Miracle-dz/UniFAR-FTUs huggingface dataset:
Chronic ethanol administration alters gamma-aminobutyric acidA receptor gene expression.

Chronic ethanol (alcohol) administration has been associated with alterations in the binding and function of the gamma-aminobutyric acid (GABAA) receptor. To evaluate the mechanism underlying these changes, we measured the steady state levels of the mRNAs for the alpha 1, alpha 2, alpha 3, alpha 5, and alpha 6 subunits of the GABAA receptor after chronic ethanol administration to rats and ethanol withdrawal for 24 hr. The results indicated that chronic ethanol administration resulted in a 61% decline in the level of the GABAA receptor alpha 1 subunit mRNAs [3.8 and 4.3 kilobases (kb)] in the cerebral cortex in rats. The levels of the alpha 2 subunit mRNAs (6 and 3 kb) and the alpha 5 subunit mRNA (2.8 kb) were also reduced, by 61, 45, and 51%, respectively, whereas there was no change in the level of the alpha 3 subunit mRNA (3 kb). Furthermore, the ethanol-induced decrease in receptor mRNA levels persisted for 24 hr, after withdrawal of ethanol and returned to control values at 36 hr of withdrawal. alpha 1 mRNA levels in cerebellum also decreased by 28%. The level of the alpha 6 subunit mRNA, which selectively encodes Ro15-4513 binding sites, was found to be increased by approximately 76% in the cerebellum. Also, the photoaffinity labeling studies using [3H]Ro15-4513 indicated an increase in the levels of various protein components of the GABAA receptor, in the cerebellum and the cerebral cortex (e.g., 50- and 55-kDa proteins in the cerebellum and 41- and 50-kDa proteins in the cortex), after chronic ethanol treatment. The increase in alpha 6 mRNA in the cerebellum might be related to the increased labeling of the 55-kDa (approximately 56-kDa) protein and partially responsible for the increased binding, as reported previously by us. Because the alpha 6 subunit is not expressed in cortex, involvement of an as yet unknown subunit in this region cannot be ruled out. The effect of chronic ethanol treatment appears to be specific for GABAA receptor subunit mRNAs, because the same treatment did not alter the levels of glyceraldehyde-3-dehydrogenase mRNA or poly(A)+ RNA. In summary, these data indicate that chronic ethanol treatment results in an alteration in the regulation of expression of GABAA receptor subunit-encoding mRNAs, which could be due to alterations in transcription or mRNA stability.
Pathfinding and target selection by developing geniculocortical axons

During development of the mammalian cerebral cortex, thalamic axons must grow into the telencephalon and select appropriate cortical targets. In order to begin to understand the cellular interactions that are important in cortical target selection by thalamic axons, we have examined the morphology of axons from the lateral geniculate nucleus (LGN) as they navigate their way to the primary visual cortex. The morphology of geniculocortical axons was revealed by placing the lipophilic tracer Dil into the LGN of paraformaldehyde-fixed brains from fetal and neonatal cats between embryonic day 26 (E26; gestation is 65 d) and postnatal day 7 (P7). This morphological approach has led to three major observations. (1) As LGN axons grow within the intermediate zone of the telencephalon toward future visual cortex (E30– 40), many give off distinct interstitial axon collaterals that penetrate the subplate of nonvisual cortical areas. These collaterals are transient and are not seen postnatally. (2) There is a prolonged period during which LGN axons are restricted to the visual subplate prior to their ingrowth into the cortical plate; the first LGN axons arrive within visual subplate by E36 but are not detected in layer 6 of visual cortex until about E50. (3) Within the visual subplate, LGN axons extend widespread terminal branches. This represents a marked change in their morphology from the simple growth cones present earlier as LGN axons navigate en route to visual cortex. The presence of interstitial collaterals suggests that there may be ongoing interactions between LGN axons and subplate neurons along the entire intracortical route traversed by the axons. From the extensive branching of LGN axons within the visual subplate during the waiting period, it appears that they are not simply “waiting. ” Rather, LGN axons may participate in dynamic cellular interactions within the subplate long before they contact their ultimate target neurons in layer 4. These observations confirm the existence of a prolonged waiting period in the development of thalamocortical connections and provide important morphological evidence in support of the previous suggestion that interactions between thalamic axons and subplate neurons are necessary for cortical target selection.
Effectiveness of VIA, Pap, and HPV DNA Testing in a Cervical Cancer Screening Program in a Peri-Urban Community in Andhra Pradesh, India

Background While many studies have compared the efficacy of Pap cytology, visual inspection with acetic acid (VIA) and human papillomavirus (HPV) DNA assays for the detection cervical intraepithelial neoplasia and cancer, few have evaluated the program effectiveness. Methods and Findings A population-based sample of 5603 women from Medchal Mandal in Andhra Pradesh, India were invited to participate in a study comparing Pap cytology, VIA, and HPV DNA screening for the detection of CIN3+. Participation in primary screening and all subsequent follow-up visits was rigorously tracked. A 20% random sample of all women screened, in addition to all women with a positive screening test result underwent colposcopy with directed biopsy for final diagnosis. Sensitivity, specificity, positive and negative predictive values were adjusted for verification bias. HPV testing had a higher sensitivity (100%) and specificity (90.6%) compared to Pap cytology (sensitivity = 78.2%; specificity = 86.0%) and VIA (sensitivity = 31.6%; specificity = 87.5%). Since 58% of the sample refused involvement and another 28% refused colposcopy or biopsy, we estimated that potentially 87.6% of the total underlying cases of CIN3 and cancer may have been missed due to program failures. Conclusions We conclude that despite our use of available resources, infrastructure, and guidelines for cervical cancer screening implementation in resource limited areas, community participation and non-compliance remain the major obstacles to successful reduction in cervical cancer mortality in this Indian population. HPV DNA testing was both more sensitive and specific than Pap cytology and VIA. The use of a less invasive and more user-friendly primary screening strategy (such as self-collected swabs for HPV DNA testing) may be required to achieve the coverage necessary for effective reduction in cervical cancer mortality.
Inhibition of effects of flow on potassium permeability in single perfused frog mesenteric capillaries

1 We have investigated the effects of various potential inhibitors on flow‐dependent K+ permeability (PK) of single perfused mesenteric microvessels in pithed frogs. 2 Neither superfusion with a nitric oxide synthase inhibitor, NG‐monomethyl‐L‐arginine (10 or 100 μmol l−1), nor the addition of indomethacin (30 μmol l−1) to both perfusate and superfusate reduced the positive correlation between PK and flow velocity (U). 3 In the presence of agents known to raise intracellular levels of adenosine 3′,5′‐cyclic monophosphate (noradrenaline, 8‐bromo‐cAMP and a combination of forskolin and rolipram) the slope of the relation between PK and U was no longer significant, so that PK was no longer flow dependent. 4 These results confirm that the flow dependence of PK is a biological process and not an artefact of measurement and suggest a role for intracellular cAMP rather than nitric oxide or prostacyclin in the flow‐dependent modulation of PK in frog mesenteric microvessels.
Ordering Phrases with Function Words

This paper presents a Function Word centered, Syntax-based (FWS) solution to address phrase ordering in the context of statistical machine translation (SMT). Motivated by the observation that function words often encode grammatical relationship among phrases within a sentence, we propose a probabilistic synchronous grammar to model the ordering of function words and their left and right arguments. We improve phrase ordering performance by lexicalizing the resulting rules in a small number of cases corresponding to function words. The experiments show that the FWS approach consistently outperforms the baseline system in ordering function words’ arguments and improving translation quality in both perfect and noisy word alignment scenarios.
Reengineering Object-Oriented Applications

Reengineering ob ject-oriented applications is becoming a vital activity in today industry where the developer turnover drains the system oral memory out of the systems themselves and where applications should constantly evolve to meet new requirements. This document summarizes the research effort led on reverse engineering and reengineering ob ject-oriented legacy systems. It includes (1) the definition of a suitable meta-model for reengineering, FAMIX. This meta-model, even if flat, supports both reverse engineering and code refac- toring analysis, (2) the presentation of a reengineering platform, MOOSE, (3) the evalution of software metrics for reengineer, (4) the definition of simple visual techniques to support large system understanding or finer grain code element, (5) the identification and cure sup- port for duplicated code, (6) the use of dynamic information to support composable views and collaboration extraction, and (7) the identification of reengineer patterns. Keywords. Meta-Modeling, Language Independence, Reengineering, Reverse Engineering, Code Duplica- tion, Reengineering Patterns, Program Traces, Dynamic Information, Program Visualization, Software Metrics, Refactorings, Interexchange Format, CODECRAWLER, FAMIX, MOOSE, FAMOOS, Smalltalk, Java, C++.
Estudio del valor pronóstico de serpina e1 y su papel en el crecimiento y la diseminación metastática del carcinoma escamoso de cabeza y cuello

RESUMEN: En multiples tipos tumorales, SERPINA E1 se asocia con una peor evolucion clinica de los pacientes. En el carcinoma escamoso de cabeza y cuello (CECC), el aumento del nivel de expresion de SERPINA E1 por parte de las celulas tumorales se considera un evento frecuente pero todavia se desconoce si tambien tiene un papel determinante en la evolucion clinica de los pacientes. En este trabajo de tesis doctoral estudiamos la relacion del nivel de expresion de SERPINA E1 con el pronostico de los pacientes con CECC en dos cohortes independientes de pacientes (estudio retrospectivo y prospectivo). En el estudio restrospectivo (n=80) los pacientes con niveles elevados de SERPINA E1 presentaron mayor riesgo de recidiva metastatica (p=0.045) y una supervivencia libre de progresion (SLP) (p=0.022) y especifica de cancer (SEC) (p=0.040) mas cortas que los pacientes con niveles bajos. En el estudio retrospectivo (n=180), el mayor nivel de SERPINA E1 se asocio con mayor probabilidad recidiva local (p=0.028) y metastatica (p=0.029) en los pacientes, asi como a peor supervivencia libre de recidiva local (SLRL) (p=0.022), peor SLP (p=0.002) y peor SEC (p=0.006). En un tercer estudio con una cohorte de pacientes incluida en The Cancer Genome Atlas (n=507), confirmamos la asociacion entre el nivel de SERPINA E1 y la supervivencia de los pacientes con CECC, apareciendo el nivel de expresion de SERPINA E1 como un factor pronostico independiente (p=0.027). Ademas, en nuestros ensayos in vitro observamos que la sobre-expresion de SERPINA E1 en lineas celulares de CECC aumento la capacidad de migracion y la resistencia de las celulas tumorales a la apoptosis a traves de las activacion de Akt, a la vez que disminuyo su proliferacion. Por otro lado, la infra-expresion de SERPINA E1 produjo los efectos opuestos. El desarrollo de un modelo murino ortotopico en la cepa NSG nos permitio estudiar el efecto de SERPINA E1 en el crecimiento tumoral y la diseminacion metastatica de las celulas de CECC. En nuestro modelo in vivo, SERPINA E1 aumento el crecimiento invasivo (p<0.000), la proporcion de estroma (p=0.02) y la resistencia a la apoptosis en el tumor primario (p=0.001). Asimismo, incremento la diseminacion de las celulas tumorales a ganglios cervicales (p=0.009) y su tasa de crecimiento. En relacion con las metastasis en pulmon, SERPINA E1 estimulo la dispersion de las celulas tumorales durante la colonizacion del pulmon (p=0.034) y favorecio la generacion de focos tumorales de mayor tamano (p=0.01). En base a nuestros resultados con muestras de pacientes con CECC que son tambien consistentes con nuestros resultados obtenidos en los ensayos con lineas celulares de CECC y en el modelo in vivo, proponemos que la sobre-expresion de SERPINA E1 podria ser un marcador util para estratificar a los pacientes en relacion con su riesgo de recidiva.
Rec-I-DCM3: a fast algorithmic technique for reconstructing phylogenetic trees

Phylogenetic trees are commonly reconstructed based on hard optimization problems such as maximum parsimony (MP) and maximum likelihood (ML). Conventional MP heuristics for producing phylogenetic trees produce good solutions within reasonable time on small datasets (up to a few thousand sequences), while ML heuristics are limited to smaller datasets (up to a few hundred sequences). However, since MP (and presumably ML) is NP-hard, such approaches do not scale when applied to large datasets. In this paper, we present a new technique called Recursive-Iterative-DCM3 (Rec-I-DCM3), which belongs to our family of disk-covering methods (DCMs). We tested this new technique on ten large biological datasets ranging from 1,322 to 13,921 sequences and obtained dramatic speedups as well as significant improvements in accuracy (better than 99.99%) in comparison to existing approaches. Thus, high-quality reconstructions can be obtained for datasets at least ten times larger than was previously possible.
Medical ultrasound systems

Medical ultrasound imaging has advanced dramatically since its introduction only a few decades ago. This paper provides a short historical background, and then briefly describes many of the system features and concepts required in a modern commercial ultrasound system. The topics addressed include array beam formation, steering and focusing; array and matrix transducers; echo image formation; tissue harmonic imaging; speckle reduction through frequency and spatial compounding, and image processing; tissue aberration; Doppler flow detection; and system architectures. It then describes some of the more practical aspects of ultrasound system design necessary to be taken into account for today's marketplace. It finally discusses the recent explosion of portable and handheld devices and their potential to expand the clinical footprint of ultrasound into regions of the world where medical care is practically non-existent. Throughout the article reference is made to ways in which ultrasound imaging has benefited from advances in the commercial electronics industry. It is meant to be an overview of the field as an introduction to other more detailed papers in this special issue.
Sparse coded decomposition for single image-based specular removal

In this paper, we propose a method to separate diffuse and specular images from a single image based on sparse representation. The proposed method relax the recent sparse-based technique for removing specular highlights that require multiple input images. Instead, we use only a single input image and then generate multiple specular-free images from this image. The specular removal problem is formulated as the recovery of a sparse representation and an outlier representation. From the obtained specular-free images, a dictionary is reconstructed as the basis function for sparse representation. The sparse signal and the dictionary is used to estimate diffuse image while the specular image is obtained from the outlier. The sparse coding was solved using alternating direction method of multiplier. In addition, a new variant of the specular-free image based on XYZ color space is also proposed to improve sparse representation. The experimental results showed that this method outperformed the accuracy of standard specular removal methods.
LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome

MOTIVATION Despite the increasing notions of the functional importance of antisense transcripts in gene regulation, the genome-wide overview on the ontology of antisense genes has not been obtained. Therefore, we tried to find novel antisense genes genome-wide by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries. RESULTS We identified 1260 potential antisense genes, of which 1001 are not annotated in EnsEMBL, thereby being regarded as novel. Interestingly their sense counterparts were co-expressed in the majority of the cases. CONCLUSIONS The use of LongSAGE transcriptome data is extremely powerful in the identification of thus-far unknown antisense transcripts, even in the case of well-characterized organisms like the mouse. CONTACT imai@gsf.de.
Maternal pre-pregnancy body mass index explains infant’s weight and BMI at 14 months: results from a multi-ethnic birth cohort study

Objective: To investigate the association between (self-reported) maternal pre-pregnancy body mass index (pBMI), and child’s weight, height and BMI at age 14 months. Design: Prospective multi-ethnic community-based cohort study. Setting: Amsterdam, The Netherlands. Participants: 8266 pregnant women from the Amsterdam Born Children and their Development study, filled out a questionnaire covering socio-demographic data, obstetric history, lifestyle, dietary habits and psychosocial factors, 2 weeks after their first antenatal visit. 7730 gave birth to a viable term singleton infant with information on birth weight, gender and pregnancy duration. Growth data were available for 3171 of these children. Main outcome measures: Weight (g), height (cm) and BMI (kg/m2) of the child at age 14 months. Results: pBMI was linearly associated with weight and BMI of the child at age 14 months. One unit increase in pBMI resulted in an increment of 29 g (95% CI 19 to 39) in weight and 0.041 kg/m2 (95% CI 0.030 to 0.053) in BMI. The effect size decreased after adjustment for birth weight (weight: β coefficient 19 g, 95% CI 10 to 28; BMI: β coefficient 0.034 kg/m2, 95% CI 0.023 to 0.046) and hardly changed after adjustment for all other variables (weight: β coefficient 21 g, 95% CI 11 to 30; BMI: β coefficient 0.031 kg/m2, 95% CI 0.019 to 0.043). pBMI was not related to height. Conclusions: pBMI is an independent determinant of weight and BMI of the child at age 14 months. At least one third of this effect is mediated through birth weight.
A molecular dynamics approach to nano-scale lubrication

Une approche numerique basee sur des simulations Dynamique Moleculaire a ete developpee dans le but d'etudier les mecanismes locaux de la lubrification a l'echelle nanometrique. Les elements du modele ont ete presentes et caracterises afin de reproduire les proprietes les plus realistes des materiaux et de l'interface du contact. En raison de leur relation etroite avec le frottement, les methodes de dissipation energetique pour la dynamique moleculaire ont ete revisitees et des recommandations ont ete proposees pour le choix d'une methode correcte adaptee aux differentes conditions operatoires. Pour le regime de fort cisaillement et donc de forte dissipation, une nouvelle methode mieux fondee physiquement a ete developpee, combinant simplicite et vitesse de calcul. Le modele a ensuite ete utilise pour etudier les effets lies a la structure moleculaire des surfaces et du lubrifiant confine. Afin d'etudier differentes surfaces tribologiques, une methode originale a ete utilisee pour mesurer quantitativement les potentiels physiques d'adsorption et de corrugation. Ces proprietes influencent directement la stratification dans le film et son glissement a l'interface solide. D'autre part, l'influence de la forme moleculaire du lubrifiant sur sa performance tribologique a ete etudiee, en solution pure et en melange, pour les surfaces mouillantes et non-mouillantes. Les simulations moleculaires ont permis une analyse locale du frottement lubrifie a l'echelle moleculaire et ainsi une meilleure comprehension des interactions physiques entre les elements mis en jeu.
The Dynamics of Poor Systems of Galaxies

We assemble and observe a sample of poor galaxy systems that is suitable for testing N-body simulations of hierarchical clustering and other dynamical halo models. We (1) determine the parameters of the density profile ρ(r) and the velocity dispersion profile σp(R), (2) separate emission-line galaxies from absorption-line galaxies, examining the model parameters and as a function of spectroscopic type, and (3) for the best-behaved subsample, constrain the velocity anisotropy parameter, β, which determines the shapes of the galaxy orbits. Our sample consists of 20 systems, 12 of which have extended X-ray emission in the ROSAT All-Sky Survey. We measure the 877 optical spectra of galaxies brighter than mR≈15.4 within 1.5 h-1 Mpc of the system centers (we take H0=100 h km s-1 Mpc-1). Thus, we sample the system membership to a radius typically three times larger than other recent optical group surveys. The average system population is 30 galaxies, and the average line-of-sight velocity dispersion is ≈300 km s-1. The Navarro, Frenk, & White universal profile and the Hernquist model both provide good descriptions of the spatial data. In most cases an isothermal sphere is ruled out. Systems with declining σp(R) are well-matched by theoretical profiles in which the star-forming galaxies have predominantly radial orbits (β>0); many of these galaxies are probably falling in for the first time. There is significant evidence for spatial segregation of the spectroscopic classes regardless of σp(R).
El ajuste entre formación y empleo de los universitarios en España = The match between education and work of the Spanish graduates

La finalidad basica de la presente tesis es la de describir la calidad de la empleabilidad de los universitarios espanoles, a traves de la identificacion de las variables que mejor predicen el ajuste laboral de tipo horizontal. Dentro de este marco global se senalan los siguientes objetivos: 1. Describir la relacion que la universidad ha mantenido con la sociedad y con el mercado desde una perspectiva historica, situando la preocupacion por el empleo de los graduados como uno de los elementos que se derivan de la misma. 2. Analizar, desde una perspectiva critica, el tratamiento dado al concepto de empleabilidad por distintos autores, las estrategias de investigacion desarrolladas y los principales resultados obtenidos, asi como ofrecer un marco de referencia que permita organizar los distintos elementos que este concepto engloba. 3. Ofrecer una sintesis de las aproximaciones teoricas relativas al concepto de competencia y describir cuales han sido los factores que han provocado la incorporacion de los modelos de competencias en el sistema de educacion superior actual y las implicaciones, pedagogicas y curriculares, que esta reforma conlleva. 4. Conocer, como indicador de exito o calidad en el empleo, el ajuste laboral horizontal de los egresados universitarios espanoles
A Rear Vehicle Location Algorithm for Lane Change Assist

A monocular vision based location algorithm is presented to detect and track rear vehicles for lane change assist. The algorithm uses the shadow underneath the vehicle to extract regions of interest (ROI), and then locates vehicles with the combination of symmetry, contour and the shadow underneath a vehicle. Three symmetry criterions are proposed to compute the vehicle symmetry axis: contour symmetry, gray symmetry and S component symmetry in HSV color space. Experimental results have shown better accuracy and robustness in different road and environmental conditions. 1 General Instructions In recent years, because of the increasing of vehi �» cles