Miracle-dz/UniFAR-FTUs huggingface dataset:
Vascular Smooth Muscle Cell–Derived Transforming Growth Factor-&bgr; Promotes Maturation of Activated, Neointima Lesion–Like Macrophages

Objective—To define the contribution of vascular smooth muscle cell (SMC)–derived factors to macrophage phenotypic modulation in the setting of vascular injury. Approach and Results—By flow cytometry, macrophages (M4) were the predominant myeloid cell type recruited to wire-injured femoral arteries, in mouse, compared with neutrophils or eosinophils. Recruited macrophages from injured vessels exhibited a distinct expression profile relative to circulating mononuclear cells (peripheral blood monocytes; increased: interleukin-6, interleukin-10, interleukin-12b, CC chemokine receptor [CCR]3, CCR7, tumor necrosis factor-&agr;, inducible nitric oxide synthase, arginase 1; decreased: interleukin-12a, matrix metalloproteinase [MMP]9). This phenotype was recapitulated in vitro by maturing rat bone marrow cells in the presence of macrophage-colony stimulating factor and 20% conditioned media from cultured rat SMC (sM&phgr;) compared with maturation in macrophage-colony stimulating factor alone (M0). Recombinant transforming growth factor (TGF)-&bgr;1 recapitulated the effect of SMC conditioned media. Macrophage maturation studies performed in the presence of a pan-TGF-&bgr; neutralizing antibody, a TGF-&bgr; receptor inhibitor, or conditioned media from TGF-&bgr;–depleted SMCs confirmed that the SMC-derived factor responsible for macrophage activation was TGF-&bgr;. Finally, the effect of SMC-mediated macrophage activation on SMC biology was assessed. SMCs cocultured with sM&phgr; exhibited increased rates of proliferation relative to SMCs cultured alone or with M0 macrophages. Conclusions—SMC-derived TGF-&bgr; modulates the phenotype of maturing macrophages in vitro, recapitulating the phenotype found in vascular lesions in vivo. SMC-modulated macrophages induce SMC activation to a greater extent than control macrophages.
Effects of Trichostatin A on In vitro Development of Porcine Embryos Derived from Somatic Cell Nuclear Transfer

Many different approaches have been developed to improve the efficiency of animal cloning by somatic cell nuclear transfer (SCNT), one of which is to modify histone acetylation levels using histone deacetylase inhibitors (HDACi) such as trichostatin A (TSA). In the present study, we examined the effect of TSA on in vitro development of porcine embryos derived from SCNT. We found that TSA treatment (50 nM) for 24 h following oocyte activation improved blastocyst formation rates (to 22.0%) compared with 8.9% in the non-treatment group and total cell number of the blastocysts for determining embryo quality also increased significantly (88.9→114.4). Changes in histone acetylation levels as a result of TSA treatment were examined using indirect immunofluorescence and confocal microscopy scanning. Results showed that the histone acetylation level in TSA-treated embryos was higher than that in controls at both acetylated histone H3 lysine 9 (AcH3K9) and acetylated histone H4 lysine 12 (AcH4K12). Next, we compared the expression patterns of seven genes (OCT4, ID1; the pluripotent genes, H19, NNAT, PEG1; the imprinting genes, cytokeratin 8 and 18; the trophoblast marker genes). The SCNT blastocysts both with and without TSA treatment showed lower levels of OCT4, ID1, cytokeratin 8 and 18 than those of the in vivo blastocysts. In the case of the imprinting genes H19 and NNAT, except PEG1, the SCNT blastocysts both with and without TSA treatment showed higher levels than those of the in vivo blastocysts. Although the gene expression patterns between cloned blastocysts and their in vivo counterparts were different regardless of TSA treatment, it appears that several genes in NT blastocysts after TSA treatment showed a slight tendency toward expression patterns of in vivo blastocysts. Our results suggest that TSA treatment may improve preimplantation porcine embryo development following SCNT.
Counting in Team Semantics

We explore several counting constructs for logics with team semantics. Counting is an important task in numerous applications, but with a somewhat delicate relationship to logic. Team semantics on the other side is the mathematical basis of modern logics of dependence and independence, in which formulae are evaluated not for a single assignment of values to variables, but for a set of such assignments. It is therefore interesting to ask what kind of counting constructs are adequate in this context, and how such constructs influence the expressive power, and the model-theoretic and algorithmic properties of logics with team semantics. Due to the second-order features of team semantics there is a rich variety of potential counting constructs. Here we study variations of two main ideas: forking atoms and counting quantifiers. Forking counts how many different values for a tuple w occur in assignments with coinciding values for v. We call this the forking degree of bar v with respect to bar w. Forking is powerful enough to capture many of the previously studied atomic dependency properties. In particular we exhibit logics with forking atoms that have, respectively, precisely the power of dependence logic and independence logic. Our second approach uses counting quantifiers E^{geq mu} of a similar kind as used in logics with Tarski semantics. The difference is that these quantifiers are now applied to teams of assignments that may give different values to mu. We show that, on finite structures, there is an intimate connection between inclusion logic with counting quantifiers and FPC, fixed-point logic with counting, which is a logic of fundamental importance for descriptive complexity theory. For sentences, the two logics have the same expressive power. Our analysis is based on a new variant of model-checking games, called threshold safety games, on a trap condition for such games, and on game interpretations.
Serum cholesterol changes in long-term survivors of liver transplantation: a comparison between cyclosporine and tacrolimus therapy.

The aim of this study was to compare the long-term effect of tacrolimus and cyclosporine therapies on serum cholesterol levels in liver transplant recipients. We retrospectively studied 127 consecutive adult liver transplant recipients who survived for at least 1 year after transplantation. Basal immunosuppression consisted of cyclosporine plus prednisone in 100 patients and tacrolimus plus prednisone in 27 patients. Hypercholesterolemia was defined as a fasting serum cholesterol level greater than 220 mg/dL. Mean follow-up was 39 months. No statistical significance was found between cyclosporine- and tacrolimus-treated patients regarding age, sex, diagnosis, and previous cholesterol levels; both groups were similar. Significantly more tacrolimus-treated patients were steroid free in the first and second year of follow-up (tacrolimus, 37% and 63%; cyclosporine, 13% and 32%, respectively; P <.01). In the third year of follow-up, this difference was not significant (77% v 56%). The overall incidence of hypercholesterolemia was 34.6% (44 patients). At the end of the study, hypercholesterolemia was found in 24 of 51 and 14 of 70 patients with and without steroids, respectively (P <.002). Also, mean cholesterol levels were 224 +/- 70 and 191 +/- 48 mg/dL before and after steroid withdrawal, respectively, P <. 001. Hypercholesterolemia was found in 43.7% of the patients during cyclosporine plus prednisone therapy compared with 46.1% of the patients during tacrolimus plus prednisone therapy (P <.9). Greater mean cholesterol levels were found in the cyclosporine group, particularly in the second and third years of follow-up (P <.01). Hypercholesterolemia was found in 22% of the patients during cyclosporine monotherapy compared with 15% during tacrolimus monotherapy (P <.5). No differences were found in mean cholesterol levels during follow-up when both monotherapy groups were compared. In conclusion, a lower incidence of hypercholesterolemia was achieved in tacrolimus-treated patients, mainly when steroids were still part of the immunosuppressive treatment.
A review of the applications of the hydrofiber dressing with silver (Aquacel Ag®) in wound care

Aquacel Ag((R)) (ConvaTec, Princeton, NJ, USA) is a new hydrofiber wound dressing consisting of soft non-woven sodium carboxymethylcellulose fibers integrated with ionic silver. It is a moisture-retention dressing, which forms a gel on contact with wound fluid and has antimicrobial properties of ionic silver. We present a current literature review on Aquacel Ag((R)), of both in vitro and in vivo efficacy and clinical applications. In vitro and in vivo studies have demonstrated the wide antimicrobial properties of Aquacel Ag((R)), and additionally demonstrated the cytotoxicity of ionic silver to keratinocytes and fibroblasts that cause delay in wound re-epithelialization. Clinical studies confirmed that Aquacel Ag((R)) is an effective and safe dressing for a variety of wound types, both acute and chronic. Incorporation of ionic silver into the hydrofibers does not cause undue alteration in the performance properties of the base dressing, which continues to provide favorable wound moisture and exudate management. The addition of ionic silver reduces local pain and dressing changes, and provides significant broad-spectrum antimicrobial properties, with no delay in wound healing.
ICDAR 2013 Competition on Historical Book Recognition (HBR 2013)

This paper presents an objective comparative evaluation of layout analysis and recognition methods for scanned historical books. It describes the competition (modus operandi, dataset and evaluation methodology) held in the context of ICDAR2013 and the 2nd International Workshop on Historical Document Imaging and Processing (HIP2013), presenting the results of the evaluation of five methods - three submitted and two state-of-the-art systems (one commercial and one open-source). Three scenarios are reported in this paper, one evaluating the ability of methods to accurately segment regions, one evaluating segmentation and region classification (with a text extraction goal) and the other the whole pipeline including recognition. The results indicate that there is a convergence to a certain methodology, in terms of layout analysis, with some variations in the approach. However, there is still a considerable need to develop robust methods that deal with the idiosyncrasies of historical books, especially for OCR.
The Effectiveness of Parental Screening of At-Risk Infants

This study examined the validity, reliability, and cost of a parent-completed screening system called the Infant Monitoring Questionnaires. This system relies on parents to complete developmental questionnaires on their at-risk infants at specific time intervals. The present work replicated and extended a previous study of the questionnaires. The primary analyses included determining (a) the agreement between the infant's classification based on the parent-completed questionnaire and a criterion measure (e.g., Bayley Scales of Infant Development, Stanford-Binet Intelligence Test, Revised Gesell Developmental Schedules); (b) interobserver and test-retest reliability of the questionnaires; and (c) the cost of the questionnaire system. The results indicated that percentage agreement between classifications of infants made using the standardized tests and the questionnaires was high, ranging from 86% to 91%. Underscreening rates were low, ranging from zero to 6%; overscreening rates were also low, ranging from 3% to 11%. Interobserver and test-retest agreement were very high. At a cost of about $2.50 per questionnaire, the screening system provides an economical and flexible means of screening at-risk infants while at the same time involving parents in the assessment process.
Density based clustering for detection of robotic operations

This paper tackles the problem of processing measured values in time series of energy consumption data obtained in robotic production cells. The consumed energy is measured at each robot in the cell to get information about the robotic operations that are performed. Such knowledge may serve as a basis for further steps such as minimization of the energy consumption or diagnosis of the robot behavior. For the modeling of the robots, Continuous State Hidden Gaussian-Markov Models (CS-HGMM) were developed in the previous work, which rely on a set of training examples of sequences for unsupervised training. In this paper, segmentation based on signal information contents and unsupervised clustering of the acquired segments is presented. The used clustering methods have been adapted from the OPTICS algorithm, which is a generalization of the popular DBSCAN algorithm. This approach has resulted in the ability to process irregular artefacts in measured data that do not represent any particular robotic operation, and to process and cluster segment candidates that do not have the same length which happens quite often in the industrial applications.
Fibroblast Growth Factor 21 Predicts the Metabolic Syndrome and Type 2 Diabetes in Caucasians

OBJECTIVE The incidence of the metabolic syndrome and type 2 diabetes mellitus (T2DM) is rising worldwide. Liver-derived fibroblast growth factor (FGF)-21 affects glucose and lipid metabolism. The aim of this study was to analyze the predictive value of FGF-21 on the incidence of T2DM and the metabolic syndrome. RESEARCH DESIGN AND METHODS The Metabolic Syndrome Berlin Potsdam (MeSyBePo) recall study includes 440 individuals. Glucose metabolism was analyzed using an oral glucose tolerance test, including insulin measurements. FGF-21 was measured using enzyme-linked immunosorbent assay. Primary study outcome was diabetes and the metabolic syndrome incidence and change of glucose subtraits. RESULTS During a mean follow-up of 5.30 ± 0.1 years, 54 individuals developed the metabolic syndrome, 35 developed T2DM, and 69 with normal glucose tolerance at baseline progressed to impaired glucose metabolism, defined as impaired fasting glucose, impaired glucose tolerance, or T2DM. FGF-21 predicted incident metabolic syndrome (lnFGF-21 odds ratio [OR] 2.6 [95% CI 1.5 – 4.5]; P = 0.001), T2DM (2.4 [1.2–4.7]; P = 0.01), and progression to impaired glucose metabolism (2.2 [1.3 – 3.6]; P = 0.002) after adjustment for age, sex, BMI, and follow-up time. Additional adjustment for waist-to-hip ratio, systolic blood pressure, HDL cholesterol, triglycerides, and fasting glucose did not substantially modify the predictive value of FGF-21. CONCLUSIONS FGF-21 is an independent predictor of the metabolic syndrome and T2DM in apparently healthy Caucasians. These results may indicate FGF-21 resistance precedes the onset of the metabolic syndrome and T2DM.
Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano

Significance The availability of high-quality genome and transcriptome assemblies is critical for enabling full exploitation of any model organism. Here we present genome and transcriptome assemblies for Macrostomum lignano, a free-living flatworm that can regenerate nearly its entire body following injury. The resources we present here will promote not only the studies of mechanisms of stem cell self-renewal, but also of regeneration and differentiation. The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50 = 222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
Racial Differences in Left Atrial Size: Results from the Coronary Artery Risk Development in Young Adults (CARDIA) Study

Whites have an increased risk of atrial fibrillation (AF) compared to Blacks. The mechanism underlying this association is unknown. Left atrial (LA) size is an important AF risk factor, and studies in older adults suggest Whites have larger LA diameters. However, because AF itself causes LA dilation, LA size differences may be due to greater subclinical AF among older Whites. We therefore assessed for racial differences in LA size among young adults at low AF risk. The Coronary Artery Risk Development in Young Adults (CARDIA) study enrolled White and Black participants between 18 and 30 years of age. LA diameter was measured in a subset of participants using echocardiography at Year 5 (n = 4,201) and Year 25 (n = 3,373) of follow up. LA volume was also assessed at Year 5 (n = 2,489). Multivariate linear regression models were used to determine the adjusted association between race and LA size. In unadjusted analyses, mean LA diameter was significantly larger among Blacks compared to Whites both at Year 5 (35.5 ± 4.8 mm versus 35.1 ± 4.5 mm, p = 0.01) and Year 25 (37.4 ± 5.1 mm versus 36.8 ± 4.9 mm, p = 0.002). After adjusting for demographics, comorbidities, and echocardiographic parameters, Whites demonstrated an increased LA diameter (0.7 mm larger at Year 5, 95% CI 0.3–1.1, p<0.001; 0.6 mm larger at Year 25, 95% CI 0.3–1.0, p<0.001). There was no significant association between race and adjusted Year 5 LA volume. In conclusion, in a young, well-characterized cohort, the larger adjusted LA diameter among White participants suggests inherent differences in atrial structure may partially explain the higher risk of AF in Whites. The incongruent associations between race, LA diameter, and LA volume suggest that LA geometry, rather than size alone, may have implications for AF risk.
Culture +Rhetoric: Studies in Rhetoric and Culture (review)

Th e publication two decades ago of a collection of essays on the “rhetorical turn” in the natural and social sciences consolidated what had already become a peculiar academic ritual, wherein discipline after discipline discovered, or found itself confronted by, the rhetorical foundations of its own knowledge claims (Simons 1990). Th e discovery should not have been as shocking as it was, since a robust if often dormant or suppressed tradition dating back to the Sophists had insisted, frequently against fashion, that all truth is the product of rhetorical operations. Nonetheless, the book’s editor, Herbert Simons, and most of its contributors eagerly welcomed this belated but auspicious acknowledgment of rhetoric’s primacy by its erstwhile rivals. Yet one dissenter, Dilip Gaonkar, expressed skepticism about the enthusiasm with which rhetoricians greeted the rhetorical turn (1990). For Gaonkar, the longing to be taken seriously by its adversaries betokened an anxiety that has plagued rhetoric since its birth as a vocation, the worry that rhetoric had no object, method, or content properly its own. Indeed, the price of this recognition, ironically, would be the confi rmation that this anxiety
Randomized parallel algorithms for backtrack search and branch-and-bound computation

Universal randomized methods for parallelizing sequential backtrack search and branch-and-bound computation are presented. These methods execute on message-passing multi- processor systems, and require no global data structures or complex communication protocols. For backtrack search, it is shown that, uniformly on all instances, the method described in this paper is likely to yield a speed-up within a small constant factor from optimal, when all solutions to the problem instance are required. For branch-and-bound computation, it is shown that, uniformly on all instances, the execution time of this method is unlikely to exceed a certain inherent lower bound by more than a constant factor. These randomized methods demonstrate the effectiveness of randomization in distributed parallel computation. Categories and Subject Descriptors: F.2. 2 (Analysis of Algorithms and Problem Complexity): Non-numerical Algorithms-computation
Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice

Pre-existing immunity to human adenovirus serotype 5 (Ad5) is common in the general population. Bypassing pre-existing immunity could maximize Ad5 vaccine efficacy. Vaccination by the intramuscular (I.M.), nasal (I.N.) or oral (P.O.) route with Ad5 expressing Ebola Zaire glycoprotein (Ad5-ZGP) fully protected naïve mice against lethal challenge with Ebola. In the presence of pre-existing immunity, only mice vaccinated I.N. survived. The frequency of IFN-γ+ CD8+ T cells was reduced by 80% and by 15% in animals vaccinated by the I.M. and P.O. routes respectively. Neutralizing antibodies could not be detected in serum from either treatment group. Pre-existing immunity did not compromise the frequency of IFN-γ+ CD8+ T cells (3.9±1% naïve vs. 3.6±1% pre-existing immunity, PEI) nor anti-Ebola neutralizing antibody (NAB, 40±10 reciprocal dilution, both groups). The number of INF-γ+ CD8+ cells detected in bronchioalveolar lavage fluid (BAL) after I.N. immunization was not compromised by pre-existing immunity to Ad5 (146±14, naïve vs. 120±16 SFC/million MNCs, PEI). However, pre-existing immunity reduced NAB levels in BAL by ∼25% in this group. To improve the immune response after oral vaccination, the Ad5-based vaccine was PEGylated. Mice given the modified vaccine did not survive challenge and had reduced levels of IFN-γ+ CD8+ T cells 10 days after administration (0.3±0.3% PEG vs. 1.7±0.5% unmodified). PEGylation did increase NAB levels 2-fold. These results provide some insight about the degree of T and B cell mediated immunity necessary for protection against Ebola virus and suggest that modification of the virus capsid can influence the type of immune response elicited by an Ad5-based vaccine.
Adverse hospital outcomes associated with the choice of empiric antibiotics in Klebsiella pneumoniae pneumonia: a retrospective observational study.

INTRODUCTION In Malaysia, Klebsiella pneumoniae ranks high as a cause of adult pneumonia requiring hospitalisation. PATIENTS AND METHODS With concern over its rising microbial resistance, we explored the association of empiric antibiotics choices with the hospital outcomes of patients treated for microbial proven K. pneumoniae pneumonia in an urban-based teaching hospital. RESULTS In 313 eligible cases reviewed retrospectively, hospital mortality and requirement for ventilation were 14.3% and 10.8% respectively. Empiric regimes that had in vitro resistance to at least one empiric antibiotic (n = 90) were associated with higher hospital mortality (23.3% vs. 10.8%, P = 0.004) with risk increased by about two-fold [Odds ratio (OR), 2.5; 95% confidence interval (CI), 1.3 to 4.8]. Regimes (n = 84) other than the commonly recommended "standard" regimes (a beta-lactam stable antibiotic with or without a acrolide) were associated with higher ventilation rates (16.7% vs. 8.8%, P = 0.047) with similar increased risk [OR, 2.0; 95% CI, 1.0 to 4.3]. CONCLUSIONS Our findings reiterate the clinical relevance of in vitro microbial resistance in adult K. pneumoniae pneumonia and support empiric regimes that contain beta-lactam stable antibiotics.