Miracle-dz/UniFAR-FTUs huggingface dataset:
A quantitative proteomic analysis of soluble bronchoalveolar fluid proteins from patients with sarcoidosis and chronic beryllium disease.

BACKGROUND Sarcoidosis and chronic beryllium disease (CBD) are granulomatous disorders which can lead to development of chronic inflammation and fibrosis. These diseases have several similarities from their clinical aspects. The aim of this study was to compare the protein profile at the site of active inflammation i.e. the lungs of patients with sarcoidosis and CBD. METHODS Bronchoalveolar lavage (BAL) proteins from patients having sarcoidosis or CBD were studied using two dimensional gel based proteomics. In this study, we used Difference Gel Electrophoresis (DIGE) proteomics approach to analyse the protein expression profiles from sarcoidosis patients (n=4), CBD (n=4) and healthy controls (n = 5). Subsequently, differentially expressed proteins were identified by using mass spectrometry. RESULTS We found 37 protein-spots with statistically different expression levels, and identified 14 of these proteins. The protein expression levels of peroxiredoxin 5, heat shock protein 70, complement C3, annexin A2 and transthyretin were significantly different in sarcoidosis versus control group. The proteins; hemopexin, beta2-microglobulin, alpha-1 antitrypsin, cystatin B, IgG kappa chain, apolipoprotein A1, and albumin were significantly different between CBD versus control group. When comparing CBD versus sarcoidosis, we found superoxide dismutase and hemoglobin upregulated in the CBD group. CONCLUSION By using quantitative proteomics, we were able to find proteins with different expression levels in both diseases.
Isolation, partial characterization, and mode of action of Acidocin J1132, a two-component bacteriocin produced by Lactobacillus acidophilus JCM 1132

Lactobacillus acidophilus JCM 1132 produces a heat-stable, two-component bacteriocin designated acidocin J1132 that has a narrow inhibitory spectrum. Maximum production of acidocin J1132 in MRS broth was detected at pH 5.0. Acidocin J1132 was purified by ammonium sulfate precipitation and sequential cation exchange and reversed-phase chromatographies. Acidocin J1132 activity was associated with two components, termed alpha and beta. On the basis of N-terminal amino acid sequencing and the molecular masses of the alpha and beta components, it is interpreted that the compounds differ by an additional glycine residue in the beta component. Both alpha and beta had inhibitory activity, and an increase in activity by the complementary action of the two components was observed. Acidocin J1132 is bactericidal and dissipates the membrane potential and the pH gradient in sensitive cells, which affect such proton motive force-dependent processes as amino acid transport. Acidocin J1132 also caused efflux of preaccumulated amino acid taken up via a unidirectional ATP-driven transport system. Secondary structure prediction revealed the presence of an amphiphilic alpha-helix region that could form hydrophilic pores. These results suggest that acidocin J1132 is a pore-forming bacteriocin that creates cell membrane channels through the "barrel-stave" mechanism.
Wealth Accumulation, On-the-Job Search and Inequality

To study equilibrium interactions between wealth accumulation and labor market search, this paper constructs a model where individuals can accumulate non-contingent assets under a borrowing limit, all workers can search for jobs, and search is directed. On-the-job search generates a wage ladder, which affects inequalities in earnings, wealth and consumption. Employed workers have incentive to save as a precaution for exogenous separation into unemployment. In the reverse direction, wealth and earnings affect search decisions by changing the optimal tradeoff between the wage and the matching probability. The calibrated model reveals that wealth significantly reduces a worker's transition rates from unemployment to employment and from one job to another. Moreover, search frictions increase wealth inequality significantly by increasing the mass of wealthy individuals and lengthening the right tail of the wealth distribution. However, the effect of wealth on job search widens frictional wage dispersion by only a small amount. In addition, on-the-job search is important for frictional wage dispersion.
Monetary Independence in a Financially Integrated World: What Do Measures of Interest Rate Co-Movement Tell Us?

Does global financial integration reduce the independence of monetary policy or its effectiveness? Do flexible exchange rates offer sufficient insulation from foreign monetary and financial developments? To provide an answer to these questions, this paper summarises the outcome of ongoing research conducted at the BIS on the measurement of co-movements in short- and long-term interest rates across countries. The sensitivities of domestic short-term interest rates to their foreign counterparts are found to be increasing in financial openness and exchange rate stability, as predicted by Mundell’s trilemma hypothesis. By contrast, long-term yield sensitivities are increasing in financial openness, but their relationship with exchange rate stability is non-monotonic. Excluding pegged exchange rates or very stable currencies, which display a high degree of sensitivity, the relationship for other currencies is negative: that is, a more volatile exchange rate is associated with larger long-term interest rate spillovers from core countries. Estimates of domestic short-to long-run interest rate pass-through also show that greater exchange rate flexibility does not necessarily translate into stronger control of the long end of the yield curve. Full Publication: Expanding the Boundaries of Monetary Policy in Asia and the Pacific
Detection of Architectural Distortion in Prior Mammograms

We present methods for the detection of sites of architectural distortion in prior mammograms of interval-cancer cases. We hypothesize that screening mammograms obtained prior to the detection of cancer could contain subtle signs of early stages of breast cancer, in particular, architectural distortion. The methods are based upon Gabor filters, phase portrait analysis, a novel method for the analysis of the angular spread of power, fractal analysis, Laws' texture energy measures derived from geometrically transformed regions of interest (ROIs), and Haralick's texture features. With Gabor filters and phase portrait analysis, 4224 ROIs were automatically obtained from 106 prior mammograms of 56 interval-cancer cases, including 301 true-positive ROIs related to architectural distortion, and from 52 mammograms of 13 normal cases. For each ROI, the fractal dimension, the entropy of the angular spread of power, 10 Laws' measures, and Haralick's 14 features were computed. The areas under the receiver operating characteristic curves obtained using the features selected by stepwise logistic regression and the leave-one-ROI-out method are 0.76 with the Bayesian classifier, 0.75 with Fisher linear discriminant analysis, and 0.78 with a single-layer feed-forward neural network. Free-response receiver operating characteristics indicated sensitivities of 0.80 and 0.90 at 5.8 and 8.1 false positives per image, respectively, with the Bayesian classifier and the leave-one-image-out method.
Evaluation of Low Density Spine Software for the Assessment of Bone Mineral Density in Children

Pediatric dual‐energy X‐ray absorptiometry spine scans often cannot be analyzed with standard software due to a failure to identify the bone edges of low density vertebrae. Low density spine (LDS) software improves bone detection compared with standard software. The objective of this study was to compare bone mineral density (BMD) measurements obtained with the standard and LDS software in 27 healthy nonobese, 32 obese, and 41 chronically ill children, ages 2–18 years. Lumbar spine (L1–L4) BMD, measured by standard analysis, ranged from 0.531–1.244 gm/cm2. Reanalysis with the LDS software resulted in a systematic increase (mean ± SD) in estimated bone area of 17.0 ± 5.0%, an increase in bone mineral content of 6.1 ± 6.3%, and a mean decrease in BMD of 8.7 ± 1.7% (all p < 0.001). This resulted in a mean decrease in BMD Z score of 0.7 ± 0.2. Linear regression models, predicting standard BMD from LDS BMD, were fit for the three subject groups (R2 = 0.993–0.995). Small differences in slopes were detected across groups (p = 0.07); LDS BMD predicted higher standard BMD in obese subjects. In conclusion, LDS analysis resulted in a clinically significant decrease in measured BMD. The association between analysis methods was exceptionally high (R2 > 0.99), indicating that LDS BMD accurately predicts standard BMD. Although LDS BMD in obese subjects predicts higher standard BMD results than in nonobese subjects, the small difference is of questionable clinical significance. LDS software is a useful tool for the assessment of BMD in children.
Adaptive composite disturbance observer based control for PMSM subject to multiple disturbances

This paper aims to investigate an adaptive composite disturbance observer based control (ACDOBC) approach for permanent magnet synchronous motors (PMSMs) subject to multiple disturbances, especially constant or slowly-varying disturbances and periodic disturbances. Different from most of the existing disturbance and uncertainty estimation and attenuation (DUEA) methods, a new adaptive mechanism is proposed in this paper for disturbance compensation. An adaptive composite disturbance observer (ACDO) is first employed to estimate the disturbances of multiple sources, even the periodic disturbances with unknown frequencies, a controller which contains a feedforward compensation item and a proportional feedback item is then employed to attenuate the disturbances. Simulation studies of the proposed method demonstrate the elegant tracking performance in the presence of multiple disturbances.
Estrogen is a critical determinant that specifies the duration of the window of uterine receptivity for implantation

Many underlying causes of human infertility have been overcome by using in vitro fertilization (IVF) and embryo transfer (ET) techniques. Nevertheless, implantation rates in IVF programs remain low despite the transfer of apparently healthy embryos. This suggests that there are problems with the differentiation of the uterus to the receptive state in response to the ovarian hormones estrogen and progesterone. The molecular basis of this receptive state when the uterine environment is conducive to blastocyst acceptance and implantation remains poorly understood. Normally, the “window” of uterine receptivity lasts for a limited time. Using ETs and the progesterone-treated delayed-implantation model in mice, we demonstrate here that levels of estrogen within a very narrow range determine the duration of the window of uterine receptivity. Although estrogen at different physiological concentrations can initiate implantation, we find that the window of uterine receptivity remains open for an extended period at lower estrogen levels but rapidly closes at higher levels. The uterine refractoriness that follows the receptive state at high estrogen levels is accompanied by aberrant uterine expression of implantation-related genes. These results suggest that careful regulation of estrogen levels is one of the important factors for improvement of female fertility in IVF/ET programs.
The Facilitator-Supported Online Method: Using Problem-Based Remote Learning Techniques for Engineering Students

This paper describes the Facilitator-Supported Online (FSO) pedagogical method and its use to deliver advanced engineering concepts to undergraduate students. To bridge large knowledge gaps in advanced topics, this method comprises strict teacher supervision and Problem-Based Learning techniques, where the students are guided by the teacher in a way that they construct the knowledge required to solve the problem (constructivist learning). It is specifically designed to cover the high-demanding Generation-Y requirements, with the contents being delivered mostly remotely using common commercial software for online collaboration, relying heavily on Web 2.0 paradigms. Three successful course implementations using this approach are described in detail: the first implementation at the Pontifical Catholic University of Campinas (PUC-Campinas - Brazil) in 2007, and two experiences held at the University of Campinas (UNICAMP - Brazil) during 2009. Initial results of an ongoing experience are also presented: a research support, were three undergraduate UNICAMP Computer Engineering students, supported through FSO by the authors and global companies (all located on different places, from the United States to southern Brazil) are developing a new method to analyze and optimize resources for "Smart Buildings", in a highly demanding hands-on task. Advantages and disadvantages of this approach are also addressed.
Chronic clenbuterol treatment compromises force production without directly altering skeletal muscle contractile machinery

Clenbuterol is an adrenergic receptor agonist known to induce skeletal muscle hypertrophy and a shift towards faster muscle fibres, when administered chronically at high doses. However, when normalized to the muscle surface area, the increase in muscle force is no longer increased and even depressed. We show that muscle contraction and relaxation force kinetics were significantly reduced particularly in fast contracting muscles. We show that action potential‐elicited Ca2+ transients were depressed in the fast contracting muscle. Our data show that chronic clenbuterol treatment reduces contractile efficiency, with altered contraction and relaxation kinetics, but without directly altering the contractile machinery. Lower Ca2+ release during contraction could partially explain these deleterious effects.
Isolation of circulating tumor cells using a microvortex-generating herringbone-chip

Rare circulating tumor cells (CTCs) present in the bloodstream of patients with cancer provide a potentially accessible source for detection, characterization, and monitoring of nonhematological cancers. We previously demonstrated the effectiveness of a microfluidic device, the CTC-Chip, in capturing these epithelial cell adhesion molecule (EpCAM)-expressing cells using antibody-coated microposts. Here, we describe a high-throughput microfluidic mixing device, the herringbone-chip, or “HB-Chip,” which provides an enhanced platform for CTC isolation. The HB-Chip design applies passive mixing of blood cells through the generation of microvortices to significantly increase the number of interactions between target CTCs and the antibody-coated chip surface. Efficient cell capture was validated using defined numbers of cancer cells spiked into control blood, and clinical utility was demonstrated in specimens from patients with prostate cancer. CTCs were detected in 14 of 15 (93%) patients with metastatic disease (median = 63 CTCs/mL, mean = 386 ± 238 CTCs/mL), and the tumor-specific TMPRSS2-ERG translocation was readily identified following RNA isolation and RT-PCR analysis. The use of transparent materials allowed for imaging of the captured CTCs using standard clinical histopathological stains, in addition to immunofluorescence-conjugated antibodies. In a subset of patient samples, the low shear design of the HB-Chip revealed microclusters of CTCs, previously unappreciated tumor cell aggregates that may contribute to the hematogenous dissemination of cancer.
Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of H2A.Z acetylation and H3K36 trimethylation from embryonic genome activation

Early embryonic development is characterized by dramatic changes in cell potency and chromatin organization. The role of histone variants in the context of chromatin remodeling during embryogenesis remains under investigated. In particular, the nuclear distribution of the histone variant H2A.Z and its modifications have not been examined. Here we investigated the dynamics of acetylation of H2A.Z and two other active chromatin marks, H3K9ac and H3K36me3, throughout murine and bovine pre-implantation development. We show that H2A.Z distribution is dynamic during the earliest stages of mouse development, with protein levels significantly varying across stages and lowest at the 2-cell stage. When present, H2A.Z localizes preferentially to euchromatin at all stages analyzed. H2A.Z is acetylated in pre-implantation blastomeres and is preferentially localized to euchromatin, in line with the known role of H2A.Zac in transcriptional activation. Interestingly, however, H2A.Zac is undetectable in mouse embryos at the 2-cell stage, the time of major embryonic genome activation (EGA). Similarly, H3K36me3 is present exclusively in the maternal chromatin immediately after fertilization but becomes undetectable in interphase nuclei at the 2-cell stage, suggesting uncoupling of these active marks with global embryonic transcription activation. In bovine embryos, which undergo EGA at the 8-cell stage, H2A.Zac can be detected in zygotes, 4-, 8- and 16-cell stage embryos as well as in blastocysts, indicating that the dynamics of H2A.Zac is not conserved in mammals. In contrast, H3K36me3 displays mostly undetectable and heterogeneous localization pattern throughout bovine pre-implantation development. Thus, our results suggest that 'canonical' active chromatin marks exhibit a dynamic behavior in embryonic nuclei, which is both stage- and species-specific. We hypothesize that chromatin of early embryonic nuclei is subject to fine-tuning through differential acquisition of histone marks, allowing for proper chromatin remodeling and developmental progression in a species-specific fashion.
Developing a classification system for haemoglobin management in patients with end-stage renal disease on haemodialysis: a secondary data analysis

Background Ongoing discussion on anaemia management and target haemoglobin (Hb) levels in patients on haemodialysis with erythropoietin treatment require a systematic approach in evaluating current practice. Aim of the present study was to develop a new classification system to easily monitor Hb trajectories and categorise patients on haemodialysis. Methods Routine data from five dialysis centres in the USA collected between 2010 and 2016. Data were anonymised and only those from patients with fortnightly Hb values were included in the analysis. Entries on blood parameters and medication were standardised to achieve overall comparability. Data from each patient was grouped in periods of 120 days. Hb values above or below the target level of 10–12 g/dL were counted for each period. Periods were then assigned to Hb-classes according to the number of Hb values out of range per period: Hb-class I with 0–2, Hb-class II for 3–5 and Hb-class III for ≥6 values out of range. Results Records from 3349 patients with fortnightly Hb values, information on haemodialysis data, laboratory parameters correlated to red blood cells and data on medication with erythropoiesis-stimulating agents (ESAs) were available. Patients were 64.4±15.9 years old; 55.0% were men. Statistical analysis revealed significant differences between Hb-classes in all of the examined parameters, except erythrocytes mean corpuscular volume and C reactive protein above the threshold, with more critical values in higher Hb-classes. The usage of ESAs showed a mean difference between Hb-class III and Hb-class I of 6.4 units/day and kilogram body weight in a 120-day period. Conclusion Our classification system allows an easily achievable overview of the patients’ responsiveness and performance of Hb management. Integrated into a disease management programme or continuous quality improvement, the classification delivers an instant appraisal without complex statistical or mathematical processing.
Argon laser photocoagulation of port wine stain hemangiomas

A total of 66 patients with port wine stains is reported. All of these were tested and 46 patients treated (80 treatments). Good to excellent results (significant lightening of color and/or smoother texture of skin) was achieved in 74% of tests (0 scar) and in 82% of treatments (4.3% scar). Treatment results correlate well with test spots but vary somewhat as the lesions are not homogenous and skin textures vary. The lowest energy density commensurate with successful treatment should be used to reduce the incidence of scarring. Future methods of manipulating the PWS may make it possible to achieve better results with less scarring. Teenagers fared well in this series, while the problem of successful treatment in the young child remains unsolved.
Novel method using 3-dimensional segmentation in spectral domain-optical coherence tomography imaging in the chick reveals defocus-induced regional and time-sensitive asymmetries in the choroidal thickness

Abstract Studies into the mechanisms underlying the active emmetropization process by which neonatal refractive errors are corrected, have described rapid, compensatory changes in the thickness of the choroidal layer in response to imposed optical defocus. While high frequency A-scan ultrasonography, as traditionally used to characterize such changes, offers good resolution of central (on-axis) changes, evidence of local retinal control mechanisms make it imperative that more peripheral, off-axis changes also be tracked. In this study, we used in vivo high resolution spectral domain-optical coherence tomography (SD-OCT) imaging in combination with the Iowa Reference Algorithms for 3-dimensional segmentation, to more fully characterize these changes, both spatially and temporally, in young, 7-day old chicks (n = 15), which were fitted with monocular +15 D defocusing lenses to induce choroidal thickening. With these tools, we were also able to localize the retinal area centralis, which was used as a landmark along with the ocular pectin in standardizing the location of scans and aligning them for subsequent analyses of choroidal thickness (CT) changes across time and between eyes. Values were derived for each of four quadrants, centered on the area centralis, and global CT values were also derived for all eyes. Data were compared with on-axis changes measured using ultrasonography. There were significant on-axis choroidal thickening that was detected after just one day of lens wear (∼190 µm), and regional (quadrant-related) differences in choroidal responses were also found, as well as global thickness changes 1 day after treatment. The ratio of global to on-axis choroidal thicknesses, used as an index of regional variability in responses, was also found to change significantly, reflecting the significant central changes. In summary, we demonstrated in vivo high resolution SD-OCT imaging, used in combination with segmentation algorithms, to be a viable and informative approach for characterizing regional (spatial), time-sensitive changes in CT in small animals such as the chick.
Dreher High School and the University of South Carolina College of Education: A Long-Standing PDS Relationship That Works.

Dating back to 1990, the PDS relationship between the University of South Carolina and Dreher High School in Columbia, South Carolina, has had a persistent dedication to a partnership that not only benefits pre-service teacher candidates but also empowers early career teachers to actively engage in their school. This article describes how this long-standing PDS partnership has created a framework for preparing teacher candidates to work with diverse populations of students, improving ideas of selfefficacy among early career teachers, and professional development driven by teacher-identified needs all for the central purpose of enhancing student achievement. NAPDS Essentials Addressed: All of the ‘‘Nine Essentials’’ are addressed in this article.