Miracle-dz/UniFAR-FTUs huggingface dataset:
Hypermethylation in Histologically Distinct Classes of Breast Cancer

Purpose: A number of different genes are known to be inactivated by aberrant hypermethylation in breast cancer, but it is still unknown to what extent these epigenetic alterations differ according to specific breast cancer phenotypes. We sought to determine whether the extent of hypermethylation or defined profiles of gene hypermethylation are associated with biological characteristics of breast cancers. Experimental Design: We evaluated methylation status of 12 different genes in a series of 109 invasive breast tumors, representing the ductal, lobular, and mucinous histologic subtypes using methylation-specific PCR. Frequencies of methylation were compared across the recognized histologic classes, and multivariate techniques (latent class analysis, factor analysis, recursive partitioning, and hierarchical clustering) were used to seek patterns of methylation for individual genes that distinguish recognized histologic types of breast cancer or define breast cancer phenotypes on a molecular level. Results: All 109 cases studied have aberrant methylation of multiple genes (3 to 10 genes per case), demonstrating that gene hypermethylation is pervasive in breast cancer. Lobular cancers and mucinous cancers, which often have relatively low levels of chromosomal changes, have higher overall frequencies of hypermethylation than ductal cancers (49% in lobular and mucinous versus 40% in ductal), but there is a relatively unimodal distribution of methylation frequency for all three histologic types. Only one of the individual genes studied, BRCA1, has a variable frequency of methylation that is significantly dependent on histologic pattern of tumor growth, with a higher frequency of methylation in mucinous cancers than ductal or lobular cancers. Although some trends of histology-specific gene methylation were seen, methylation patterns could not definitively classify breast cancers according to histologic type. Conclusions: Although a more comprehensive hypermethylation profile could potentially be useful for breast cancer classification and understanding the biology of this disease, it appears that the hypermethylation patterns across various forms of breast cancer are less distinct than those between breast cancer and cancers of different tissue origins. Furthermore, the relatively unimodal distribution of methylation frequency for all three histologic types does not support there being a distinct CpG island methylator phenotype for breast cancer.
A Transcriptional Activator, Homologous to theBacillus subtilis PurR Repressor, Is Required for Expression of Purine Biosynthetic Genes in Lactococcus lactis

ABSTRACT A purR::pGh9:ISS1 mutant ofLactococcus lactis was obtained following transposon mutagenesis of strain MG1363 and selection for purine auxotrophs. After determination of the nucleotide sequence and deduction of thepurR reading frame, the PurR product was found to be highly similar to the purR-encoded repressor from Bacillus subtilis. The wild-type purR gene complemented the purine auxotrophy of a purR::ISS1mutant, and it was shown that thepurR::ISS1 mutation lowered the level of transcription from the purine-regulated L. lactis purDpromoter. In a parallel study on the regulation of purC andpurD expression in L. lactis (M. Kilstrup, S. G. Jessing, S. B. Wichmand-Jørgensen, M. Madsen, and D. Nilsson, J. Bacteriol. 180:3900–3906, 1998), we identified regions (PurBox sequences: AWWWCCGAACWWT) upstream of the promoters with a central G residue at exactly position −76 relative to the transcriptional start site. The PurBox sequences were found to be required for high-level promoter activity and purine regulation. We identified a PurBox sequence overlapping the −35 region of theL. lactis purR promoter and found, by studies of apurR-lacLM fusion plasmid, that purR is autoregulated. Because of the high degree of similarity of the PurR proteins from B. subtilis and L. lactis, we looked for PurBox sequences in the promoter regions of the PurR-regulated genes in B. subtilis and identified a perfectly matching PurBox sequence in the purA promoter region and slightly degenerate PurBox-like sequences in the promoter regions for the pur operon and the purR gene. Interestingly, the PurBox in the pur operon of B. subtilis is located almost identically, with respect to the promoter, to the PurBox sequences located in front of purCand purD in L. lactis. We present a hypothesis to explain how an ancestral PurR protein in B. subtiliscould have evolved from an activator of the pur operon into a repressor which regulates transcription initiation from the samepur promoter by using the same PurR binding site and a similar response toward its effectors.
Prevalence of Masked Hypertension and Its Association With Subclinical Cardiovascular Disease in African Americans: Results From the Jackson Heart Study

Background Studies consisting mostly of whites have shown that the prevalence of masked hypertension differs by prehypertension status. Using data from the Jackson Heart Study, an exclusively African American population‐based cohort, we evaluated the association of masked hypertension and prehypertension with left ventricular mass index and common carotid intima media thickness. Methods and Results At the baseline visit, clinic blood pressure (CBP) measurement and 24‐hour ambulatory blood pressure monitoring were performed. Masked hypertension was defined as mean systolic/diastolic CBP <140/90 mm Hg and mean daytime systolic/diastolic ambulatory blood pressure ≥135/85 mm Hg. Clinic hypertension was defined as mean systolic/diastolic CBP ≥140/90 mm Hg. Normal CBP was defined as mean systolic/diastolic CBP <120/80 mm Hg and prehypertension as mean systolic/diastolic CBP 120 to 139/80 to 89 mm Hg. The analytic sample included 909 participants. Among participants with systolic/diastolic CBP <140/90 mm Hg, the prevalence of masked hypertension and prehypertension was 27.5% and 62.4%, respectively. The prevalence of masked hypertension among those with normal CBP and prehypertension was 12.9% and 36.3%, respectively. In a fully adjusted model, which included prehypertension status and antihypertensive medication use as covariates, left ventricular mass index was 7.94 g/m2 lower among those without masked hypertension compared to participants with masked hypertension (P<0.001). Left ventricular mass index was also 4.77 g/m2 lower among those with clinic hypertension, but this difference was not statistically significant (P=0.068). There were no significant differences in left ventricular mass index between participants with and without masked hypertension, or clinic hypertension. Conclusions Masked hypertension was common among African Americans with prehypertension and also normal CBP, and was associated with subclinical cardiovascular disease.
Variation of Soil Aggregation along the Weathering Gradient: Comparison of Grain Size Distribution under Different Disruptive Forces

The formation and stabilization of soil aggregates play a key role in soil functions. To date, few studies have been performed on the variation of soil aggregation with increasing soil weathering degree. Here, soil aggregation and its influencing factors along the weathering gradient were investigated. Six typical zonal soils (derived from similar parent materials) were sampled from temperate to tropical regions. Grain size distribution (GSD) in aggregate fragmentation with increasing disruptive forces (air-dried, water dispersion and chemical dispersion) was determined by laser diffraction particle size analyzer. Different forms of sesquioxides were determined by selective chemical extraction and their contributions to soil aggregation were identified by multiple stepwise regression analysis. The high variability of sesquioxides in different forms appeared with increasing free oxide content (Fed and Ald) from the temperate to tropical soils. The transformation of GSD peak to small size varied with increasing disruptive forces (p<0.05). Although in different weathering degrees, zonal soils showed a similar fragmentation process. Aggregate water stability generally increased with increasing soil weathering (p<0.01), with higher stability in eluvium (A) horizon than in illuvium (B) horizon (p<0.01). Crystalline oxides and amorphous iron oxides (Feo), especially (Fed-Feo) contributed to the formation of air-dried macroaggregates and their stability against slaking (R2 = 55%, p<0.01), while fine particles (<50μm) and Feo (excluding the complex form Fep) played a positive role in the formation of water stable aggregates (R2 = 93%, p<0.01). Additionally, water stable aggregates (including stability, size distribution and specific surface area) were closely related with pH, organic matter, cation exchange capacity (CEC), bulk density (BD), and free oxides (including various forms) (p<0.05). The overall results indicate that soil aggregation conforms to aggregate hierarchy theory to some extent along the weathering gradient and different forms of sesquioxides perform their specific roles in the formation and stabilization of different size aggregates.
Functional Compensation of Primary and Secondary Metabolites by Duplicate Genes in Arabidopsis thaliana

It is well known that knocking out a gene in an organism often causes no phenotypic effect. One possible explanation is the existence of duplicate genes; that is, the effect of knocking out a gene is compensated by a duplicate copy. Another explanation is the existence of alternative pathways. In terms of metabolic products, the relative roles of the two mechanisms have been extensively studied in yeast but not in any multi-cellular organisms. Here, to address the functional compensation of metabolic products by duplicate genes, we quantified 35 metabolic products from 1,976 genes in knockout mutants of Arabidopsis thaliana by a high-throughput Liquid chromatography-Mass spectrometer (LC-MS) analysis. We found that knocking out either a singleton gene or a duplicate gene with distant paralogs in the genome tends to induce stronger metabolic effects than knocking out a duplicate gene with a close paralog in the genome, indicating that only duplicate genes with close paralogs play a significant role in functional compensation for metabolic products in A. thaliana. To extend the analysis, we examined metabolic products with either high or low connectivity in a metabolic network. We found that the compensatory role of duplicate genes is less important when the metabolite has a high connectivity, indicating that functional compensation by alternative pathways is common in the case of high connectivity. In conclusion, recently duplicated genes play an important role in the compensation of metabolic products only when the number of alternative pathways is small.
System productivity and profitability of sugarcane (Saccharum spp. hybrid complex) + grain amaranth (Amaranthus hypochondriacus) intercropping system

Field experiments were conducted during 2003-04 and 2004-05 at Lucknow, to study performance of sugar- cane ( Saccharum spp hybrid complex) + grain amaranth ( Amaranthus hypochondriacus L.) intercropping at . various planting geometries (sugarcane sole at 90 cm row spacing, amaranth sole at 45 cm row spacing, sugar- cane + amaranth in 1:1 row ratio and sugarcane paired (45:135 cm) + amaranth 2 rows in 135 cm spacing in 2:2
Estimating International R&D Knowledge Spillovers

This paper develops an equation of national knowledge accumulation and uses it to estimate the size of international innovator-to-imitator R&D knowledge spillovers using aggregate data. The equation is compared to existing measures of international spillovers from foreign R&D. Because these measures do not distinguish between imitative and innovative research efforts, their estimates of spillovers from foreign R&D may be biased. The empirical results are preliminary, but suggest that the magnitude of spillovers may be consistent with the case study work of Mansfield et al. [1981].
Trade Liberalization, Financial Development and Economic Growth: Evidence from Pakistan (1980-2009)

This study investigates the impact of financial development and trade openness on GDP growth in Pakistan using annual data over the period 1980-2009. The analysis is based on the bound testing approach of co-integration advanced by Pesaran et al (2001). The empirical results confirm the validity of trade led growth and financial led growth hypothesis in Pakistan. A co-integrated relationship between economic growth, trade openness and financial development was noticed in both the long-run and short-runs. Further analysis showed that trade openness and financial development Granger-cause economic growth in the period of study.
Model equations in rarefied gas dynamics: Viscous-slip and thermal-slip coefficients

Various model equations are used to define the viscous-slip and the thermal-slip coefficients in rarefied gas dynamics. More specifically, the BGK model, the S model, the variable collision model and the CES model are used to establish the slip coefficients basic to Kramers’ problem and the half-space problem of thermal creep. While the most general results are developed from use of the Maxwell boundary condition, results for the BGK model and the S model as defined by the Cercignani–Lampis boundary condition are also reported. An analytical discrete-ordinates method is used to establish the reported numerical results, and when available results from a numerical solution of the linearized Boltzmann equation are used as reference values. In addition to the numerical work based on model equations, the important issue of how to define meaningful ways (appropriate mean-free paths) to compare the results for the various models is discussed.
Amperean pairing and the pseudogap phase of cuprate superconductors

The enigmatic pseudogap phase in underdoped cuprate high T_c superconductors has long been recognized as a central puzzle of the T_c problem. Recent data show that the pseudogap is likely a distinct phase, characterized by a medium range and quasi-static charge ordering. However, the origin of the ordering wavevector and the mechanism of the charge order is unknown. At the same time, earlier data show that precursive superconducting fluctuations are also associated with this phase. We propose that the pseudogap phase is a novel pairing state where electrons on the same side of the Fermi surface are paired, in strong contrast with conventional BCS theory which pair electrons on opposite sides of the Fermi surface. In this state the Cooper pair carries a net momentum and belong to a general class called pair density wave (PDW). The microscopic pairing mechanism comes from a gauge theory formulation of the resonating valence bond (RVB) picture, where electrons traveling in the same direction feel an attractive force in analogy with Ampere's effects in electromagnetism. We call this Amperean pairing. Charge order automatically appears as a subsidiary order parameter. Our theory gives a prediction of the ordering wavevector which is in good agreement with experiment. Furthermore, the quasiparticle spectrum from our model explains many of the unusual features reported in photoemission experiments. The Fermi arc and the unusual way the tip of the arc terminates also come out naturally. We also discuss how the onset of the Kerr effect in this state can be accommodated. Finally, we propose an experiment which can directly test the notion of Amperean pairing.
Involvement of NADPH oxidase in high-dose phenolic acid-induced pro-oxidant activity on rat mesenteric venules

In the present study, we investigated the potential role of phenolic acids in initiating oxidative damage to microvascular endothelial cells and the underlying mechanism mediating the pro-oxidant action. Male Wistar rats received high doses of phenolic acid [caffeic acid (CA), salvianolic acid B (SAB), chlorogenic acid (ChA) or ferulic acid (FA)]. The creation of reactive oxygen species in mesenteric microcirculation endothelial cells and adherent leukocytes along with venules were assessed using intravital microscopy. The expression levels of NADPH oxidase subunits (Nox4 and p22phox) in terminal ileum tissues were determined by western blot analysis. Intravenous injection of high-dose ChA or CA (7 mg/kg) markedly increased the peroxide production in the venular walls and upregulated the protein expression levels of Nox4 and p22phox in the ileum tissues, while the same dose of CA and SAB made no difference within the observation period. No changes were observed in the number of leukocytes adhering to the venular walls. High-dose ChA and FA led to an imbalance between the oxidant and antioxidant mechanism by boosting the expression levels of NADPH oxidase. Thus, we clarified the rationale behind the adverse effects of a herbal injection containing high levels of phenolic acid compounds.
Webbens vägar : om webbjournalistikens etablering och utveckling vid tre svenska regionala och lokala dagstidningar 1995-2013

In this dissertion in Media History I study the history and development of online journalism in three Swedish local and regional newspapers: Helsingborgs Dagblad, Sydostran and Ystads Allehanda. The starting point is historical: I have tried to anchor the three newspapers' decision to start their online newspapers in their own history and surrounding society. By following the three newspapers' work with the Web from the first attempts to today's eleborated online newspapers, I try to give a concrete picture of a development that does not follow a straight track. Rather I underscore how the management and online journalists instead make different attempts to try to find new solutions to the problems in this new journalistic field. Through my empirical studies (interviews and observations in the newsrooms) and a review of the research literature, I study how the general features of web journalism work concretely in a local context. This includes examining the news’ fast – and slow – cycles, how the form of web pages remediates other media, in what ways online journalism forms a semi-dependent subfield in the journalistic field, what an online journalist really does in his/her job, the introduction of a paywall in one of the online newspapers, and how the three newspapers' web journalism relate to the surrounding digital media ecosystem in the form of social media.
Primary Neural Precursors and Intermitotic Nuclear Migration in the Ventricular Zone of Adult Canaries

New neurons continue to be born in the ventricular zone (VZ) of the lateral ventricles in the brain of adult birds. On the basis of serial section reconstruction and electron microscopy, we determined that the VZ of the adult canary brain is composed of three main cell types (A, B, and E). Type A cells were never found in contact with the ventricle and had microtubule-rich processes typical of young migrating neurons. Type B cells were organized as a pseudostratified epithelium, all contacted the ventricle, and most had a characteristic single cilium. Type E cells, also in contact with ventricle, were ultrastructurally similar to the mammalian multiciliated ependymal cells. After six injections of [3H]-thymidine (1 every 12 hr), Types A and B cells were found labeled. Type E cells were never [3H]-thymidine labeled. One to two hours after a single injection of [3H]-thymidine, all labeled cells corresponded to Type B cells. At survivals of 5, 24, and 74 hr after [3H]-thymidine injection, the proportion of labeled Type B cells decreased and that of Type A cells increased, indicating that Type B cells were the primary precursors. Most [3H]-labeled nuclei at 1–2 hr after [3H]-thymidine injection were separated from the ventricular cavity, but most of the mitotic cells were adjacent to the ventricle. This observation and measurements of the distance between labeled nuclei and the ventricular surface at 1, 5, 7, and 11 hr after [3H]-thymidine injection indicate that Type B cell nuclei move toward the ventricle to divide. This work reveals the architecture of the VZ in an adult vertebrate brain, identifies the primary precursor of new neurons, and describes nuclear translocation of these precursors during the cell cycle.
The Role of Consumer Characteristics and Attitudes in Purchase Behavior of Domestic versus Foreign Made Products

Abstract The aim of this study was to investigate the role of factors underlying consumer choice of domestic vs. foreign products on a sample of consumers in a less traditional post-socialist economy of Slovenia. Empirical results confirmed the postulated relationships among the protectionism dimension of ethnocentric attitudes, familiarity with global brands and consumer domestic purchase decisions for the product categories examined in this study. However, findings did not lend support for theoretical propositions related to demographic variables. Implications for domestic and global brand managers are outlined in the conclusions.
Outpatient Day-care Neuroangiography and Neurointervention of Unruptured Intracranial Aneurysms

Purpose Day-care management of unruptured intracranial aneurysms can shorten hospital stay, reduce medical cost and improve outcome. We present the process, outcome and duration of hospital stay for the management of unruptured intracranial aneurysms via a neurointervention clinic in a single center during the past four years. Materials and Methods We analyzed 403 patients who were referred to Neurointervention Clinic at Asan Medical Center for aneurysm evaluation between January 1, 2011 and December 31, 2014. There were 141 (41%) diagnostic catheter angiographies, 202 (59%) neurointerventional procedures and 2 (0.6%) neurointerventional procedures followed by operation. We analyzed the process, outcome of angiography or neurointervention, and duration of hospital stay. Results There was no aneurysm in 58 patients who were reported as having an aneurysm in MRA or CTA (14 %). Among 345 patients with aneurysm, there were 283 patients with a single aneurysm (82%) and 62 patients with multiple aneurysms (n=62, 18%). Aneurysm coiling was performed in 202 patients (59%), surgical clipping in 14 patients (4%), coiling followed by clipping in 2 patients (0.6%) and no intervention was required in 127 patients (37%). The hospital stay for diagnostic angiography was less than 6 hours and the mean duration of hospital stay was 2.1 days for neurointervention. There were 4 procedure-related adverse events (2%) including 3 minor and 1 major ischemic strokes. Conclusion Our study revealed that day-care management of unruptured intracranial aneurysms could be performed without an additional risk. It could enable rapid patient flow, shorten hospital stay and thus reduce hospital costs.
Improving fold recognition of protein threading by experimental distance constraints

We present a comprehensive analysis of methods for improving the fold recognition rate of the threading approach to protein structure prediction by the utilization of few additional distance constraints. The distance constraints between protein residues may be obtained by experiments such as mass spectrometry or NMR spectroscopy. We applied a post-filtering step with new scoring functions incorporating measures of constraint satisfaction to ranking lists of 123D threading alignments. The detailed analysis of the results on a small representative benchmark set show that the fold recognition rate can be improved significantly by up to 30% from about 54%-65% to 77%-84%, approaching the maximal attainable performance of 90% estimated by structural superposition alignments. This gain in performance adds about 10% to the recognition rate already achieved in our previous study with cross-link constraints only. Additional recent results on a larger benchmark set involving a confidence function for threading predictions also indicate notable improvements by our combined approach, which should be particularly valuable for rapid structure determination and validation of protein models.