Miracle-dz/UniFAR-FTUs huggingface dataset:
MR imaging of poststenotic flow phenomena: Experimental studies

Poststenotic flow patterns were analyzed in a flow phantom with a 1.5‐T magnetic resonance (MR) imager, with use of different MR imaging and MR angiographic pulse sequences. Spin‐echo, fast field‐echo, two‐dimensional inflow (multiple single‐section technique), and flow‐adjusted‐gradient sequences were applied. For the spin‐echo sequences, modulus and phase images were reconstructed from each data set. The length of the region of poststenotic changes in signal amplitude and phase measured at a constant flow rate increased with stenosis grade. Likewise, the length of the region of poststenotic changes measured at a constant stenosis grade increased with flow rate. Moreover, the results depended on the alignment of the flow direction with the readout gradient. Comparison of modulus and phase images allowed discrimination of turbulent and nonturbulent flow, which yields additional information on stenosis grade in clinical MR angiography.
Low-level visual cortex and motion perception: an MRI study. (Système visuel cortical de bas niveau et perception du mouvement: une caractérisation par IRM)

L'evolution des technologies d'imagerie cerebrale alliee au developpement d'algorithmes specifiques de traitement d'images permettent d'ameliorer nos connaissances sur le fonctionnement du cerveau, en particulier s'agissant de la perception visuelle. L'objectif de ce travail de these est de contribuer a la comprehension des aires corticales impliquees dans la perception visuelle du mouvement chez l'homme, en analysant l'information des signaux de differentes modalites complementaires d'Imagerie par Resonance Magnetique (IRM). Une premiere partie concerne l'identification individuelle des aires visuelles de bas-niveau. Nous detaillons la methode de cartographie retinotopique par IRM fonctionnelle (IRMf) que nous avons developpee, depuis la conception des stimuli visuels a l'analyse anatomo-fonctionnelle finale. Par ailleurs, une localisation fonctionnelle du complexe hMT/V5+ est obtenue par un paradigme en bloc. Ces methodes, optimisees suivant certains parametres de la stimulation, permettent d'extraire pour tout individu des Regions d'Interet homogenes. Dans un deuxieme temps, nous proposons une caracterisation fonctionnelle des differentes aires visuelles primaires. En se fondant sur le paradigme recent d'IRM d'adaptation qui permet d'etudier la sensibilite d'une region cerebrale a des variations quantitatives d'un parametre de la stimulation, nous demontrons une differenciation de la sensibilite a la direction du mouvement dans les aires etudiees. Enfin, nous decrivons une experience combinant les modalites d'IRMf et d'IRM de diffusion (IRMd) dans le but d'etudier la connectivite anatomique au sein du cortex visuel primaire. Cette caracterisation, etablie en s'appuyant sur des algorithmes recents de cartographie des fibres de matiere blanche, donne des indices sur le reseau d'aires notamment impliquees dans le traitement du mouvement visuel.
Relativity of value and the consequentialist umbrella

Does the real difference between non-consequentialist and consequentialist theories lie in their approach to value? Non-consequentialist theories are thought either to allow a different kind of value (namely, agent-relative value) or to advocate a different response to value (‘honouring’ rather than ‘promoting’). One objection to this idea implies that all normative theories are describable as consequentialist. But then the distinction between honouring and promoting collapses into the distinction between relative and neutral value. A proper description of non-consequentialist theories can only be achieved by including a distinction between temporal relativity and neutrality in addition to the distinction between agent-relativity and agent-neutrality.
Streptococcal M1 Protein-Provoked CXC Chemokine Formation, Neutrophil Recruitment and Lung Damage Are Regulated by Rho-Kinase Signaling

Streptococcal toxic shock syndrome is frequently caused by Streptococcus pyogenes of the M1 serotype. The aim of this study was to determine the role of Ras-homologous (Rho)-kinase signaling in M1 protein-provoked lung damage. Male C57BL/6 mice received the Rho-kinase-specific inhibitor Y-27632 before administration of M1 protein. Edema, neutrophil accumulation and CXC chemokines were quantified in the lung 4 h after M1 protein challenge. Flow cytometry was used to determine Mac-1 expression. Quantitative RT-PCR was used to determine gene expression of CXC chemokine mRNA in alveolar macrophages. M1 protein increased neutrophil accumulation, edema and CXC chemokine formation in the lung as well as enhanced Mac-1 expression on neutrophils. Inhibition of Rho-kinase signaling significantly reduced M1 protein-provoked neutrophil accumulation and edema formation in the lung. M1 protein-triggered pulmonary production of CXC chemokine and gene expression of CXC chemokines in alveolar macrophages was decreased by Y-27632. Moreover, Rho-kinase inhibition attenuated M1 protein-induced Mac-1 expression on neutrophils. We conclude that Rho-kinase-dependent neutrophil infiltration controls pulmonary tissue damage in response to streptococcal M1 protein and that Rho-kinase signaling regulates M1 protein-induced lung recruitment of neutrophils via the formation of CXC chemokines and Mac-1 expression.
Object proposals using CNN-based edge filtering

With the success of deep learning in the last few years, the object detection community shifted from processing on exhaustive sliding windows to smaller set of object proposals using more powerful and deep visual representations. Object proposals increase the accuracy and speed up detection process by reducing the search space. In this paper we propose a novel idea of filtering irrelevant edges using semantic image filtering and true objectness learnt within convolutional layers of CNN. Our approach localizes well proposals by producing highly accurate bounding boxes and reduces the number of proposals. The greatest benefit of our approach is that it can be integrated into any existing method exploiting edge-based objectness to achieve consistently high recall across various intersection over union thresholds. Unlike other supervised methods, our approach does not require bounding box annotations for training. Experiments on PASCAL VOC 2007 dataset demonstrate that our approach improves the state-of-the-art model with a significant margin.
Analyzing the Stability of Convolutional Neural Networks against Image Degradation

Understanding the underlying process of Convolutional Neural Networks (ConvNets) is usually done through visualization techniques. However, these techniques do not provide accurate information about the stability of ConvNets. In this paper, our aim is to analyze the stability of ConvNets through different techniques. First, we propose a new method for finding the minimum noisy image which is located in the minimum distance from the decision boundary but it is misclassified by its ConvNet. Second, we exploratorly and quanitatively analyze the stability of the ConvNets trained on the CIFAR10, the MNIST and the GTSRB datasets. We observe that the ConvNets might make mistakes by adding a Gaussian noise with σ = 1 (barely perceivable by human eyes) to the clean image. This suggests that the inter-class margin of the feature space obtained from a ConvNet is slim. Our second founding is that augmenting the clean dataset with many noisy images does not increase the inter-class margin. Consequently, a ConvNet trained on a dataset augmented with noisy images might incorrectly classify the images degraded with a low magnitude noise. The third founding reveals that even though an ensemble improves the stability, its performance is considerably reduced by a noisy dataset.
Antibody responses to Epstein‐Barr virus‐encoded latent membrane protein‐1 (LMP1) and expression of LMP1 in juvenile Hodgkin's disease

A large group of juvenile Hodgkin's disease patients (n = 242, mean age 11.7 years, 75% [n = 181] seropositive) was evaluated for anti‐Epstein‐Barr virus (EBV) antibody responses and the presence of EBV‐encoded EBER‐RNA and latent membrane protein‐1 (LMP1)‐protein expression in the tumor. The molecular diversity of anti‐EBV antibody responses in Hodgkin's disease patients with EBV‐positive and‐negative tumors was studied by enzyme‐linked immunosorbent assay (ELISA) and immunoblot. Using purified recombinant LMP1 protein as antigen, the presence of antibodies to LMP1 was related to expression of LMP1 in the tumor cells and specific EBV‐serological patterns. Antibodies to LMP1 were detected in 30% of the EBV‐seropositive Hodgkin's disease patients. The presence of antibodies to LMP1 was not associated with a distinct anti‐EBV antibody diversity profile (ELISA), but a significantly higher percentage of patients with antibodies to LMP1 had antibodies to ZEBRA and viral capsid antigen (VCA)‐p18 (Immunoblot). Significantly more patients with an EBV‐positive tumor had detectable antibody responses to LMP1, but the presence of antibodies to LMP1 did not reflect the expression of LMP1 protein in the tumor cells. Interestingly, all patients with the strongest antibody responses to LMP1 had EBV‐negative tumors, suggesting immunological selection in vivo. J. Med. Virol. 68:370–377, 2002. © 2002 Wiley‐Liss, Inc.
Improvements to B cell clonality analysis using PCR amplification of immunoglobulin light chain genes

Aims: Clonality analysis using polymerase chain reaction (PCR) amplification of the immunoglobulin heavy chain (IgH) gene is an important aid to the diagnosis of B cell lymphoproliferative diseases. However, the method has a relatively high false negative rate. In an attempt to improve detection rates simple PCR strategies for clonality analysis of B cell populations using amplification of Ig light chain genes have been developed. Methods: Novel PCR protocols, designed to amplify Igκ and Igλ light chain genes, were evaluated using high molecular weight DNA samples from 28 selected cases of B cell lymphoma with known light chain expression and 12 reactive lymphoid specimens. Products were run on 10% polyacrylamide minigels using heteroduplex analysis. Conventional IgH PCR analysis was also performed. Twelve randomly selected formalin fixed, paraffin wax processed samples from cases submitted for molecular genetic analysis were also studied. Results: Polyclonal products were seen in all reactive lymphoid samples. Using Igκ PCR, 24 of 28 lymphomas, including four of five IgH negative cases, displayed monoclonal patterns. Using Igλ PCR, eight of 12 Igλ expressing tumours, including two of five IgH negative cases, showed monoclonal patterns. Standard IgH PCR demonstrated monoclonality in 23 of 28 B cell lymphomas. The detection rate was improved to 27 of 28 lymphomas using heavy and light chain PCR. Efficient amplification was achieved using paraffin wax processed samples, seven of which showed monoclonality compared with eight using IgH PCR. Conclusions: Ig light chain PCR, used in conjunction with heavy chain analysis, enables improved detection of B cell monoclonality using routine histological specimens and can provide additional clone specific markers for the study of the biology of B cell tumours.
Flow cytometric DNA index and S-phase fraction in breast cancer in relation to other prognostic variables and to clinical outcome.

One frequently used classification of flow cytometric DNA ploidy status (diploid versus nondiploid) was compared with a division into seven ploidy classes based on DNA index (DI) and number of cell populations (hypodiploid, diploid, near-hyperdiploid, hyperdiploid, tetraploid, hypertetraploid, and multiploid). The latter ploidy classification showed a better correlation with prognosis and other prognostic factors (i.e., lymph node involvement, estrogen and progesterone receptor status, and S-phase fraction). The improvement in correlation was mainly due to the identification of near-hyperdiploid cases (DI 1.00-1.14) which could be combined with the diploid cases to form a group with favourable prognosis. In contrast to cases with a small increase in DNA content (near-hyperdiploid), those with a small decrease of DNA content (hypodiploid) manifested a more aggressive disease. In multivariate analysis, S-phase fraction (SPF) was a more important prognostic factor than both the improved or the conventional ploidy classification.
Impact of Surgery and Valvuloplasty on Liver Stiffness in a Patient With Pericarditis and Pulmonary Valvulopathy

Liver stiffness (LS) is associated with the presence of fibrosis; however, hepatic congestion due to elevated central venous pressure has also been shown to correlate with LS values. We report here the case of a 35-year-old woman with operated pulmonary stenosis and chronic pericarditis in whom longitudinal follow-up of LS was correlated with the changes in her hemodynamic conditions before and after surgical or percutaneous treatment of residual lesions. This case highlights the potential interest of LS as a reliable marker of hepatic congestion and elevated right ventricle (RV) filling pressures.
Regulation of the Rev 1-Pol ζ complex during bypass of a DNA interstrand crosslink

Thank you for submitting your manuscript on ICL replication after unhooking to The EMBO Journal. It has now been reviewed by three expert referees, whose reports are copied below for your information. I am happy to say that all of them consider this work in principle of interest and potential importance, and we would therefore be interested in considering a revised version further for publication. The referees nevertheless raise a number of seemingly well-taken concerns that would need to be satisfactorily answered before eventual acceptance of the paper.
Computerized cognition assessment during acetylcholinesterase inhibitor treatment in Alzheimer’s disease

Wesnes K, Edgar C, Andreasen N, Annas P, Basun H, Lannfelt L, Zetterberg H, Blennow K, Minthon L. Computerized cognition assessment during acetylcholinesterase inhibitor treatment in Alzheimer’s disease. Acta Neurol Scand: 2010: 122: 270–277. © 2009 The Authors Journal compilation © 2009 Blackwell Munksgaard.
In Response: From Manchikanti et al

We appreciate the lengthy letter by Chou entitled “Critiquing the Critiques. ” At the outset, the letter reminded us of an exchange between Bogduk and Carragee in 2007 (1) criticizing each other – Bogduk claiming that Carragee et al utilized sophistry to discredit the study, whereas Carragee described Bogduk’s argument as “inflated albeit entertaining rhetoric”. Bogduk elaborated that the defense to sophistry is to inform the listeners of the fallacy of the argument, and to point out the opposite when it applies. In contrast, Carragee borrows Aristotle’s caution in The Art of Rhetoric, that when one hears bombastic and exaggerated styles of argument, the substance is likely deficient (2). Here, it appears that Chou’s argument could qualify for sophistry, and the art of rhetoric by rehashing the same arguments over and over again while leaving the substance out. ASIPP rigorously supports peer-reviewed and bias free research including evidence synthesis, as well as government funding of such efforts. The criticism is extremely important, especially when the work is generously supported by taxpayer funds or even membership dues as in the case of the American Pain Society (APS). It appears that Chou, instead of aiming at imagined inappropriate issues should focus and concern himself with valid points raised in the critique. Further, it appears Chou is begging for shielding for funding from government grants as well as membership dues from the societies from open scientific critical reviews by concerned professional societies, which is grossly improper. Physicians specializing in methodology, either working with the government or insurers or guideline developers, have a right to claim the supremacy of their methodology – at least in their own minds. However, they have a responsibility to understand the flaws in their vaunted methodology. Consequently, it is difficult to understand the wisdom of recommending or not recommending techniques without understanding them. Further, it has become quite a bit of a phenomenon and tradition for the experts who disagree with clinicians to act as victims. However, history shows it to be different. For example, if we look at the demise of Agency for Health Care Policy and Research (AHCPR) with its $75 million expenditures per guideline and proposed expenses of $200,000 to $300,000 for each systematic review, it would appear that this network
Clique finding-a genetic approach

Presents a novel and efficient genetic approach for finding maximal cliques in a graph. A binary alphabet has been chosen to represent the presence or absence of nodes in a subgraph. The approach is to start with an initial population having small sized graphs, and then to effectively generate larger ones using a new crossover mechanism called 'partial copy crossover'. The splitting of the mutation operator into two operators, namely 'addition' and 'deletion', has been found to be effective for both increasing the diversity of the population and controlling the number of relevant subgraphs, i.e. those with the potentiality to become cliques. Experimental results on graphs with between 5 and 50 nodes and varying edge densities establish the efficacy and robustness of the approach. <<ETX>>
Inflammatory markers and physical performance in older persons: the InCHIANTI study.

BACKGROUND Some studies have proposed chronic inflammation as an underlying biological mechanism responsible for physical function decline in elderly people. The aim of this study is to evaluate the relationship between several inflammatory markers and physical performance in an older population. METHODS This study is part of the "Invecchiare in Chianti" (InCHIANTI) study, a prospective population-based study of older people, aimed at identifying risk factors for late-life disability. The study sample consisted of 1020 participants aged 65 years and older living in the Chianti area of Italy. Physical performance was assessed using walking speed, the chair-stand test, and the standing balance test. Hand-grip strength was assessed using a hand-held dynamometer. Serum levels of C-reactive protein (CRP), interleukin (IL)-6, tumor necrosis factor-alpha (TNF-alpha), IL-10, IL-1beta, IL-6sR, and IL-1RA were determined. Linear regression analyses were used to assess the multivariate relationship of inflammatory marker levels with physical performance, scored as a continuous variable from 0 to 3, and hand-grip strength after adjustment for demographics, chronic conditions, medication use, and other biological variables. RESULTS CRP, IL-6, and IL1RA were significantly correlated with physical performance (r=-0.162, r=-0.251, and r=-0.127, respectively). Significant correlations with hand-grip strength were found for CRP and IL-6 (r=-0.081 and r=-0.089, respectively). After adjustment for covariates, high levels of IL-6 and IL-1RA continued to be strongly associated with worse physical performance (p<.001 and p=0.004, respectively). High levels of CRP (p<.001) and IL-6 (p<.001) were associated with low hand-grip strength. Mean adjusted physical performance scores ranged from 2.21 in the CRP<0.59 mg/dl group to 2.07 in the CRP>0.60 mg/dl group (p for trend=.004), and from 2.25 in the lowest IL-6 quartile to 2.08 in the highest IL-6 quartile (p for trend<.001). This trend was also reflected in mean adjusted hand-grip strength, with a range from 28.8 kg for the CRP<0.59 mg/dl group to 26.0 kg for the CRP>0.60 mg/dl group (p for trend=.001), and from 27.4 kg for the lowest IL-6 quartile to 25.1 kg for the highest IL-6 quartile (p for trend=.001). CONCLUSIONS Inflammation, measured as high levels of IL-6, CRP, and IL-1RA, is significantly associated with poor physical performance and muscle strength in older persons. These data also support the biological face validity of physical performance measures. The assessment of inflammatory markers may represent a useful screening test and perhaps a potential target of intervention.
Statistical Applications in Genetics and Molecular Biology Survival Analysis with High-Dimensional Covariates : An Application in Microarray Studies

Use of microarray technology often leads to high-dimensional and low-sample size (HDLSS) data settings. A variety of approaches have been proposed for variable selection in this context. However, only a small number of these have been adapted for time-to-event data where censoring is present. Among standard variable selection methods shown both to have good predictive accuracy and to be computationally efficient is the elastic net penalization approach. In this paper, adaptations of the elastic net approach are presented for variable selection both under the Cox proportional hazards model and under an accelerated failure time (AFT) model. Assessment of the two methods is conducted through simulation studies and through analysis of microarray data obtained from a set of patients with diffuse large B-cell lymphoma where time to survival is of interest. The approaches are shown to match or exceed the predictive performance of a Cox-based and an AFT-based variable selection method. The methods are moreover shown to be much more computationally efficient than their respective Coxand AFT-based counterparts.
Inhibition of Homologous Recombination by DNA-Dependent Protein Kinase Requires Kinase Activity, Is Titratable, and Is Modulated by Autophosphorylation

ABSTRACT How a cell chooses between nonhomologous end joining (NHEJ) and homologous recombination (HR) to repair a double-strand break (DSB) is a central and largely unanswered question. Although there is evidence of competition between HR and NHEJ, because of the DNA-dependent protein kinase (DNA-PK)'s cellular abundance, it seems that there must be more to the repair pathway choice than direct competition. Both a mutational approach and chemical inhibition were utilized to address how DNA-PK affects HR. We find that DNA-PK's ability to repress HR is both titratable and entirely dependent on its enzymatic activity. Still, although requisite, robust enzymatic activity is not sufficient to inhibit HR. Emerging data (including the data presented here) document the functional complexities of DNA-PK's extensive phosphorylations that likely occur on more than 40 sites. Even more, we show here that certain phosphorylations of the DNA-PK large catalytic subunit (DNA-PKcs) clearly promote HR while inhibiting NHEJ, and we conclude that the phosphorylation status of DNA-PK impacts how a cell chooses to repair a DSB.