Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors associated with failure to publish large randomized trials presented at an oncology meeting.

CONTEXT Large clinical trials are the criterion standard for making treatment decisions, and nonpublication of the results of such trials can lead to bias in the literature and contribute to inappropriate medical decisions. OBJECTIVES To determine the rate of full publication of large randomized trials presented at annual meetings of the American Society of Clinical Oncology (ASCO), quantify bias against publishing nonsignificant results, and identify factors associated with time to publication. DESIGN Survey of 510 abstracts from large (sample size, > or =200), phase 3, randomized controlled trials presented at ASCO meetings between 1989 and 1998. Trial results were classified as significant (P< or =.05 for the primary outcome measure) or nonsignificant (P>.05 or not reported), and the type of presentation and sponsorship were identified. Subsequent full publication was identified using a search of MEDLINE and EMBASE, completed November 1, 2001; the search was updated in November 2002, using the Cochrane Register of Controlled Trials. Authors were contacted if the searches did not find evidence of publication. MAIN OUTCOME MEASURES Publication rate at 5 years; time from presentation to full publication. RESULTS Of 510 randomized trials, 26% were not published in full within 5 years after presentation at the meeting. Eighty-one percent of the studies with significant results had been published by this time compared with 68% of the studies with nonsignificant results (P<.001). Studies with oral or plenary presentation were published sooner than those not presented (P =.002), and studies with pharmaceutical sponsorship were published sooner than studies with cooperative group sponsorship or studies for which sponsorship was not specified (P =.02). These factors remained significant in a multivariable model. The most frequent reason cited by authors for not publishing was lack of time, funds, or other resources. CONCLUSIONS A substantial number of large phase 3 trials presented at an international oncology meeting remain unpublished 5 years after presentation. Bias against publishing nonsignificant results is a problem even for large randomized trials. Nonpublication breaks the contract that investigators make with trial participants, funding agencies, and ethics boards.
Influence of the quality factor on the signal to noise ratio of magnetoelectric sensors based on the delta-E effect

Recently, there has been much interest in magnetoelectric magnetic field sensors utilizing the delta-E effect. Such sensors are fully integrable and combine the advantages of high sensitivity at low frequencies with broad bandwidth. Here, we report the influence of the quality factor Q on the signal-to-noise ratio of magnetoelectric magnetic field sensors utilizing the delta-E effect. The sensor consists of a silicon cantilever covered by a magnetostrictive and a piezoelectric thin film. The magnetization-dependent elasticity of the magnetostrictive film leads to detuning of the sensor's resonance, which is excited and read out via the piezoelectric layer. The signal-to-noise ratio is experimentally analyzed as a function of the quality factor, the excitation amplitude and the signal frequency. The results are compared with a signal and noise model to describe general tendencies. The model demonstrates that, in contrast to the conventional direct operation of magnetoelectric sensors, an improvement in the limit of detection proportional to Q3/2 can be achieved if thermal-mechanical noise is dominant. The relationship still holds for frequencies far away from the resonance frequency. This reveals the potential for improving the limit of detection significantly by increasing the quality factor, if magnetic and electronic noise can be suppressed.Recently, there has been much interest in magnetoelectric magnetic field sensors utilizing the delta-E effect. Such sensors are fully integrable and combine the advantages of high sensitivity at low frequencies with broad bandwidth. Here, we report the influence of the quality factor Q on the signal-to-noise ratio of magnetoelectric magnetic field sensors utilizing the delta-E effect. The sensor consists of a silicon cantilever covered by a magnetostrictive and a piezoelectric thin film. The magnetization-dependent elasticity of the magnetostrictive film leads to detuning of the sensor's resonance, which is excited and read out via the piezoelectric layer. The signal-to-noise ratio is experimentally analyzed as a function of the quality factor, the excitation amplitude and the signal frequency. The results are compared with a signal and noise model to describe general tendencies. The model demonstrates that, in contrast to the conventional direct operation of magnetoelectric sensors, an improvement in the.
Compressed video sensing using adaptive sampling rate

Compressive video sampling is an application of compressed sensing (CS) theory which samples a signal below the Shannon-Nyquist rate. In this paper, we present a compressed video sensing method that samples the blocks with adaptive sampling rate. The edge of the image is exploited to define a deficiency factor for blocks. Considering this factor, we determine sampling rates independently for each block. The simulation results show that the proposed method outperforms the conventional CS in image quality for the same compression ratio.
Incorporation of zidovudine into leukocyte DNA from HIV-1-positive adults and pregnant women, and cord blood from infants exposed in utero.

OBJECTIVE The nucleoside analog 3'-azido-3'-deoxythymidine (ZDV) has widespread clinical use but also is carcinogenic in newborn mice exposed to the drug in utero and becomes incorporated into newborn mouse DNA. This pilot study was designed to determine ZDV incorporation into human blood cell DNA from adults and newborn infants. DESIGN In this prospective cohort study, peripheral blood mononuclear cells (PBMC) were obtained from 28 non-pregnant adults and 12 pregnant women given ZDV therapy, six non-pregnant adults with no exposure to ZDV, and six non-pregnant adults who last received ZDV > or = 6 months previously. In addition, cord blood leukocytes were obtained from 22 infants of HIV-1-positive, ZDV-exposed women and from 12 infants unexposed to ZDV. There were 11 mother-infant pairs involving HIV-1 -positive women. METHODS DNA was extracted from PBMC obtained from non-pregnant HIV-1-positive adults taking ZDV, pregnant HIV-1-positive women given ZDV during pregnancy, and from adults not taking ZDV. Cord blood leukocytes were examined from infants exposed to ZDV in utero and from unexposed controls. DNA samples were assayed for ZDV incorporation by anti-ZDV radioimmunoassay (RIA). RESULTS The majority (76%) of samples from ZDV-exposed individuals, pregnant women (8 of 12), non-pregnant adults (24 of 28), or infants at delivery (15 of 22), had detectable ZDV-DNA levels. The range of positive values for ZDV-treated adults and infants was 25-544 and 22-452 molecules ZDV/10(6) nucleotides, respectively. Analysis of 11 mother-infant pairs showed variable ZDV-DNA incorporation in both, with no correlation by pair or by duration of drug treatment during pregnancy. Two of the 24 samples from individuals designated as controls were positive by anti-ZDV RIA. The 20-fold range for ZDV-DNA values in both adults and infants suggested large interindividual differences in ZDV phosphorylation. CONCLUSIONS Incorporation of ZDV into DNA was detected in most of the samples from ZDV-exposed adults and infants. Therefore, the biologic significance of ZDV-DNA damage and potential subsequent events, such as mutagenicity, should be
Non‐invasive determination of tissue thermal parameters from high intensity focused ultrasound treatment monitored by volumetric MRI thermometry

A method is proposed for estimating the perfusion rate, thermal diffusivity, and the absorption coefficient that influence the local temperature during high intensity focused ultrasound (HIFU) thermotherapy procedures. For this purpose, HIFU heating experiments (N = 100) were performed ex vivo on perfused porcine kidney (N = 5) under different flow conditions. The resulting spatio‐temporal temperature variations were measured non‐invasively by rapid volumetric MR‐temperature imaging. The bio‐heat transfer (BHT) model was adapted to describe the spatio‐temporal evolution of tissue temperature in the cortex. Absorption and perfusion coefficients were determined by fitting the integrated thermal load (spatial integration of the thermal maps) curves in time with an analytical solution of the BHT equation proposed for single point HIFU heating. Thermal diffusivity was determined independently by analyzing the spatial spread of the temperature in time during the cooling period. Absorption coefficient and thermal diffusivity were found to be independent of flow, with mean and average values of 11.0 ± 1.85 mm3 · K · J−1 and 0.172 ± 0.003 mm2 · s−1, respectively. A linear dependence of the calculated perfusion rate with flow was observed with a slope of 9.20 ± 0.75 mm−3. The perfusion was found to act as a scaling term with respect to temperature but with no effect on the spatial spread of temperature which only depends on the thermal diffusivity. All results were in excellent agreement with the BHT model, indicating that this model is suitable to predict the evolution of temperature in perfused organs. This quantitative approach allows for determination of tissue thermal parameters with excellent precision (within 10%) and may thus help in quantifying the influence of perfusion during MR guided high intensity focused ultrasound (MRgHIFU). Copyright © 2009 John Wiley & Sons, Ltd.
A structural analysis of job search methods and subsequent wages

In most studies on individual labor market transitions, the search process leading to job offers is a black box. In this paper we specify and estimate a search model that distinguishes between formal (applications) and informal (referrals) search methods. Job offers can be obtained by either method, and the corresponding wage offer distributions are allowed to differ. The model allows for search during unemployment as well as search on the job. We conclude that although the method by which jobs are found varies considerably with education and occupation, the use of a particular search method does not result in a higher wage. Moreover, individuals who have an advantage in informal search do not find a job more rapidly, which casts doubt on the hypothesis that the search method is freely chosen by the searcher by comparing costs and returns.
The Cultural Tailoring of a Substance use Prevention Curriculum for American Indian Youth

In this article we discuss the importance of the cultural tailoring (CT) of classroom-based prevention curricula to ensure their relevance to, and increase their receptivity by, racial and ethnic minority adolescent populations. Following a review of the pertinent literature, we develop an integrated model of CT that conceptualizes such adaptations into “superficial/peripheral,” “deep structure/sociocultural,” and “evidential,” and subclassifies the first of these into “language” and “images. ” We then describe the results of the application of this model post hoc to the adaptation of a specific alcohol use prevention curriculum, “Protecting You/Protecting Me,” to enhance its suitability for youth in three American Indian tribes in Nebraska. We conclude with a discussion of the adequacy of the model of CT we developed and the potential challenges and benefits of subjecting other curricula to this process.
La queue GABAergique de l’aire tegmentale ventrale : un nouveau centre de contrôle des systèmes dopaminergiques

Les systemes dopaminergiques (DA) mesencephaliques jouent un role cle dans de nombreuses fonctions cerebrales. A l’origine de ces systemes, se trouve notamment l’aire tegmentale ventrale (VTA). Dans les annees 2000, une nouvelle sous-region de la VTA a ete identifiee et nommee tVTA. Essentiellement GABAergique, elle accumule le facteur de transcription DeltaFosB en reponse a la cocaine ou aux amphetamines. Nous avons realise chez le rat un criblage d’une vingtaine de molecules pour evaluer leur capacite a exprimer FosB dans la tVTA. Les resultats montrent que l’induction de FosB dans la tVTA est specifique aux psychostimulants et n’a lieu que dans les neurones GABAergiques. Notre travail a egalement permis de delimiter les frontieres neuroanatomiques de la tVTA et d’analyser les connexions de cette region. Les afferences sont nombreuses et essentiellement similaires a celles de la VTA, suggerant l’appartenance de la tVTA a la VTA. Par contre, les efferences sont plus restreintes. La tVTA projette surtout vers les groupes DA A9 et A10. Ces projections sont GABAergiques et forment des appositions avec les somas des neurones DA de la VTA, notamment ceux projetant vers le noyau accumbens. Enfin, en utilisant l’electrophysiologie in vivo, nous avons demontre que la stimulation de la tVTA inhibe les neurones DA de la VTA. Ces resultats ont permis de definir une nouvelle region cerebrale pouvant etre un centre de controle des systemes dopaminergiques. Cette decouverte devrait deboucher sur de nombreuses etudes permettant de mieux comprendre comment la tVTA participe a la physiologie et aux pathologies des systemes dopaminergiques.
Renal hyalin

This describes the sodium sulphate-Alcian Blue (SAB) method for staining amyloid in paraffin sections. Its value lies in the possibility of subsequent counterstaining and thus of revealing the structural relationships of amyloid. In the kidney the topical disposition of amyloid closely resembles the disposition of fibrin in the kidney of diabetics; this suggests that upset in vascular permeability plays a part in determining the site of the amyloid deposits. Furthermore, an aging process in amyloid can now be envisaged resembling the aging of extraluminal fibrin. Both materials proceed to a hyalin material that, staining like collagen, merits the name pseudo-collagen. This term we apply to a hyalin, staining like collagen, for which, we can postulate a specific precursor.
Interactions between c-Jun, Nuclear Factor 1, and JC Virus Promoter Sequences: Implications for Viral Tropism

ABSTRACT The infectious cycle of the human polyomavirus JC (JCV) is ultimately regulated in cellular nuclei at the level of viral protein expression and genomic replication. Such activity is prompted by interactions between variant nucleotide sequences within the JCV regulatory region (promoter) and cellular transcription factors that bind specific DNA consensus sites. In previous work we identified an NF-1 class member, NF-1X, as a critical transcription factor affecting the JCV cellular host range. Within variant JCV promoters, as well as other viral and cellular promoters, adjacently located NF-1 and AP-1 consensus sites are often found. The close proximity of these two binding sites suggests the opportunity for interaction between NF-1 and AP-1 proteins. Here, by electrophoretic mobility shift assays, we show temporal and dose-dependent interference by an AP-1 family member, c-Jun, upon NF-1 proteins binding an NF-1 consensus site derived from JCV promoter sequence. Moreover, as demonstrated by protein-protein interaction assays, we identify specific binding affinity independent of DNA binding between NF-1X and c-Jun. Finally, to compare the binding profiles of NF-1X and c-Jun on JCV promoter sequence in parallel with in vivo detection of viral activity levels, we developed an anchored transcriptional promoter (ATP) assay. With use of extracts from JCV-infected cells transfected to overexpress either NF-1X or c-Jun, ATP assays showed concurrent increases in NF-1X binding and viral protein expression. Conversely, increased c-Jun binding accompanied decreases in both NF-1X binding and viral protein expression. Therefore, inhibition of NF-1X binding by c-Jun appears to play a role in regulating levels of JCV activity.
Association of the X-linked Lymphoproliferative Disease Gene Product SAP/SH2D1A with 2B4, a Natural Killer Cell-activating Molecule, Is Dependent on Phosphoinositide 3-Kinase*

Natural killer (NK) cells express an activating receptor, 2B4, that enhances cellular cytotoxicity. Upon NK cell activation by ligation of 2B4, the intracellular domain of 2B4 associates with the X-linked lymphoproliferative disease (XLP) gene product, signaling lymphocytic activation molecule-associated protein/SH2D1A (SAP/SH2D1A). Defective intracellular association of 2B4 with mutated SAP/SH2D1A is likely to underlie the defects in cytotoxicity observed in NK cells from patients with XLP. We report here a role for phosphoinositide 3-kinase (PI3K) in the recruitment and association of SAP/SH2D1A to 2B4 in human NK cells. The activation of normal NK cells by ligation of 2B4 leads to the phosphorylation of 2B4, recruitment of SAP/SH2D1A, and association of the p85 regulatory subunit of PI3K. The inhibition of PI3K enzymatic activity with either wortmannin or LY294002 prior to 2B4 ligation does not alter the association of 2B4 with the p85 subunit but prevents the recruitment of SAP/SH2D1A to 2B4. In addition, PI3K inhibitors significantly diminish the cytotoxic function of primary NK cells. This observed inhibition of cytotoxicity, present in normal NK cells, was less apparent or absent in NK cells derived from a patient with XLP. These data indicate that the cytotoxicity of activated NK cells is mediated by the association of 2B4 and SAP/SH2D1A, and that this association is dependent upon the activity of PI3K.
Identification and Mapping of Self-Assembling Protein Domains Encoded by the Escherichia coli K-12 Genome by Use of λ Repressor Fusions

ABSTRACT Self-assembling proteins and protein fragments encoded by the Escherichia coli genome were identified from E. coli K-12 strain MG1655. Libraries of random DNA fragments cloned into a series of λ repressor fusion vectors were subjected to selection for immunity to infection by phage λ. Survivors were identified by sequencing the ends of the inserts, and the fused protein sequence was inferred from the known genomic sequence. Four hundred sixty-three nonredundant open reading frame-encoded interacting sequence tags (ISTs) were recovered from sequencing 2,089 candidates. These ISTs, which range from 16 to 794 amino acids in length, were clustered into families of overlapping fragments, identifying potential homotypic interactions encoded by 232 E. coli genes. Repressor fusions identified ISTs from genes in every protein-based functional category, but membrane proteins were underrepresented. The IST-containing genes were enriched for regulatory proteins and for proteins that form higher-order oligomers. Forty-eight (20.7%) homotypic proteins identified by ISTs are predicted to contain coiled coils. Although most of the IST-containing genes are identifiably related to proteins in other bacterial genomes, more than half of the ISTs do not have identifiable homologs in the Protein Data Bank, suggesting that they may include many novel structures. The data are available online at http://oligomers.tamu. edu/ .
Effects of Neonatal Thymectomy on the Densities of Nicotinic Cholinergic Receptors in Skeletal Muscle and Brain

It has been suggested that the thymic polypeptide thymopoietin interacts with skeletal muscle nicotinic acetylcholine receptors (nAChRs) and brain nicotinic receptors labeled by alpha-bungarotoxin (alpha-BuTX). In this study, the effects of neonatal thymectomy on the density of skeletal muscle nAChRs and the density of brain alpha-BuTX binding sites at 7 and 45 days postnatal were investigated. In addition, the densities of receptors in the skeletal muscle and brain of the athymic nu/nu mouse at 42 days postnatal were measured. We found little evidence that the absence of the thymus alters the density of nicotinic receptors in either skeletal muscle or brain.
Mutation Analysis of Autosomal Dominant Polycystic Kidney Disease Genes in Han Chinese

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in two genes, PKD1 and PKD2. The complexity of these genes, particularly PKD1, has complicated genetic screening, though recent advances have provided new opportunities for amplifying these genes. In the Han Chinese population, no complete mutational analysis has previously been conducted across the entire span of PKD1 and PKD2. Here, we used single-strand conformation polymorphism (SSCP) analysis to screen the entire coding sequence of PKD1 and PKD2 in 85 healthy controls and 72 Han Chinese from 24 ADPKD pedigrees. In addition to 11 normal variants, we identified 17 mutations (12 in PKD1 and 5 in PKD2), 15 of which were novel ones (11 for PKD1 and 4 for PKD2). We did not identify any seeming mutational hot spots in PKD1 and PKD2. Notably, we found several disease-associated C–T or G–A mutations that led to charge or hydrophobicity changes in the corresponding amino acids. This suggests that the mutations cause conformational alterations in the PKD1 and PKD2 protein products that may impact the normal protein functions. Our study is the first report of screenable mutations in the full-length PKD1 and PKD2 genes of the Han Chinese, and also offers a benchmark for comparisons between Caucasian and Han ADPKD pedigrees and patients.
Bridging the Gap between Vision and Reality: A Methodological Assessment Tool for Long-term Normative Planning Implementation

SUMMARY Action plans and spatial organization should reflect a long-term normative vision of a desired future for a given area. In practice, however, the attempt to translate a normative long-term vision, utopian in nature, into operational steps is often overpowered by obstacles and difficulties inherent in current realities. Reality overpowering vision reduces the ability of vision to influence at the local level and contributes to weakening the ability to achieve overall sustainability. The increasing complexity and dynamics characterizing the present planning field create a demand for applicability, quality and reliability. At the same time, the field is directed by strong pressures for reduced time scales and delivery at a reasonable cost. This reality calls for the development of new methodologies tailored to those specifications. The present paper presents a novel, integrative methodology that stimulates action to mitigate significant challenges addressed by long-term normative vision by means of strategies that bridge the gap between vision and reality. The methodological tool offered aims at assisting planners to formulate an implementation-oriented spatial plan rooted in long-term vision, yet flexible and adaptable to temporal changes. The suggested methodology originates in diverse theoretical disciplines and fields of public governance, planning, economics and social science, and relies on methodologies developed in other countries.
Application of multi-class support vector machines for power system on-line static security assessment using DT - based feature and data selection algorithms

This paper presents a multi-class Support Vector Machine (SVM) based algorithm for on-line static security assessment of the power systems. The proposed SVM based security assessment algorithm has a very small training time and space in comparison with the traditional machine learning methods such as Artificial Neural Networks (ANN) based algorithms. In addition, the proposed algorithm is faster than existing algorithms. One of the main points, to apply a machine learning method is feature selection. In this paper, a new Decision Tree (DT) based feature selection algorithm has been presented. The proposed SVM algorithm has been applied to New England 39-bus power system. The simulation results show the effectiveness and the stability of the proposed method for on-line static security assessment. The effectiveness of the proposed feature selection algorithm has been investigated, too. The proposed feature selection algorithm has been compared with different feature selection algorithms. The simulation results demonstrate the effectiveness of the proposed feature algorithm.