Miracle-dz/UniFAR-FTUs huggingface dataset:
The Pu.1 Locus Is Differentially Regulated at the Level of Chromatin Structure and Noncoding Transcription by Alternate Mechanisms at Distinct Developmental Stages of Hematopoiesis

ABSTRACT The Ets family transcription factor PU.1 is crucial for the regulation of hematopoietic development. Pu.1 is activated in hematopoietic stem cells and is expressed in mast cells, B cells, granulocytes, and macrophages but is switched off in T cells. Many of the transcription factors regulating Pu.1 have been identified, but little is known about how they organize Pu.1 chromatin in development. We analyzed the Pu.1 promoter and the upstream regulatory element (URE) using in vivo footprinting and chromatin immunoprecipitation assays. In B cells, Pu.1 was bound by a set of transcription factors different from that in myeloid cells and adopted alternative chromatin architectures. In T cells, Pu.1 chromatin at the URE was open and the same transcription factor binding sites were occupied as in B cells. The transcription factor RUNX1 was bound to the URE in precursor cells, but binding was down-regulated in maturing cells. In PU.1 knockout precursor cells, the Ets factor Fli-1 compensated for the lack of PU.1, and both proteins could occupy a subset of Pu.1 cis elements in PU.1-expressing cells. In addition, we identified novel URE-derived noncoding transcripts subject to tissue-specific regulation. Our results provide important insights into how overlapping, but different, sets of transcription factors program tissue-specific chromatin structures in the hematopoietic system.
Polarimetric invariants for detection by forward-looking ground penetrating radar

The usefulness of ground penetrating radar to detect landmines has been limited because of low signal-to-clutter ratios which result in high false alarm rates. We describe a method using polarimetric radar to measure the polarizability angle, the relative phase, and the target magnitude. These three independent quantities are directly related to target shape and dimensions and are invariant to rotation about the sensor-to-target axis. Data collected on an automobile disk brake rotor over a frequency range of 1.35–2.14 GHz showed that the polarizability angle and the relative phase varied less with frequency when the rotor was buried than when laying on the surface. The target magnitude showed similarities to interference patterns from scattering centers at the edges of a cylinder.
Measuring social inclusion--a key outcome in global mental health.

BACKGROUND Social inclusion is increasingly recognized as a key outcome for evaluating global mental health programmes and interventions. Whereas social inclusion as an outcome is not a new concept in the field of mental health, its measurement has been hampered by varying definitions, concepts and instruments. To move the field forward, this paper reviews the currently available instruments which measure social inclusion and are reported in the literature, realizing that no single measure will be appropriate for all studies or contexts. METHODS A systematic literature search of English language peer-reviewed articles published through February 2013 was undertaken to identify scales specifically developed to measure social inclusion or social/community integration among populations with mental disorders. RESULTS Five instruments were identified through the search criteria. The scales are discussed in terms of their theoretical underpinnings, domains and/or key items and their potential for use in global settings. Whereas numerous reviewed abstracts discussed mental health and social inclusion or social integration, very few were concerned with direct measurement of the construct. All identified scales were developed in high-income countries with limited attention paid to how the scale could be adapted for cross-cultural use. CONCLUSIONS Social inclusion is increasingly highlighted as a key outcome for global mental health policies and programmes, yet its measurement is underdeveloped. There is need for a global cross-cultural measure that has been developed and tested in diverse settings. However, until that need is met, some of the scales presented here may be amenable to adaptation.
Semi-Mechanistic Modeling of an Osmotic Dehydration Process

This article presents a semi-mechanistic model (a hybrid of the classic and fuzzy models) of an osmotic dehydration process of pineapple. The fuzzy model (Takagi-Sugeno) represents a kinetic parameter of the physical process and it is developed through fuzzy clasification of data (Gustaffson-Kessel algorithm). The fuzzy model is then incorporated in the mass conservation equation (classic model) aiming at the numerical prediction of the process. Experiments and validations are presented
Functional and Transcriptional Characterization of Human Embryonic Stem Cell-Derived Endothelial Cells for Treatment of Myocardial Infarction

Background Differentiation of human embryonic stem cells into endothelial cells (hESC-ECs) has the potential to provide an unlimited source of cells for novel transplantation therapies of ischemic diseases by supporting angiogenesis and vasculogenesis. However, the endothelial differentiation efficiency of the conventional embryoid body (EB) method is low while the 2-dimensional method of co-culturing with mouse embryonic fibroblasts (MEFs) require animal product, both of which can limit the future clinical application of hESC-ECs. Moreover, to fully understand the beneficial effects of stem cell therapy, investigators must be able to track the functional biology and physiology of transplanted cells in living subjects over time. Methodology In this study, we developed an extracellular matrix (ECM) culture system for increasing endothelial differentiation and free from contaminating animal cells. We investigated the transcriptional changes that occur during endothelial differentiation of hESCs using whole genome microarray, and compared to human umbilical vein endothelial cells (HUVECs). We also showed functional vascular formation by hESC-ECs in a mouse dorsal window model. Moreover, our study is the first so far to transplant hESC-ECs in a myocardial infarction model and monitor cell fate using molecular imaging methods. Conclusion Taken together, we report a more efficient method for derivation of hESC-ECs that express appropriate patterns of endothelial genes, form functional vessels in vivo, and improve cardiac function. These studies suggest that hESC-ECs may provide a novel therapy for ischemic heart disease in the future.
Amantadine Revisited: An Open Trial of Amantadinesulfate Treatment in Chronically Depressed Patients with Borna Disease Virus Infection

Amantadinesulfate is a well known substance which has proven useful in the treatment and prophylaxis of viral infections, in treating symptoms of Parkinson's disease, cocaine dependence, and apathy in multiple sclerosis. It has also been reported as having mild antidepressive effects not sufficient to warrant its use as an antidepressant. Striking antidepressive effects in some patients have been attributed to its antiviral activity against human Borna disease virus (BDV) infection which is frequently seen in patients with depressive episodes. In this 8 to 12 week open study of oral amantadine in 30 depressed patients with various states of BDV infection we found a significant antidepressive response in 19 of 30. Peripheral BDV antigen indicating acute infection was cleared in both responders and non-responders, but only in responders peripheral infection was significantly reduced.
Paclitaxel, cisplatin and gemcitabine in treatment of carcinomas of unknown primary site, a phase II study

Abstract Background. The present study was conducted to evaluate the efficacy and toxicity of a combination of paclitaxel, cisplatin and gemcitabine in patients with carcinoma of unknown primary site (CUP). Patients and methods. Patients with CUP, ECOG performance status 0–1 and age between 18 and 65 years old were treated with paclitaxel 175 mg/m2 day 1, cisplatin 75 mg/m2 day 1 and gemcitabine 1000 mg/m2 day 1 and 8 in a three-week schedule. Results. Ninety-eight patients were enrolled between 1998 and 2008. Ninety-one patients had target lesions according to the RECIST guidelines. The overall response rate was 42.9% (39 patients), including five complete responses (5.5%) and 34 partial responses (37.4%). The median survival time was 10.7 months, and the survival rates at one and two years were 42% and 14%, respectively. The most frequent grade 3 or more adverse events were neutropenia and thrombocytopenia. There were 3 treatment-related deaths. Conclusions. Combination of paclitaxel, cisplatin and gemcitabine is an active regimen in patients with CUP with response and survival rates at least similar to other platinum- and taxane-containing regimens. The treatment was well tolerated by most patients although neutropenia and thrombocytopenia were relatively common. The present regimen represents an attractive regimen in younger CUP patients with a good performance status.
Chemistry and liquid chromatography methods for the analyses of primary oxidation products of triacylglycerols

Abstract Triacylglycerols (TAGs) are one of the major components of the cells in higher biological systems, which can act as an energy reservoir in the living cells. The unsaturated fatty acid moiety is the key site of oxidation and formation of oxidation compounds. The TAG free radical generates several primary oxidation compounds. These include hydroperoxides, hydroxides, epidioxides, hydroperoxy epidioxides, hydroxyl epidioxides, and epoxides. The presence of these oxidized TAGs in the cell increases the chances of several detrimental processes. For this purpose, several liquid chromatography (LC) methods were reported in their analyses. This review is therefore focused on the chemistry, oxidation, extraction, and the LC methods reported in the analyses of oxidized TAGs. The studies on thin-layer chromatography were mostly focused on the total oxidized TAGs separation and employ hexane as major solvent. High-performance LC (HPLC) methods were discussed in details along with their merits and demerits. It was found that most of the HPLC methods employed isocratic elution with methanol and acetonitrile as major solvents with an ultraviolet detector. The coupling of HPLC with mass spectrometry (MS) highly increases the efficiency of analysis as well as enables reliable structural elucidation. The use of MS was found to be helpful in studying the oxidation chemistry of TAGs and needs to be extended to the complex biological systems.
Mixed-integer method for optimal UPFC placement based on line flow-based equations

Flexible AC transmission systems (FACTS) is an evolving technology, which can be used to improve power system utilisation. Determining the type, location, device number, and device compensation are critical to successfully utilizing FACTS controllers, and this paper presents a method of Unified Power Flow Controller (UPFC) placement, which is capable of simultaneously determining number of UPFCs, their location(s), and minimum compensation to maximise the system loadability. A mixed integer linear programming approach is considered, and the method utilises line flow based equations to formulate the problem. The method is successfully demonstrated on the IEEE 9-bus and IEEE 30-bus test systems.
Enterprise systems, business process management and UK-management accounting practices: Cross-sectional case studies

Purpose This paper aims to address the extant and arguable role of enterprise systems (ES) in relation to management accounting practices (MAPs) through an inclusion relative neglect account of business process management (BPM). This is also extended to draw out an analytical framework to advance our understanding of how BPM mediate ES-MAPs interplay. Design/methodology/approach A cross-sectional case study was adopted as a research strategy with which to collect data about the ES-BPM-MAPs interplay as a unit of analysis. The latter, in the first stage, was examined across (89) mini-case studies operating in the UK context through reports and documentations collected from cases’ websites, vendors and consultants of information systems. Drawn insights from cross-sectional analysis and contributions made by prior studies are blended together to inform the second stage that outlines an analytical framework for ES-BPM-MAPs interplay. Findings Different ES are mobilised to address different orientations of BPMs and being used for different managerial functions and purposes. Different patterns of ES-BPM-MAPs interplay are identified across (89) UK-case studies and the BPM is a fulcrum understanding. These patterns are centred around three key BPM including customer, logistics and control processes and all oriented by a continuum of an organisation intention focus on control, understanding and strategising. Both processes and orientations explain ES development and MAPs evolution processes. Standardisation, integration and intelligence are key characteristics sought through ES mobilisations. By complementary, information provision, analytics and simulation are three sophisticated ways of using MA information facilitated by ES characteristics. Research limitations/implications Dynamic processes of MAPs change over time and are beyond the reach of this study. Such approach requires full access to case studies. BPM is fulcrum understanding of MAPs change and/or stability in relation to ES implementation including other components. Practical implications Findings and analytical framework could be used as a base for establishing the best approach in adopting ES to fully exploit the potential of future ES applications as well as to avoid organisations pitfalls of implementations. Organisations are advised to understand their existing business processes, characteristics of MA information would be achieved first upon which decision of ES components selection and implementation could be outlined. Originality/value The indirect interplay between ES and MAPs through business processes is rarely examined. By the inclusion of BPM and using cross-sectional case studies, this research contributes to the existing shortcomings of ES-MAPs interplay by broadening the picture and proposing an analytical framework. The latter advances our understanding by focusing on attributes of ES-BPM-MAPs upon which informal changes in-the use of MAPs are recognised.
3,3′,5,5′-Tetra-tert-butyl-2′-hydroxy-[1,1′-biphenyl]-2-yl 4-methylbenzenesulfonate

In the title molecule, C37H48O4S, the benzene rings in the biphenyl fragment are inclined to each other at 61.1 (1)°. The hydroxy group is involved in a weak intramolecular O—H⋯Osulfonate hydrogen bond. One tert-butyl group is disodered over two orientations in a 0.682 (17):0.318 (17) ratio. In the crystal, weak C—H⋯O hydrogen bonds link the molecules into columns in direction [100].
Treatment outcome of women with a single ovary undergoing in vitro fertilisation cycles.

INTRODUCTION Women with a single ovary present a unique problem in assisted reproductive techniques. The aim of our study was to compare the ovarian response and pregnancy rates of women with one ovary and those with two ovaries in assisted reproduction. METHODS A total of 18 consecutive women with a single ovary (n is 22 cycles) were identified. The control group included 44 women with two ovaries and mechanical infertility, who were selected as frequency-matched samples (2:1) to meet the distribution of age at treatment and race in the single ovary group. All patients underwent controlled ovarian hyperstimulation treatment via the long down-regulation protocol using a gonadotropin-releasing hormone agonist. Standard procedures were carried out for gamete-embryo handling, and embryo transfer was performed using a soft catheter on day two in all cases. The luteal phase was supported by progesterone or Pregnyl after oocyte pick-up. RESULTS The duration of stimulation (11.3 +/- 1.7 versus 10.1 +/- 1.4 days) and the total follicle stimulating hormone (FSH) consumption (3906.8 +/- 1860.6 mIU/ml versus 2900.0 +/- 1440.0 mIU/ml) were significantly higher, and the mean number of oocytes (10.8 +/- 4.5 versus 16.8 +/- 10.9) and metaphase II oocytes collected (9.5 +/- 4.5 versus 13.3 +/- 7.7) were significantly lower in the single ovary group (p is less than 0.05). The clinical pregnancy rates (31.8 percent versus 43.2 percent) were comparable between the two groups. CONCLUSION Although women with a single ovary required significantly higher doses of FSH and a longer duration of stimulation, as well as produced less oocytes, their clinical pregnancy rates were comparable to those of women with two ovaries in assisted reproduction.
Activation Domain-Specific and General Transcription Stimulation by Native Histone Acetyltransferase Complexes

ABSTRACT Recent progress in identifying the catalytic subunits of histone acetyltransferase (HAT) complexes has implicated histone acetylation in the regulation of transcription. Here, we have analyzed the function of two native yeast HAT complexes, SAGA (Spt-Ada-Gcn5 Acetyltransferase) and NuA4 (nucleosome acetyltransferase of H4), in activating transcription from preassembled nucleosomal array templates in vitro. Each complex was tested for the ability to enhance transcription driven by GAL4 derivatives containing either acidic, glutamine-rich, or proline-rich activation domains. On nucleosomal array templates, the SAGA complex selectively stimulates transcription driven by the VP16 acidic activation domain in an acetyl coenzyme A-dependent manner. In contrast, the NuA4 complex facilitates transcription mediated by any of the activation domains tested if allowed to preacetylate the nucleosomal template, indicating a general stimulatory effect of histone H4 acetylation. However, when the extent of acetylation by NuA4 is limited, the complex also preferentially stimulates VP16-driven transcription. SAGA and NuA4 interact directly with the VP16 activation domain but not with a glutamine-rich or proline-rich activation domain. These data suggest that recruitment of the SAGA and NuA4 HAT complexes by the VP16 activation domain contributes to HAT-dependent activation. In addition, extensive H4/H2B acetylation by NuA4 leads to a general activation of transcription, which is independent of activator-NuA4 interactions.
2D and 3D radial multi‐gradient‐echo DCE MRI in murine tumor models with dynamic R*2‐corrected R1 mapping

Dynamic contrast‐enhanced MRI is extensively studied to define and evaluate biomarkers for early assessment of vasculature‐targeting therapies. In this study, two‐dimensional and three‐dimensional radial multi‐gradient‐echo techniques for dynamic R*2‐corrected R1 mapping based on the spoiled gradient recalled signal equation were implemented and validated at 4.7 T. The techniques were evaluated on phantoms and on a respiratory motion animated tumor model. R1 measurements were validated with respect to a standard inversion‐recovery spin‐echo sequence in a four‐compartment phantom covering a range of relaxation rates typically found in tumor tissue. In the range of [0.4, 3] sec−1, R1 differences were less than 10% for both two‐dimensional and three‐dimensional experiments. A dynamic contrast‐enhanced MRI pilot study was performed on a colorectal tumor model subcutaneously implanted in mice at the abdominal level. Low motion sensitivity of radial acquisition allowed image recording without respiratory triggering. Three‐dimensional Ktrans maps and significantly different mean Ktrans values were obtained for two contrast agents with different molecular weights. The radial multi‐gradient‐echo approach should be most useful for preclinical experimental conditions where the tissue of interest experiences physiologic motion, like spontaneous extracerebral tumors developed by transgenic mice, and where dynamic contrast‐enhanced MRI is performed with high‐relaxivity contrast agents. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Optimal Macroprudential Policies and House Prices in Korea

ABSTRACT This article investigates the impacts of the macroprudential policy of limitation on credit growth in housing market on Korean economy to find empirical and theoretical implications. Empirical results based on VAR models show that macroprudential policies like LTV and DTI in Korea have significant and persistent effect on real household credit and real house price. This article further addresses implications of optimal macroprudential and monetary policy in Korea by employing a standard DSGE model. The results suggest that the time-varying macroprudential policy responding to the borrower’s debt to income ratio is most effective in stabilizing household debt among the macroprudential policy rules considered, but produces a moderate downturn of the economy.
Anti‐tumor activity and tumor vessel normalization by the vascular endothelial growth factor receptor tyrosine kinase inhibitor KRN951 in a rat peritoneal disseminated tumor model

We assessed the antitumor efficacy of KRN951, a novel tyrosine kinase inhibitor of vascular endothelial growth factor receptors, using a rat colon cancer RCN‐9 syngeneic model in which the tumor cells are transplanted into the peritoneal cavity of F344 rats. KRN951 treatments that commenced 4 days after tumor transplantation (day 4) significantly inhibited tumor‐induced angiogenesis, the formation of tumor nodules in the mesenteric windows, and the accumulation of malignant ascites. Moreover, KRN951 treatments initiated on day 14, by which time angiogenesis and malignant ascites have already been well established, resulted in the regression of newly formed tumor vasculatures with aberrant structures and also in the apparent loss of malignant ascites by the end of the study period. Quantitative analysis of the vessel architecture on mesenteric windows revealed that KRN951 not only regressed, but also normalized the tumor‐induced neovasculature. Continuous daily treatments with KRN951 significantly prolonged the survival of rats bearing both early stage and more advanced‐stage tumors, compared with the vehicle‐treated animals. The results of our current study thus show that KRN951 inhibits colon carcinoma progression in the peritoneal cavity by blocking tumor angiogenesis, ascites formation, and tumor spread, thereby prolonging survival. Moreover, these studies clearly demonstrate the therapeutic effects of KRN951 against established tumors in the peritoneal cavity, including the regression and normalization of the tumor neovasculature. Our findings therefore suggest that KRN951 has significant potential as a future therapeutic agent in the treatment of peritoneal cancers with ascites. (Cancer Sci 2008; 99: 623–630)
Looking for reference genes for real‐time quantitative PCR experiments in Rhodnius prolixus (Hemiptera: Reduviidae)

Quantitative real‐time PCR (qPCR) has become one of the most used techniques to measure gene expression. However, normalization of gene expression data against reference genes is essential, although these are usually used without any kind of validation. The expression of seven genes was compared in organs of Rhodnius prolixus under diverse conditions, using published software to test gene expression stability. Rp18S and elongation factor 1 (RpEF ‐1) were the most reliable genes for normalization in qPCR when gene expression in different organs was compared. Moreover, both genes were found to be the best references when transcript levels were compared in the posterior midgut of insects infected with Trypanosoma cruzi. Rp18S was also the best reference gene in the fat bodies of unfed and fed insects. By contrast, RpEF‐1 was found to be the best reference gene for comparison between posterior midguts, and RpMIP or RpActin should be used to compare gene expression in the ovaries. Although Rp18S is indicated here as the best reference in most cases, reports from the literature show that it is difficult to find an optimum reference gene. Nevertheless, validation of candidate genes to be taken as references is important when new experimental conditions are tested to avoid incorrect data interpretation.