Miracle-dz/UniFAR-FTUs huggingface dataset:
Blockade of transforming growth factor β upregulates T-box transcription factor T-bet, and increases T helper cell type 1 cytokine and matrix metalloproteinase-3 production in the human gut mucosa

Background and Aims: The role of transforming growth factor β (TGFβ) in inhibiting T cell function in the normal gut has been studied in animal models. However, the impact of TGFβ inhibition on T cells in the normal human gut remains poorly understood. The effect of TGFβ blockade in normal intestinal biopsies grown ex vivo and lamina propria mononuclear cells (LPMCs) on T-bet, a T-box transcription factor required for T helper cell type (Th)1 differentiation, interferon γ (IFNγ) production, T cell apoptosis and matrix metalloproteinase (MMP)-3 production has therefore been tested. Methods: TGFβ transcripts were determined by quantitative reverse transcription-PCR in laser-captured gut epithelium and lamina propria. Biopsies and LPMCs were cultured with anti-TGFβ neutralising antibody. After 24 h culture, T-bet was determined by immunoblotting, and T cell apoptosis was assessed by flow cytometry. IFNγ, tumour necrosis factor α (TNFα), interleukin (IL) 2, IL6, IL8, IL10, IL12p70 and IL17 were measured by ELISA. MMP-3 and tissue inhibitor of matrix metalloproteinase (TIMP)-1 were assessed by immunoblotting. Results: A higher number of TGFβ transcripts was found in the lamina propria than in the epithelium in normal gut. T-bet expression was significantly higher in biopsies and LPMCs cultured with anti-TGFβ antibody than in those cultured with control antibody. TGFβ blockade downregulated T cell apoptosis, and induced a significant increase in IFNγ, TNFα, IL2, IL6, IL8 and IL17 production. A higher expression of MMP-3, but not TIMP-1, was observed in the tissue and supernatant of biopsies treated with anti-TGFβ antibody. Conclusions: The findings support a crucial role for TGFβ in dampening T cell-mediated tissue-damaging responses in the human gut.
The stable carbon isotopic composition of Daphnia ephippia in small, temperate lakes reflects in‐lake methane availability

Daphnia can ingest methane‐oxidizing bacteria and incorporate methanogenic carbon into their biomass, leading to low stable carbon isotope ratios (expressed as δ13C values) of their tissue. Therefore, δ13C analysis of Daphnia resting eggs (ephippia) in lake sediment records can potentially be used to reconstruct past in‐lake availability of methane (CH4). However, detailed multilake studies demonstrating that δ13C values of recently deposited Daphnia ephippia (δ13Cephippia) are systematically related to in‐lake CH4 concentrations ([CH4]aq) are still missing. We measured δ13Cephippia from surface sediments of 15 small lakes in Europe, and compared these values with late‐summer [CH4]aq. δ13Cephippia ranged from −51.6‰ to −25.9‰, and was strongly correlated with [CH4]aq in the surface water and above the sediment (r −0.73 and −0.77, respectively), whereas a negative rather than the expected positive correlation was found with δ13C values of carbon dioxide (CO2) (r −0.54), and no correlation was observed with [CO2]aq. At eight sites, offsets between δ13 CCO2 and δ13Cephippia exceeded offsets between δ13 CCO2 and δ13Calgae reported in literature. δ13Cephippia was positively correlated with δ13C values of sedimentary organic matter (r 0.54), but up to 20.7‰ lower in all except one of the lakes (average −6.1‰). We conclude that incorporation of methanogenic carbon prior to ephippia formation must have been widespread by Daphnia in our study lakes, especially those with high [CH4]aq. Our results suggest a systematic relationship between δ13Cephippia values and [CH4]aq in small temperate lakes, and that δ13Cephippia analysis on sediment records may provide insights into past changes in in‐lake [CH4]aq.
Efficiency Gain from Ownership Deregulation: Estimates for the Radio Industry

Reducing fixed cost duplication - a common justification for concentrated market structure - motivated the US government to relax the number of radio stations a firm could operate in any local market. After deregulation the number of firms per market decreased. The implied cost saving depends on the per market fixed costs incurred by each firm. Using data from 140 markets we estimate upper and lower bounds to fixed costs using (i) an empirical model of gross profit and (ii) the assumption that the observed post-deregulation market structure is a Nash equilibrium. The estimates suggest that the efficiency savings were significant.
The magic of a name.

ABSTRACT In a recent article ("In the End Is the Word." New Scientist 85:37-38, 1980) Colin Tudge tells how important it is for the patient to be told the name of his disease. He contends that, unlike physicians, many patients do not view diagnosis as merely a prelude to treatment. To them, diagnosis may be the most important part of therapy. In fact, many sufferers from a chronic disease are content with a diagnostic label without detailed definition or an explanation of its underlying pathophysiology. The physician's prescription may not be even filled or complied with. According to Tudge, much of the touted noncompliance may be due to the patient's complete satisfaction with the reassurance provided by having his disease named. It is as if the name brings the disturbingly unknown into the realm of the partially known. Perhaps the less therapeutically equipped physician of the 19th century understood this need
CK2-NCoR signaling cascade promotes prostate tumorigenesis

The aberrant expressions of casein kinase 2 (CK2) was found in prostate cancer patient and cell lines, but little is known of the detailed mechanisms implicated in prostate tumorigenesis. In this study, we report that both CK2 activity and CK2-mediated NCoR phosphorylation are significantly elevated in the androgen-independent prostate cancer cell line DU145 and PC-3 compared with RWPE1 and LNCaP cells. Increased phosphorylation inversely correlates with the mRNA level of the NCoR-regulated gene, interferon-γ-inducible protein 10 (IP-10). CK2 inhibition abrogated NCoR phosphorylation, IP-10 transcriptional repression, and the invasion activity of PC-3 cells. Inhibition of the CK2-NCoR network significantly reduced in vivo PC-3 cell tumorigenicity, likely due to transcriptional derepression of IP-10. Clinicopathological analyses revealed that increased CK2-mediated NCoR phosphorylation significantly correlates with poor survival among prostate cancer patients. These findings elucidate a CK2-modulated oncogenic cascade in prostate tumorigenesis.
MODELLING THE RHEOLOGY OF COMPLEX FLUIDS : Cases of Bitumen and Heavy Oils at low temperatures.

As complex fluids such as heavy oil or bitumen pass from the field to process units, structural and compositional changes occur that are intimately linked with pressure (P), temperature (T), and shear histories. In this exploratory work, a modified Structural Kinetics Model is used to calculate the apparent shear viscosity of three complex fluids: Maya Crude Oil (MCO), Athabasca Bitumen (AB) and Safaniya Heavy Oil (SP) and their related nano-filtered fractions (permeates and retentates) at low temperatures. The proposed model involves a structural parameter λ that tracks the mechanical history of these fluids and a temperature shift factor aTP that integrates the thermal history, through the usage of the concept of fictive temperature Teff inside a modified Williams Landel Ferry (WLF) equation. Rheological data for the feedstocks were divided into a training data set, used to fit model parameters, and an extrapolation data set, used to test the asymptotic behaviour of the model with respect to temperature and shear history. Rheological data for the nano-filtered permeates and retentates, with varying mass fractions of structured phase, comprised a prediction data set. Average absolute deviations (AAD) less than 15% and R values approaching unity were obtained for the prediction data set. AAD values were less than 4 % for the training and less than 10 % for the extrapolation data sets. The modified Structure-Kinetics Model offers insights, as well as flexibility and accuracy for simulating heavy oil and bitumen rheological properties under conditions where these fluids are structured.
Citation for Published Item: Use Policy Oxi1 Protein Kinase Is Required for Plant Immunity against Pseudomonas Syringae in Arabidopsis

(2009) 'OXI1 protein kinase is required for plant immunity against Pseudomonas syringae in Arabidopsis. ', Journal of experimental botany. , 60 (13). pp. distribution, and reproduction in any medium, provided the original work is properly cited. The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full DRO policy for further details. Abstract Expression of the Arabidopsis Oxidative Signal-Inducible1 (OXI1) serine/threonine protein kinase gene (At3g25250) is induced by oxidative stress. The kinase is required for root hair development and basal defence against the oomycete pathogen Hyaloperonospora parasitica, two separate H 2 O 2-mediated processes. In this study, the role of OXI1 during pathogenesis was characterized further. Null oxi1 mutants are more susceptible to both virulent and avirulent strains of the biotrophic bacterial pathogen Pseudomonas syringae compared with the wild type, indicating that OXI1 positively regulates both basal resistance triggered by the recognition of pathogen-associated molecular patterns, as well as effector-triggered immunity. The level of OXI1 expression appears to be critical in mounting an appropriate defence response since OXI1 overexpressor lines also display increased susceptibility to biotrophic pathogens. The induction of OXI1 after P. syringae infection spatially and temporally correlates with the oxidative burst. Furthermore, induction is reduced in atrbohD mutants and after application of DPI (an inhibitor of NADPH oxidases) suggesting that reactive oxygen species produced through NADPH oxidases drives OXI1 expression during this plant–pathogen interaction.
Downregulation of p53 promotes in vitro perineural invasive activity of human salivary adenoid cystic carcinoma cells through epithelial-mesenchymal transition-like changes.

Salivary adenoid cystic carcinoma (SACC) is a malignant tumor that is characterized by perineural invasion (PNI). p53 is an essential tumor-suppressor gene and p53 mutations play a critical role in tumor occurrence and progression (e.g., pancreatic, prostate and head and neck cancer). However, the regulatory role of the p53 gene in SACC and the PNI process remains unknown. In the present study, we employed RNA interference technique to downregulate p53 gene expression in SACC-83 cells to explore the role of p53 in the PNI process. Our results showed that the downregulation of the p53 gene induced significant 'epithelial-mesenchymal transition (EMT)-like changes' in SACC-83 cells, including decreased expression levels of epithelial markers (E-cadherin, EMA and CK5) and increased expression levels of mesenchymal markers (vimentin, N-cadherin and C-cadherin). The downregulation of p53 also caused a lower apoptotic index of Annexin V-FITC/PI and a lower number of SACC-83 cells in the second G0/G1 phase of the cell cycle. Furthermore, the downregulation of the p53 gene resulted in a significant increase in PNI activity in the SACC-83 cells. Thus, our findings revealed that downregulation of p53 promoted in vitro PNI activity through 'EMT-like changes' in SACC-83 cells. The present study suggests the essential regulatory role of p53 in the PNI activity of SACC cells, and implies that p53 may be a new target gene for the clinical treatment of SACC.
Fluctuating States: What is the Probability of a Thermodynamical Transition?

If the second law of thermodynamics forbids a transition from one state to another, then it is still possible to make the transition happen by using a sufficient amount of work. But if we do not have access to this amount of work, can the transition happen probabilistically? In the thermodynamic limit, this probability tends to zero, but here we find that for finite-sized and quantum systems it can be finite. We compute the maximum probability of a transition or a thermodynamical fluctuation from any initial state to any final state and show that this maximum can be achieved for any final state that is block diagonal in the energy eigenbasis. We also find upper and lower bounds on this transition probability, in terms of the work of transition. As a by-product, we introduce a finite set of thermodynamical monotones related to the thermomajorization criteria which governs state transitions and compute the work of transition in terms of them. The trade-off between the probability of a transition and any partial work added to aid in that transition is also considered. Our results have applications in entanglement theory, and we find the amount of entanglement required (or gained) when transforming one pure entangled state into any other.
Nurses’ knowledge and attitudes toward aged sexuality in Flemish nursing homes

Background: Admission to a nursing home does not necessarily diminish an older person’s desire for sexual expression and fulfillment. Given that nursing staff directly and indirectly influence the range of acceptable sexual expressions of nursing home residents, their knowledge and attitudes toward aged sexuality can have far-reaching effects on both the quality of care they provide to residents and the self-image and well-being of these residents. Research objectives: To investigate nursing staff’s knowledge and attitudes toward aged sexuality, to determine whether certain sociodemographic factors of the nursing staff relate to their knowledge and attitudes toward later-life sexuality, and to examine the relationship between knowledge and attitudes. Research design: Descriptive cross-sectional survey study. Research participants and research context: The administered questionnaire collected sociodemographic data and data from an adapted, Dutch version of the Aging Sexual Knowledge and Attitudes Scale. Data were collected from November 2011 through April 2012. A total of 43 geographically dispersed nursing homes in Flanders, Belgium, participated. Out of a potential research sample of 2228 nursing staff respondents, 1166 participated. Ethical considerations: The study protocol was approved by the Ethics Committee of the Faculty of Medicine of the KU Leuven. Findings: Nursing staff appeared to be moderately knowledgeable about aged sexuality and displayed a rather positive attitude toward sexuality in older people. Significant relationships between various variables were found both at univariable and multivariable levels. Knowledge and attitudes proved to be positively related, indicating that a higher level of knowledge of aged sexuality is associated with a more positive attitude toward sexuality in later life. Discussion: Research findings are discussed within a broader international context. Conclusion: There is room for improvement for both nursing staff’s knowledge and attitudes toward aged sexuality. This might be aided by appropriate educational interventions. Our results identified different target groups of nursing home staff for these interventions.
Adsorption of hematite nanoparticles onto Caco-2 cells and the cellular impairments: effect of particle size

The increasing applications of engineered nanomaterials nowadays have elevated the potential of human exposure through various routes including inhalation, skin penetration and digestion. To date there is scarce information on a quantitative description of the interactions between nanoparticles (NPs) and cell surfaces and the detrimental effects from the exposure. The purpose of this work was to study in vitro exposure of Caco-2 cells to hematite (α-Fe2O3) NPs and to determine the particle size effects on the adsorption behaviors. Cellular impairment was also investigated and compared. Hematite NPs were synthesized as part of this study with a discrete size distribution and uniform morphology examined by dynamic light scattering (DLS) and confirmed by transmission electron microscopy (TEM). Caco-2 cells were cultured as a model epithelium to mirror human intestinal cells and used to evaluate the impacts of the exposure to NPs by measuring transepithelial electrical resistance (TEER). Cell surface disruption, localization and translocation of NPs through the cells were analyzed with immunocytochemical staining and confocal microscopy. Results showed that hematite NPs had mean diameters of 26, 53, 76 and 98 nm and were positively charged with minor aggregation in the buffer solution. Adsorption of the four sizes of NPs on cells reached equilibrium within approximately 5 min but adsorption kinetics were found to be size-dependent. The adsorption rates expressed as mg m − 2 min − 1 were greater for large NPs (76 and 98 nm) than those for small NPs (26 and 53 nm). However, adsorption rates, expressed in units of m − 2 min − 1, were much greater for small NPs than large ones. After the adsorption equilibrium was reached, the adsorbed mass of NPs on a unit area of cells was calculated and showed no significant size dependence. Longer exposure time (>3 h) induced adverse cellular effects as indicated by the drop in TEER compared to the control cells without the exposure to NPs. NPs initially triggered a dynamic reorganization and detachment of microvilli structures on Caco-2 cell surfaces. Following this impact, the drop in TEER occurred more significantly, particularly for the exposure to 26 nm NPs, which was consistent with the observations with confocal microscopy that the junctions were more severely disrupted by 26 nm NPs than other sizes. In conclusion, this paper demonstrates the interactions at the ultrastructural level from initial surface adsorption of NPs upon cells, to the subsequent microvilli reorganization, membrane penetration and the disruption of adherens junction and provides the fundamental information on size effects on NP behavior which is often poorly addressed for in vitro cytotoxicity studies of NPs.
PlenoPatch: Patch-Based Plenoptic Image Manipulation

Patch-based image synthesis methods have been successfully applied for various editing tasks on still images, videos and stereo pairs. In this work we extend patch-based synthesis to plenoptic images captured by consumer-level lenselet-based devices for interactive, efficient light field editing. In our method the light field is represented as a set of images captured from different viewpoints. We decompose the central view into different depth layers, and present it to the user for specifying the editing goals. Given an editing task, our method performs patch-based image synthesis on all affected layers of the central view, and then propagates the edits to all other views. Interaction is done through a conventional 2D image editing user interface that is familiar to novice users. Our method correctly handles object boundary occlusion with semi-transparency, thus can generate more realistic results than previous methods. We demonstrate compelling results on a wide range of applications such as hole-filling, object reshuffling and resizing, changing object depth, light field upscaling and parallax magnification.
Preliminary Results From a Multidisciplinary University-Based Disease State Management Program Focused on Hypertension, Hyperlipidemia, and Diabetes

Objective: To describe the implementation and evaluation of a pilot multidisciplinary disease state management (DSM) program for diabetes, hypertension, and hyperlipidemia at a private, self-insured university (over 900 covered lives). Methods: Enrollees met with a pharmacist, nurse, exercise physiologist, and students in these disciplines to improve clinical outcomes and fitness parameters. Clinical values, quality of life, patient knowledge of disease states, and patient satisfaction were assessed. Results: Of the 20 patients in the pilot program, 17 completed 1 nursing and 2 pharmacist visits; 8 completed exercise physiology visits. At baseline, elevated blood pressure readings were observed in 64.7% (11 of 17) of patients, 20% of those with diabetes (1 of 5) had an elevated hemoglobin A1c value (HbA1c), and 82.4% (14 of 17) had a cholesterol value that was not at goal. At least 1 medication-related problem was observed in 16 patients (94.1%). At 3 months, all patients with diabetes achieved HbA1c levels at or below 7%, 4 patients attained blood pressure control, and 1 achieved normal cholesterol readings. Patients characterized participation in the program as valuable and convenient. Conclusions: Patients involved in the multidisciplinary DSM showed improved clinical outcomes after 3 months. Ongoing analysis of patient outcomes will determine the long-term effectiveness of the DSM.
Shared Regulation of UGT1A7 by Hepatocyte Nuclear Factor (HNF) 1α and HNF4α

Substrates for glucuronidation include endogenous and xenobiotic compounds such as environmental carcinogens and drugs, as well as the chemotherapeutic agent irinotecan. The UDP-glucuronosyltransferase (UGT) 1A7 gene is expressed in the upper gastrointestinal tract and the lung but is not expressed in the liver. The transcriptional regulation of UGT1A7 and the putative influence of single nucleotide polymorphisms (SNPs) are incompletely characterized. UGT1A8, UGT1A9, and UGT1A10, which are highly homologous to UGT1A7, have been reported to be transcriptionally regulated by hepatocyte nuclear factors (HNFs). In this study, we show the activation of UGT1A7 by the aforementioned transcription factors. Sequence analyses, mutagenesis, reporter gene experiments, small interfering RNA silencing, chromatin immunoprecipitation, and electromobility shift assays identified five HNF binding sites in the proximal promoter region of UGT1A7 that were regulated by HNF1α and HNF4α. Activation by HNF1α was lower in the presence of the UGT1A7 −57G SNP. In contrast to liver-expressed UGT1A9, transcriptional activation of UGT1A7 by HNF4α was lower and dependent on higher HNF4α concentrations, which may contribute to the observed differences in tissue expression patterns. Therefore, a specific role of HNF in the transcriptional control of UGT1A7 is shown and characterized, which may contribute to its tissue specificity and function.
Novel Optimized Hybrid Terahertz Photoconductive Antennas

We demonstrate the results of on THz emission from hybrid THz photoconductive antenna loaded with silver nanoantenna. The results of experimental investigations are in a good agreement with numerical simulations presented in our recent work. The conversion efficiency reveals over 5-fold improvement at certain frequencies, if compared with similar photoconductive antenna without silver nanoparticles, while previous results for this type of antenna barely exceeded 2-fold conversion efficiency gain. We propose a cost-effective fabrication procedure to realize such hybrid THz antennas with optimized plasmonic nanostructures via thermal dewetting process, which does not require any post processing and makes the proposed solution very attractive for applications.