Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting Interferon-Induced Transcriptional Programs in Human Peripheral Blood Cells

Interferons are key modulators of the immune system, and are central to the control of many diseases. The response of immune cells to stimuli in complex populations is the product of direct and indirect effects, and of homotypic and heterotypic cell interactions. Dissecting the global transcriptional profiles of immune cell populations may provide insights into this regulatory interplay. The host transcriptional response may also be useful in discriminating between disease states, and in understanding pathophysiology. The transcriptional programs of cell populations in health therefore provide a paradigm for deconvoluting disease-associated gene expression profiles. We used human cDNA microarrays to (1) compare the gene expression programs in human peripheral blood mononuclear cells (PBMCs) elicited by 6 major mediators of the immune response: interferons α, β, ω and γ, IL12 and TNFα; and (2) characterize the transcriptional responses of purified immune cell populations (CD4+ and CD8+ T cells, B cells, NK cells and monocytes) to IFNγ stimulation. We defined a highly stereotyped response to type I interferons, while responses to IFNγ and IL12 were largely restricted to a subset of type I interferon-inducible genes. TNFα stimulation resulted in a distinct pattern of gene expression. Cell type-specific transcriptional programs were identified, highlighting the pronounced response of monocytes to IFNγ, and emergent properties associated with IFN-mediated activation of mixed cell populations. This information provides a detailed view of cellular activation by immune mediators, and contributes an interpretive framework for the definition of host immune responses in a variety of disease settings.
Frictional Instabilities in Ball Bearings

Computer modeling techniques are used to investigate instabilities in the motions of ball and cage in a ball bearing. As the friction at ball/race and ball/cage contacts increases, the cage mass center whirl orbit changes from circular to polygonal and then to a rather erratic shape under excessive friction. The corresponding variations in whirl velocities also increase to represent bearing squeal. It is shown that cage instabilities are directly dependent on the ball/race traction slope, under low slip velocities, and the friction coefficient at the cage interfaces. Under steep traction slopes, the variation in traction at higher slip rates is also significant in high-speed bearings. In particular, it is found that a negative traction slope, in the high-slip region, may produce appreciable ball skid which promotes excessive interaction in the cage pockets and, perhaps, the most damaging instability of the cage, where the mechanical interactions progressively increase to indicate significant potentials fo.
UCD-PN: Classification of Semantic Relations Between Nominals using WordNet and Web Counts

For our system we use the SMO implementation of a support vector machine provided with the WEKA machine learning toolkit. As with all machine learning approaches, the most important step is to choose a set of features which reliably help to predict the label of the example. We used 76 features drawn from two very different knowledge sources. The first 48 features are boolean values indicating whether or not each of the nominals in the sentence are linked to certain other words in the WordNet hypernym and meronym networks. The remaining 28 features are web frequency counts for the two nominals joined by certain common prepositions and verbs. Our system performed well on all but two of the relations; theme-tool and origin entity.
Novel sensing and control schemes for a three-mirror coupled cavity

We present two options for length sensing and control of a three-mirror coupled cavity. The control of the first cavity uses amplitude or single sideband modulation and phase modulation in combination with a beat-frequency demodulation scheme, whereas the control scheme for the second cavity incorporates phase modulation and single demodulation. The theoretical and experimental performance is discussed as well as the relevance to a research programme to develop interferometric techniques for application in future interferometric gravitational wave detectors.
Using WordNet to turn a Folksonomy into a Hierarchy of Concepts

As the volume of information in the read-write Web increases rapidly, folksonomies are becoming a widely used tool to organize and categorize resources in a bottom up, flat and inclusive way. However, due to their very structure, they show some drawbacks; in particular the lack of hierarchy bears some limitations in the possibilities of searching and browsing. In this paper we investigate a new approach, based on the idea of integrating an ontology in the navigation interface of a folksonomy, and we describe an application that filters del.icio. us keywords through the WordNet hierarchy of concepts, to enrich the possibilities of navigation.
The HIV-positive skin biopsy

Dermatological disorders are a frequent presenting feature of HIV infection and/or AIDS. More than 90% of HIV-infected patients will suffer from one or more skin diseases during the course of their illness. This trend is reflected in the increasing number of skin biopsies from HIV-positive patients in those parts of the world where HIV infection/AIDS is highly prevalent. Histopathologists are therefore required to possess a working knowledge of the broad spectrum of cutaneous manifestations of HIV infection. These include the range of dermatoses that are specific to HIV infection, the more common dermatoses occurring with greater frequency (or modified by) HIV infection/AIDS, the spectrum of infectious diseases (often opportunistic) caused by viruses, bacteria, fungi, protozoa and even arthropods, and neoplastic conditions such as Kaposi sarcoma and B-cell non-Hodgkin lymphoma. The risk for adverse skin reactions to certain drugs is also greatly increased. Although the introduction of highly active antiretroviral therapy has resulted in a dramatic decrease in opportunistic infections, several of these drugs may result in adverse reactions in the skin. Skin biopsies play a vital diagnostic role when different diseases present with clinically similar skin lesions. Biopsy material should always be examined carefully to exclude dual pathology. The diagnosis may need to be confirmed with histochemical and immunohistochemical stains, and/or molecular studies. Where indicated, additional biopsies for microbiological culture should always be recommended. The examination of multiple serial sections often proves invaluable. A diagnostic approach is given based on the predominant histological reaction pattern, with an emphasis on clinicopathological correlation.
Analysis of histological and immunological parameters of metastatic lymph nodes from colon cancer patients reveals that T-helper 1 type immune response is associated with improved overall survival

AbstractLymph node (LN) involvement in colonic carcinoma (CC) is a grave prognostic sign and mandates the addition of adjuvant treatment. However, in light of the histological variability and outcomes observed, we hypothesized that patients with LN metastases (LNM) comprise different subgroups.We retrospectively analyzed the histological sections of 82 patients with CC and LNM. We studied various histological parameters (such as tumor grade, desmoplasia, and preservation of LN architecture) as well as the prevalence of specific peritumoral immune cells (CD8+, CD20+, T-bet+, and GATA-3+). We correlated the histological and immunological data to patient outcome.Tumor grade was a significant prognostic factor even in patients with LNM. So was the number of LN involved (N1/N2 stage). From the morphological parameters tested (LN extracapsular invasion, desmoplasia in LN, LN architecture preservation, and mode of metastases distribution), none was found to be significantly associated with overall survival (OS). The mean OS of CD8+ low patients was 66.6 ± 6.25 versus 71.4 ± 5.1 months for CD8+ high patients (P = 0.79). However, T-helper (Th) 1 immune response skewing (measured by Th1/Th2 ratio >1) was significantly associated with improved OS. For patients with low ratio, the median OS was 35.5 ± 5 versus 83.5 months for patients with high Th1/Th2 ratio (P = 0.001). The histological presentation of LNM does not entail specific prognostic information. However, the finding of Th1 immune response in LN signifies a protective immune response. Future studies should be carried to verify this marker and develop a strategy that augments this immune response during subsequent adjuvant treatment.
Beyond Budgeting and change: A case study

Purpose – This paper aims to investigate reasons for going Beyond Budgeting and the practical issues organizations face when they change their management accounting system based on inspiration from the Beyond Budgeting model. Design/methodology/approach – The authors apply a case study approach. The primary data source is interviews. The case company is a global company in the agri-food industry that is organized as a cooperative. Findings – The authors propose that many organizations that change their management accounting system on the basis of inspiration from Beyond Budgeting will maintain fixed budget targets. Furthermore, the authors propose that even when the use of budgets at the corporate level focuses on few line items, the diagnostic use of budgeting at lower levels in the organization may focus on a larger number of line items. Research limitations/implications – The study is subject to the usual limitations of case-based research. The propositions made in the paper should be further investiga.
A classification of symbolic transition systems

We define five increasingly comprehensive classes of infinite-state systems, called STS1--STS5, whose state spaces have finitary structure. For four of these classes, we provide examples from hybrid systems.STS1 These are the systems with finite bisimilarity quotients. They can be analyzed symbolically by iteratively applying predecessor and Boolean operations on state sets, starting from a finite number of observable state sets. Any such iteration is guaranteed to terminate in that only a finite number of state sets can be generated. This enables model checking of the μ-calculus.STS2 These are the systems with finite similarity quotients. They can be analyzed symbolically by iterating the predecessor and positive Boolean operations. This enables model checking of the existential and universal fragments of the μ-calculus.STS3 These are the systems with finite trace-equivalence quotients. They can be analyzed symbolically by iterating the predecessor operation and a restricted form of positive Boolean operations (intersection is restricted to intersection with observables). This enables model checking of all ω-regular properties, including linear temporal logic.STS4 These are the systems with finite distance-equivalence quotients (two states are equivalent if for every distance d, the same observables can be reached in d transitions). The systems in this class can be analyzed symbolically by iterating the predecessor operation and terminating when no new state sets are generated. This enables model checking of the existential conjunction-free and universal disjunction-free fragments of the μ-calculus.STS5 These are the systems with finite bounded-reachability quotients (two states are equivalent if for every distance d, the same observables can be reached in d or fewer transitions). The systems in this class can be analyzed symbolically by iterating the predecessor operation and terminating when no new states are encountered (this is a weaker termination condition than above). This enables model checking of reachability properties.
Predictors of child psychological changes during family-based treatment for obesity.

OBJECTIVE To explore the influence of 1-year changes in child obesity and maternal psychopathology on changes in child psychological problems. DESIGN Hierarchical regression models were used to predict child psychological change, with demographic variables, maternal psychological change, and child percentage overweight change as predictors. SETTING Pediatric obesity research clinic. PARTICIPANTS Clinic sample of 116 obese 8- to 12-year-old children and their mothers. INTERVENTIONS Family-based behavioral weight-control program. MAIN OUTCOME MEASURES Child psychopathology was assessed via mother-reported Child Behavior Checklists and maternal psychopathology was determined by standardizing scores on the Cornell Medical Index and the Symptoms Checklist-90-Revised. RESULTS Significant improvements were observed in child percentage overweight (-20.1% overweight), and child and maternal psychopathology. Improved maternal psychopathology accounted for a significant amount of variance in improvements in the Child Behavior Checklist total Problems Scale and internalizing and externalizing problems subscales. Decreased obesity accounted for a significant amount of variance in improvements in the Total Competence scale and, somatic complaints, social problems and social competence subscales of the Child Behavior Checklist. Significant interactions of child obesity change by sex were found for Total Problems and externalizing scores. The interactions were due to girls with greater obesity reduction showing greater improvement in Total Problems, whereas boys with greater obesity reduction showed less improvement in externalizing problems. CONCLUSIONS These results highlight the multidimensional nature of psychosocial functioning in obese children and call attention to multiple avenues for intervention to improve their psychosocial functioning.
Tat Pathway-Mediated Translocation of the Sec Pathway Substrate OprM, an Outer Membrane Subunit of the Resistance Nodulation Division Xenobiotic Extrusion Pumps, in Pseudomonas Aeruginosa

Background: Pseudomonas aeruginosa produces the Sec and Tat protein secretion machineries. The latter appears to be involved in the secretion of virulence factors, including phospholipase C (PlcH), and hence is a potential target of chemotherapeutic agents. Methods: The signal sequence of OprM, the outer membrane subunit of the xenobiotic extrusion pumps, was substituted with that of PlcH. The antibiotic susceptibility of oprM-deficient cells expressing the hybrid protein PlcH-OprM was evaluated using the agar dilution method. Results: The PlcH-OprM-expressing cells showed resistance to various MexAB-OprM substrate antibiotics. To evaluate the translocation route of PlcH-OprM, tatC encoding an indispensable component of the Tat machinery was knocked out in oprM-deficient cells. The tatC-oprM double mutant expressing PlcH-OprM exhibited antibiotic hypersusceptibility like the oprM-deficient cells, indicating that PlcH-OprM was translocated across the inner membrane exclusively through the Tat system. Conclusions: This system can be used for the screening of Tat system inhibitors and will be an excellent model for the study of secretion and biogenesis of the β-barrel outer membrane proteins.
Sounding Board – University of Washington’s Alexa Prize Submission

This paper introduces the University of Washington’s Alexa Prize socialbot, Sounding Board, which is designed to engage users with a wide variety of content. The system models the user utterance using a multi-dimensional representation. A hierarchical dialogue manager is employed where a master manages the overall conversation and a collection of miniskills manage different conversation segments. The system constructs responses using speech acts selected by the dialogue manager, where each speech act is instantiated with randomness to introduce variation to the conversation. Further, we analyze the impact of miniskill variety, user personality, and speech recognition performance on user interaction ratings.
The natural history of fetomaternal alloimmunization to the platelet-specific antigen HPA-1a (PlA1, Zwa) as determined by antenatal screening.

Immunization against the human platelet antigen (HPA)-1 alloantigen is the most common cause of severe fetal and neonatal thrombocytopenia. Fetal therapy has substantial risks and its indications need better definition. Of 24,417 consecutive pregnant women, 618 (2.5%) were HPA-1a negative of whom 385 entered an observational study. All were HLA-DRB3*0101 genotyped and screened for anti-HPA-1a. Their partners and neonates were HPA-1 genotyped and the latter were assessed by cord blood platelet counts and cerebral ultrasound scans. Anti-HPA-1a was detected in 46 of 387 pregnancies (12.0%; 95% CI 8.7%-15.2%). All but one were HLA-DRB3*0101 positive (odds ratio 140; 95% CI 19-1035; P< .00001). One baby died in utero, and of 26 HPA-1a-positive babies born to women with persistent antenatal antibodies, 9 were severely thrombocytopenic (8 with a count <10 x 10(9)/L, 1 with a large porencephalic cyst), 10 were mildly thrombocytopenic, whereas 7 had normal platelet counts. Severe thrombocytopenia was significantly associated with a third trimester anti-HPA-1a titer >/= 1:32 (P = . 004), but was not observed in babies of women with either transient or postnatal-only antibodies. HPA-1a alloimmunization complicates 1 in 350 unselected pregnancies, resulting in severe thrombocytopenia in 1:1,200. HPA-1a and HLA-DRB3*0101 typing combined with anti-HPA-1a titration allows selection of the majority of pregnancies at risk of severe thrombocytopenia.
Carbon Overcoat Loss From the Surface of a Heat Assisted Magnetic Storage Disk due to Laser Irradiation

A pump-probe experimental technique that incorporated a 527nm wavelength pump laser and a 476nm probe laser was applied to a magnetic storage disk having a magnetic layer comprised of a FePt alloy and coated with a hydrogenated carbon overcoat (COC). The pump laser power was systematically increased while sweeping the applied field with an electromagnet to observe the temperature dependent magnetization, which is proportional to the change in the polarization of the reflected beam. In this way the laser power required to heat the media to the Curie temperature (Tc) was determined, with the Curie temperature of the media determined from a separate magnetometry measurement. Such a single point laser power-to-media temperature calibration allowed the determination of the media temperature over a small laser power range near Tc. The carbon over-coated FePt media was then irradiated for varying durations at temperatures pertinent to a Heat Assisted Magnetic Recording (HAMR) device [1]. The COC surface topography and carbon bonding structure within each irradiated zone was probed with AFM and micro-spot Raman. A subtle, systematic temperature and duration dependent change in the COC was observed. With increasing temperature and duration, the Raman D-peak became increasingly pronounced, signaling an increase of the sp2 (disorder) content in the film in the irradiated region. At incrementally higher temperatures, the loss of the carbon overcoat becomes apparent as a shallow depression in the COC film in the irradiated area. A clearer picture of the possible sensitivity and kinetics of the loss of COC on the HAMR media surface was obtained by measuring its loss over a range of irradiation temperatures and durations. The activation energy and COC loss rate were obtained and a possible mechanism for COC failure-loss was discussed within the bounds of the operating HAMR device [2]. © 2013 ASME
Fast Committee-Based Structure Learning

Current methods for causal structure learning tend to be computationally intensive or intractable for large datasets. Some recent approaches have speeded up the process by first making hard decisions about the set of parents and children for each variable, in order to break large-scale problems into sets of tractable local neighbourhoods. We use this principle in order to apply a structure learning committee for orientating edges between variables. We find that a combination of weak structure learners can be effective in recovering causal dependencies. Though such a formulation would be intractable for large problems at the global level, we show that it can run quickly when processing local neighbourhoods in turn. Experimental results show that this localized, committee-based approach has advantages over standard causal discovery algorithms both in terms of speed and accuracy.
Gold nanoparticles as a sensitising agent in external beam radiotherapy and brachytherapy: a feasibility study through Monte Carlo simulation

In recent years, gold nanoparticles (GNP) have been proposed as sensitising agents in radiotherapy. Several studies, performed both through Monte Carlo simulation of dosimetric and microdosimetric enhancement in presence of GNPs and through in–vitro experiments, have clearly shown the powerfulness of such a technique in radiotherapy. Aim of the present work is to estimate the dose enhancement during external beam radiotherapy and brachytherapy in tissues loaded with different GNP concentrations. We developed two Monte Carlo simulations in GEANT4: one reproducing a medical Linac operating at 6 MV, irradiating a volume of soft tissue containing GNP–doped sub–volumes at various depths; the second one representing an 192Ir source irradiating a cylindrical cavity, in presence of a shallow volume distribution of GNPs. The Linac simulation yielded relative percent dose increases ranging from 1.6% for GNP concentrations of 1% in weight to 18% for 10% GNP concentrations, while the high–energy brachytherapy 192Ir source gave 6% of relative dose increase at 1% of concentration up to more than 70% increase at 10% of GNP concentration. Such dose enhancements are mainly due to the increased photoelectron and characteristic X–ray production from the GNPs and, at a lower percentage, to the Auger electrons escaping from the GNPs. These scarcely penetrating radiations induce relevant microdosimetric intensifications in the surrounding of each GNP, leading to a biological damage at cellular and sub–cellular level, which depends on the biological distribution of GNPs within the target cells.
Ocular Penetration and Pharmacokinetics of Topical Gatifloxacin 0.3% and Moxifloxacin 0.5% Ophthalmic Solutions After Keratoplasty

Purpose: To compare the corneal and aqueous penetration and pharmacokinetics of gatifloxacin 0.3% and moxifloxacin 0.5% ophthalmic solutions and their effect on corneal reepithelialization after penetrating keratoplasty. Methods: In this randomized, open-label, parallel-controlled study, corneal and aqueous penetration and the pharmacokinetic parameters of topically applied gatifloxacin 0.3% and moxifloxacin 0.5% (2 preoperative doses of 1 drop given 5 minutes apart) were estimated by using a sparse sampling method. Corneal and aqueous samples were collected 0.25, 0.5, 1, or 2 hours after the final dose. The concentration was determined by a high-performance liquid chromatography method. Stromal Cmax:MBC50 (maximum drug concentration in serum to 50% minimum bactericidal concentration) ratios for selected ocular pathogens were also assessed. Postoperative corneal reepithelialization at days 1, 3, and 7 was evaluated and compared between groups. Results: The calculated pharmacokinetic parameters were higher with moxifloxacin 0.5% than with gatifloxacin 0.3%. The stromal Cmax was 48.5 versus 15.7 μg/g (P = 0.04), and the stromal AUC0-2 (area under the concentration-time curve from 0 to 2 hours) was 30.9 versus 13.6 μg·h/g (P < 0.05). The endothelial Cmax was 76.1 versus 7.3 μg/g (P > 0.05), and the endothelial AUC0-2 was 43.9 versus 9.8 μg·h/g (P < 0.05). The aqueous Cmax was 0.9 versus 0.3 μg/mL (P > 0.05), and the aqueous AUC0-2 was 1.2 versus 0.4 μg·h/mL (P < 0.05). Stromal Cmax:MBC50 ratios were higher in the moxifloxacin 0.5% group for each pathogen tested. The corneal reepithelialization rates were comparable between groups. Conclusions: Topical preoperative moxifloxacin 0.5% achieved greater corneal and aqueous penetration than did gatifloxacin 0.3%. The clinical significance of this difference is not known. Postoperative use of these agents had similar effects on corneal reepithelialization.