clinico-pathological and molecular profiles similar to GISTs. Here is a series of case reports from The National Cancer Institute (INCA) about this rare type of tumor. METHODOLOGY We retrospectively analyzed 142 patients with a diagnosis of GIST who were treated at INCA between 1997 and 2009, among which 9 were confirmed as having EGIST. RESULTS We identified 9 patients with a diagnosis of EGIST, 7 of which (77.8%) were female patients with an average age of 56.8 (36-81) years. All patients were symptomatic, with abdominal pain present in 55% of cases. The tumors were located in the pancreas (n=2), in the retroperitoneum (n=3), and in the mesocolon, in the mesentery of the small intestine, in the spleen and in the pelvis (all n=1), respectively. The average tumor size was 18(8.5-27)cm. Immunohistochemistry revealed CD 117 positive in 100% of cases and CD34 positive in 62.5%. Five patients were treated surgically, three of which were submitted to R0 resection. Among those patients, all recurred after 31, 23 and 17 months respectively, and the most frequent sites were the liver and the peritoneum. Out of these three recurrences, two were "rescued" surgically (66%). Five patients were given imatinib (three patients considered unresectable, one submitted to R2 resection and another patient with recurrent disease not amenable to surgery) two patients did not receive any treatment due to compromised clinical conditions. The average overall survival was 26.4 (04-114) months. CONCLUSION The occurrence of EGIST is extremely rare and little is known about their actual origin. They manifest through bulky masses, which compromise the prognosis. Aggressive surgical intervention is the most effective treatment associated with the use of imatinib, and a strict followup is necessary due to high recurrence rates.
Algorithmes Heuristiques et Techniques d'Apprentissage : Applications au Problème de Coloration de Graphe. (Heuristic Algorithms And Learning Techniques : Applications to the Graph Coloring Problem)

Au cours des trois dernieres decennies, les algorithmes heuristiques ont permis de realiser des progres remarquables dans la resolution des problemes diciles d'optimisation combinatoire. Cependant, la conception de ces algorithmes releve encore plusieurs challenges importants { en particulier, il semble qu'il est toujours dicile d'integrer dans une heuristique une vue d'ensemble sur l'evolution de la recherche ou sur sa trajectoire. Prenant comme cadre experimental le probleme bien connu de la coloration de graphe, nous presentons de nouvelles strategies qui font appel a certains mecanismes d'apprentissage pour rendre le processus de recherche plus \auto-conscient". Nous introduisons un algorithme qui est capable d'enregistrer sa trajectoire et d'interpreter sa propre evolution. Une analyse de l'espace de recherche a montre que les meilleures congurations visitees sont relativement proches les unes des autres, regroupees dans des spheres de rayon xe. Avec ce type d'informations apprises, nous avons concu : (i) des algorithmes de diversication qui \prennent garde" a ne pas visiter la m^eme sphere a plusieurs reprises, (ii) des algorithmes d'intensication qui se focalisent sur l'exploration d'un perimetre limite en utilisant un parcours en largeur des spheres de ce perimetre, et (iii) des approches evolutionnistes pour gerer la diversite de sorte que les individus soient a la fois de bonne qualite eu egard a la fonction objectif et susamment distants les uns des autres. En fait, nous presentons une gamme de techniques (e.g. nouvelles fonctions d'evaluation) qui peuvent rendre la recherche heuristique \bien informee".
No-inference image sharpness assessment based on wavelet transform and image saliency map

This paper combines the wavelet transform and image saliency map to construct an image sharpness index without reference image. The main idea of the proposed index is that the saliency areas in an image always get more attentions than non-saliency regions when human perceives the sharpness of the image. Specifically, an input image is firstly decomposed into three directional sub-bands by a separable discrete wavelet transform. Next, the saliency map of the inputted image is constructed by Itti's salience algorithm. Then, the log-energies of wavelet coefficients belonging to the saliency area of the input image are computed. The final scalar index corresponding to the image's overall sharpness is computed via a weighted average of these log-energies. The experiments show that, despite its simplicity, the proposed sharpness index is competitive with the current best-performance techniques for no-reference image sharpness estimation.
Local anesthetic lidocaine delivery system: chitosan and hyaluronic acid-modified layer-by-layer lipid nanoparticles

Abstract Context: Transdermal local anesthesia is one of the most applied strategies to avoid systemic adverse effects; there is an appealing need for a prolonged local anesthetic that would provide better bioavailability and longer pain relief with a single administration. Objective: Layer-by-layer (LBL) technique was used in this study to explore a nanosized drug delivery system for local anesthetic therapy. Materials and methods: LBL-coated lidocaine-loaded nanostructured lipid nanoparticles (LBL-LA/NLCs) were prepared and characterized in terms of particle size (PS), zeta potential, drug encapsulation efficiency (EE), in vitro skin permeation and in vivo local anesthetic studies. Results: Evaluation of the in vitro skin permeation and in vivo anesthesia effect illustrated that LBL-LA/NLCs can enhance and prolong the anesthetic effect of LA. Discussion and conclusion: LBL-LA/NLCs could function as a promising drug delivery strategy for overcoming the barrier function of the skin and could deliver anesthetic through the skin with sustained release behavior for local anesthetic therapy.
Myocardial Protection in Minimally Invasive Mitral Valve Surgery: Comparison of the Cold-Blood Cardioplegia of the Bretschneider Solution and the Warm-Blood Cardioplegia of the Calafiore Protocol

Objective: Minimal invasive mitral valve surgery using right thoracotomy is becoming a safe alternative and has an increasing impact in the clinical routine. The best strategy for myocardial protection for these patients is under discussion. Warm-blood cardioplegia, according to the protocol of Calafiore (group C), is well-established in coronary surgery throughout Europe, whereas the cold-crystalloid cardioplegia by Bretschneider (Custodiol®, group B) is in worldwide use in both heart surgery and organ transplantation. Methods: All 107 patients with proposed mitral valve surgical repair through a right lateral mini-thoracotomy between July 2008 and September 2009 were evaluated and randomly selected for one of the two myocardial protection strategies described above. The quality of the myocardial protection was detected using the specific ischaemia markers cTNI and CK-MB on days zero, one and two following surgery. The study population represents 80% of all patients with isolated mitral surgery from the department. Demographic, as well as operative, data did not show any differences between the groups, and the hospitalization period was 13 days for both groups. Results: The totally clinical mortality rate was 5% (2 patients in group B vs. 3 patients in group C, p=0.673). cTNI >10 μg/l levels 48 hours after the surgical procedure (p=0.055) were significantly higher in group C compared to group B, calculated by ANOVA for repeated measurement using SPSS® 17.0 software. However, the need for defibrillation was higher after Bretschneider`s cardioplegia (45% vs 10%, p
The breastfeeding self-efficacy scale: psychometric assessment of the short form.

OBJECTIVE The purpose of this study was to reduce the number of items on the original Breastfeeding Self-Efficacy Scale (BSES) and psychometrically assess the revised BSES-Short Form (BSES-SF). DESIGN As part of a longitudinal study, participants completed mailed questionnaires at 1, 4, and 8 weeks postpartum. SETTING Health region in British Columbia. PARTICIPANTS A population-based sample of 491 breastfeeding mothers. MAIN OUTCOME MEASURES BSES, Edinburgh Postnatal Depression Scale, Rosenberg Self-Esteem Scale, and Perceived Stress Scale. RESULTS Internal consistency statistics with the original BSES suggested item redundancy. As such, 18 items were deleted, using explicit reduction criteria. Based on the encouraging reliability analysis of the new 14-item BSES-SF, construct validity was assessed using principal components factor analysis, comparison of contrasted groups, and correlations with measures of similar constructs. Support for predictive validity was demonstrated through significant mean differences between breastfeeding and bottle feeding mothers at 4 (p < .001) and 8 (p < .001) weeks postpartum. Demographic response patterns suggested the BSES-SF is a unique tool to identify mothers at risk of prematurely discontinuing breastfeeding. CONCLUSIONS These psychometric results indicate the BSES-SF is an excellent measure of breastfeeding self-efficacy and considered ready for clinical use to (a) identify breastfeeding mothers at high risk, (b) assess breastfeeding behaviors and cognitions to individualize confidence-building strategies, and (c) evaluate the effectiveness of various interventions and guide program development.
Signal integrity issues due to ESD events in high-speed CMOS comparator

This paper is mainly focused on analyzing the behavior of the output data of a CMOS latched comparator subjected to the Human Body Model (HBM) Electrostatic Discharge (ESD) test event. The importance of the comparator circuit in the applications of data transmission is illustrated. Several tests using the Cadence IC 5.3 software were carried out in order to investigate the accuracy of the output data signal. The tests were computed for the high and low level of the clock. The malfunction of the comparator structure due to the effects of the electrostatic field is investigated. The functioning of the circuit was improved by adding decoupling capacitors with protective properties.
Demonstration of retrotransposition of the Tf1 element in fission yeast.

Tf1, a retrotransposon from fission yeast, has LTRs and coding sequences resembling the protease, reverse transcriptase and integrase domains of retroviral pol genes. A unique aspect of Tf1 is that it contains a single open reading frame whereas other retroviruses and retrotransposons usually possess two or more open reading frames. To determine whether Tf1 can transpose, we overproduced Tf1 transcripts encoded by a plasmid copy of the element marked with a neo gene. Approximately 0.1–4.0% of the cell population acquired chromosomally inherited resistance to G418. DNA blot analysis demonstrated that such strains had acquired both Tf1 and neo specific sequences within a restriction fragment of the same size; the size of this restriction fragment varied between different isolates. Structural analysis of the cloned DNA flanking the Tf1‐neo element of two transposition candidates with the same regions in the parent strain showed that the ability to grow on G418 was due to transposition of Tf1‐neo and not other types of recombination events.
Inverse Kinematics of Functionally-Redundant Serial Manipulators: A Comparison Study

Kinematic redundancy of a pair of manipulator-task can be classified into intrinsic and functional redundancies. This paper compares two different approaches to solve the inverse kinematics of functionally-redundant serial manipulators. First, the augmented approach add a virtual joint to the manipulator in order to render the Jacobian matrice underdetermined and project a secondary task onto the null space of theaugmented Jacobian, while the twist-decomposition approach rather decompose the instantenous twist into two orthogonal subspaces of the tool frame. The numerical simulatution of an end-milling operation shown that the twist decomposition is more effective in termes of computation time and numerical robustness then the augmented approach.
An experimental study of particle effects on drop formation

The formation of drops of particulate suspensions composed of spherical, neutrally buoyant, noncolloidal particles in a viscous liquid is examined experimentally. The suspensions are investigated over a range of particle volume fractions, φ=nπdp3/6 where n is the particle number density and dp is the particle diameter (dp=212–250 μm in most of the experiments), and for flow through three tubes of outer diameters d=0.16, 0.32 and 0.64 cm; the corresponding inner diameters are 0.10, 0.22, and 0.53 cm. Drop formation in the dripping mode and the transition from dripping to jetting are investigated. In the dripping mode, the behavior of low-φ suspensions (φ⩽0.10) is markedly different from that of higher-φ suspensions (0.15⩽φ⩽0.40), with a transition in the qualitative behavior over a relatively narrow range of concentrations. Pinch-off structures for low-φ suspensions are similar to that of the pure liquid, consisting of a long slender liquid thread connecting a hemispherical cap of liquid at the orifice to .
Forensic identification using multiple lot numbers of an implanted device

We report a case in which identification of a deceased individual was established using multiple lot numbers printed on a body implantable device. Autopsy of an unknown woman revealed an intramedullary nail inserted within her right femur. The device manufacturer was identified from the configuration of the intramedullary nail, and the “use history” was traced from lot numbers printed on the device’s multiple parts. The deceased individual was thus identified as a woman who had attempted suicide by jumping from a height about a year previously and had been transported to a hospital and undergone surgery that included implantation of the intramedullary nail. The main factor contributing to the rapid identification was the manufacturer’s and distributor’s record of the use history (traceability) of the product, because of their accountability for purposes of quality control. A second contributing factor was multiple lot numbers, resulting in extremely low probability of the same combination of lot numbers being present in multiple individuals. This case confirmed the utility of multiple lot numbers of body implantable devices in forensic identification.
Kinetics and risk of de novo hepatitis B infection in HBsAg-negative patients undergoing cytotoxic chemotherapy.

BACKGROUND & AIMS De novo hepatitis B virus (HBV)-related hepatitis after chemotherapy results in high morbidity and mortality. We evaluate the clinical course of de novo HBV-related hepatitis after chemotherapy. METHODS Two hundred forty-four consecutive hepatitis B surface antigen (HBsAg)-negative lymphoma patients treated with chemotherapy were followed up for a median of 12.4 (range, 0.1-65.0) months. Serially collected serum samples were analyzed for hepatitis, serum HBV DNA, and HBsAg seroreversion. RESULTS Eight of the 244 patients (3.3%) developed de novo HBV-related hepatitis. A 100-fold increase in serum HBV DNA preceded de novo HBV-related hepatitis by a median of 18.5 (range, 12-28) weeks. All 8 patients had normal serum alanine aminotransaminase level when the 100-fold increase in serum HBV DNA occurred. Patients with de novo HBV-related hepatitis were more likely to have occult HBV infection before chemotherapy. Direct sequencing results showed that these 8 patients had de novo HBV-related hepatitis from reactivation of occult HBV infection. Three of the 8 patients with de novo HBV-related hepatitis compared with 6 of the 236 patients without de novo HBV-related hepatitis developed fulminant hepatic failure (37.5% vs 2.5%, respectively, P < .001). On multivariate Cox analysis, de novo HBV-related hepatitis was independently associated with a higher risk of fulminant hepatic failure (relative risk, 29.854; 95% confidence interval: 4.844-183.980; P < .001). CONCLUSIONS Close surveillance for a 100-fold increase in HBV DNA is recommended for HBsAg-negative patients treated with chemotherapy so that early commencement of antiviral therapy can be initiated before the occurrence of de novo HBV-related hepatitis.