Miracle-dz/UniFAR-FTUs huggingface dataset:
Vicenin-2 inhibits Wnt/β-catenin signaling and induces apoptosis in HT-29 human colon cancer cell line

Background Colorectal cancer (CRC) is among highest prevailing cancers in the whole world, especially in western countries. For a diverse of reasons, patients prefer naturally occurring dietary substances over synthetic agents to prevent cancer. Vicenin-2 is largely available in a medicinal plant Ocimum sanctum and is an apigenin form, 6,8-di-C-glucoside, which has been reported to have a range of pharmacological values which includes antioxidant, hepatoprotective, anti-inflammatory and anti-cancer. This study was aimed to analyze the anti-proliferative effect of Vicenin-2 on human colon cancer cells via the Wnt/β-catenin signaling inhibition. Methods MTT assay was used to assess the cell viability at different concentrations and time point. Vicenin-2 at a concentration of 50 µM (IC50) decreased the phosphorylated (inactive) glycogen synthase kinase-3β, cyclin D1, and non-p-β-catenin expressions in HT-29 cells, which were evidenced through western blot analysis. Results Further, Vincenin-2 reduced the T-cell factor (TCF) / Leukocyte erythroid factor (LEF) reporter activity in HT-29 cells. Vicenin-2 also promoted substantial cell cycle arrest at the G2M phase of HT-29 cells, as well induced apoptosis in HT-29 cells, as revealed through flow cytometric analysis. Furthermore, immunoblot analysis showed that Vicenin-2 treatment enhanced the expression of Cytochrome C, Bax and caspase-3 whereas suppressed the Bcl-2 expression. Conclusion Together, these results revealed that Vicenin-2 can act as a potent inhibitor of HT-29 cell proliferation and can be used as an agent against CRC.
Financial investment and economic policy uncertainty in the UK

UK based financial firms following Brexit reported net disinvestment of 15 billion pounds. This was the fifth time financial disinvestment occurred since the production of this data: 1987. Parallel to this event, Economic Policy Uncertainty (EPU) in the UK experienced its biggest rise during Brexit June 2016. This note studies the relationship between EPU and its particular components and financial investment. I find that overall EPU and specifically fiscal policy, monetary policy, geopolitical, regulation and liquidity uncertainty have the highest negative sensitivity to financial investment.
The Impact of Industrial Odors on the Subjective Well-Being of Communities in Colorado

Odor pollution was identified as a top priority of the community of North Denver. Previous studies that investigated the impact of air pollution in North Denver focused on adverse health effects, rather than mental well-being. This study assessed the impact of odors from industrial sources on the subjective well-being (SWB) of North Denver residents, and of four similar communities in Colorado for comparison. An online survey was sent to participants from Greeley, Fort Collins, Fort Lupton, North Denver, and Pueblo, asking questions about SWB and odors in their areas (n = 351). The evaluation of SWB was performed using a novel approach that appraises three aspects of SWB. This approach of evaluating SWB has not been used in odor exposure studies. A proportional odds logistic regression model was used to estimate nine measures of SWB. The results showed that participants who reported that the air is very fresh or the odor is highly acceptable had higher levels of SWB. This association suggests that residents who live in areas exposed to strong industrial odors had lower levels of SWB. A subset of participants in this study took the survey four times in one year. Longitudinal analysis showed that evaluative satisfaction was slightly associated with seasonality. Both satisfaction with how life turned out and satisfaction with standards of living slightly increased during the fourth quarter of the year. The study also found that four of the nine measures can be used to represent SWB in future studies. Two of those measures were evaluative SWB, and the other two were positive hedonic SWB measures. A comparison between the five communities showed that well-being levels in North Denver and Greeley were not significantly different than those in Fort Collins or Fort Lupton. The comparison, however, showed that Pueblo had the lowest levels of well-being among all communities.
FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment

CpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. Here, we identify FBXL19 as a CpG island-binding protein in mouse embryonic stem (ES) cells and show that it associates with the CDK-Mediator complex. We discover that FBXL19 recruits CDK-Mediator to CpG island-associated promoters of non-transcribed developmental genes to prime these genes for activation during cell lineage commitment. We further show that recognition of CpG islands by FBXL19 is essential for mouse development. Together this reveals a new CpG island-centric mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment.
Validation of ACE-FTS v2.2 methane profiles from the upper troposphere to the lower mesosphere

The ACE-FTS (Atmospheric Chemistry Experiment – Fourier Transform Spectrometer) solar occultation instrument that was launched onboard the Canadian SCISAT-1 satellite in August 2003 is measuring vertical profiles from the upper troposphere to the lower mesosphere for a large number of atmospheric constituents. Methane is one of the key species. The version v2.2 data of the ACE-FTS CH 4 data have been compared to correlative satellite, balloon-borne and ground-based Fourier transform infrared remote sensing data to assess their quality. The comparison results indicate that the accuracy of the data is within 10% in the upper troposphere – lower stratosphere, and within 25% in the middle and higher stratosphere up to the lower mesosphere (<60 km). The observed differences are generally consistent with reported systematic uncertainties. ACE-FTS is also shown to reproduce the variability of methane in the stratosphere and lower mesosphere.
Bioengineered bile ducts recapitulate key cholangiocyte functions

Investigation of diseases of the bile duct system and identification of potential therapeutic targets are hampered by the lack of tractable in vitro systems to model cholangiocyte biology. Here, we show a step-wise method for the differentiation of murine Lgr5+ liver stem cells (organoids) into cholangiocyte-like cells (CLCs) using a combination of growth factors and extracellular matrix components. Organoid-derived CLCs display key properties of primary cholangiocytes, such as expressing cholangiocyte markers, forming primary cilia, transporting small molecules and responding to farnesoid X receptor agonist. Integration of organoid-derived cholangiocytes with collagen-coated polyethersulfone hollow fiber membranes yielded bioengineered bile ducts that morphologically resembled native bile ducts and possessed polarized bile acid transport activity. As such, we present a novel in vitro model for studying and therapeutically modulating cholangiocyte function.
Improving Long-Term Outcomes for Patients with Extra-Abdominal Soft Tissue Sarcoma Regionalization to High-Volume Centers, Improved Compliance with Guidelines or Both?

Introduction Optimization of outcomes of extra-abdominal STS is not clearly understood. We sought to determine whether hospital surgical volume and adherence to NCCN guidelines, or both, are associated with outcomes in the treatment of extra-abdominal soft tissue sarcoma (STS). Methods The National Cancer Database (NCDB) was queried for patients undergoing surgery for extra-abdominal STS diagnosed from 2003 to 2007. Mean annual hospital volume for STS surgery was divided into volume terciles (1T ≤3, 2T 4–10, and 3T ≥11 cases/year). Adherence to NCCN guidelines was determined. Primary outcome was overall survival. Results Our study population consisted of 13,684 patients with a median age of 56 years. 3T hospitals were more likely to adhere to NCCN guidelines for stage III patients (63% versus 47%; p ≤ 0.001) than 1T hospitals. On multivariable analysis, adherence to NCCN guidelines was associated with improved survival (HR = 0.79, CI 0.73–0.87; p < 0.001), but hospital volume was not (3T versus 1T: HR = 0.92, CI 0.82–1.02; p=0.12). Five-year overall survival was comparable for compliant groups at 1T, 2T, and 3T hospitals (72%, 72.4%, and 72.6%, resp.). 3T hospitals were not associated with a lower risk of 30-day mortality (OR 0.70, 95% CI 0.44–1.11) compared to 1T hospitals but did have a higher R0 resection rate (OR 1.43, 95% CI 1.32–1.54). Conclusions Adherence to NCCN guidelines, irrespective of hospital volume, is associated with improved overall survival for patients with extra-abdominal STS. High-volume hospitals more often adhere to guidelines, but low-volume hospitals that follow national guidelines may achieve comparable outcomes.
High neutrophil to lymphocyte ratio and decreased CD69+NK cells represent a phenotype of high risk in early-stage breast cancer patients

Purpose Breast cancer (BC) is a highly heterogeneous disease presenting a broad range of clinical and molecular characteristics. In the past years, a growing body of evidence demonstrated that immune response plays a significant role in cancer outcome. However, immune prognostic markers are not completely validated in clinical practice in BC patients. Materials and methods With the aim to characterize immune features, several parameters were analyzed in peripheral blood at diagnosis of 85 nonmetastatic BC patients between April 2011 and July 2014. Results With a median follow-up of 38.6 months, peripheral blood analysis of BC patients (stages I, II, and III) showed that total lymphocyte and T lymphocyte counts were augmented in nonrelapsed patients. Also, a higher neutrophil-to-lymphocytes ratio was associated with prolonged disease-free survival. Natural killer cell receptor analysis revealed that early activation receptor CD69 was associated with a better outcome. Conclusion This preliminary evidence is in accordance with the concept of immune surveillance. We suggest an “immune phenotype” that provides relevant prognostic information in early-stage BC patients and which could be useful in the decision-making process.
Association of Mild Traumatic Brain Injury With and Without Loss of Consciousness With Dementia in US Military Veterans

Importance Traumatic brain injury (TBI) is common in both veteran and civilian populations. Prior studies have linked moderate and severe TBI with increased dementia risk, but the association between dementia and mild TBI, particularly mild TBI without loss of consciousness (LOC), remains unclear. Objective To examine the association between TBI severity, LOC, and dementia diagnosis in veterans. Design, Setting, and Participants This cohort study of all patients diagnosed with a TBI in the Veterans Health Administration health care system from October 1, 2001, to September 30, 2014, and a propensity-matched comparison group. Patients with dementia at baseline were excluded. Researchers identified TBIs through the Comprehensive TBI Evaluation database, which is restricted to Iraq and Afghanistan veterans, and the National Patient Care Database, which includes veterans of all eras. The severity of each TBI was based on the most severe injury recorded and classified as mild without LOC, mild with LOC, mild with LOC status unknown, or moderate or severe using Department of Defense or Defense and Veterans Brain Injury Center criteria. International Classification of Diseases, Ninth Revision codes were used to identify dementia diagnoses during follow-up and medical and psychiatric comorbidities in the 2 years prior to the index date. Main Outcomes and Measures Dementia diagnosis in veterans who had experienced TBI with or without LOC and control participants without TBI exposure. Results The study included 178 779 patients diagnosed with a TBI in the Veterans Health Administration health care system and 178 779 patients in a propensity-matched comparison group. Veterans had a mean (SD) age of nearly 49.5 (18.2) years at baseline; 33 250 (9.3%) were women, and 259 136 (72.5%) were non-Hispanic white individuals. Differences between veterans with and without TBI were small. A total of 4698 veterans (2.6%) without TBI developed dementia compared with 10 835 (6.1%) of those with TBI. After adjustment for demographics and medical and psychiatric comobidities, adjusted hazard ratios for dementia were 2.36 (95% CI, 2.10-2.66) for mild TBI without LOC, 2.51 (95% CI, 2.29-2.76) for mild TBI with LOC, 3.19 (95% CI, 3.05-3.33) for mild TBI with LOC status unknown, and 3.77 (95% CI, 3.63-3.91) for moderate to severe TBI. Conclusions and Relevance In this cohort study of more than 350 000 veterans, even mild TBI without LOC was associated with more than a 2-fold increase in the risk of dementia diagnosis. Studies of strategies to determine mechanisms, prevention, and treatment of TBI-related dementia in veterans are urgently needed.
Characterization results of EMCCDs for extreme low-light imaging

EMCCDs are capable of extreme low light imaging thanks to sub-electron read-out noise, enabling single-photon counting. The characterization of e2v's CCD60 (128 x 128), CCD97 (512 x 512) and CCD201-20 (1024 x 1024) using a controller optimized for the driving of EMCCDs at a high (≥10 MHz) pixel rate per output with < 0.002 e- total background signal. Using the CCD Controller for Counting Photons (CCCP), the horizontal and vertical CIC, dark current and EM gain stability are characterized.
A Comparison of Perturbed Initial Conditions and Multiphysics Ensembles in a Severe Weather Episode in Spain

AbstractEnsembles of numerical model forecasts are of interest to operational early warning forecasters as the spread of the ensemble provides an indication of the uncertainty of the alerts, and the mean value is deemed to outperform the forecasts of the individual models. This paper explores two ensembles on a severe weather episode in Spain, aiming to ascertain the relative usefulness of each one. One ensemble uses sensible choices of physical parameterizations (precipitation microphysics, land surface physics, and cumulus physics) while the other follows a perturbed initial conditions approach. The results show that, depending on the parameterizations, large differences can be expected in terms of storm location, spatial structure of the precipitation field, and rain intensity. It is also found that the spread of the perturbed initial conditions ensemble is smaller than the dispersion due to physical parameterizations. This confirms that in severe weather situations operational forecasts should address.
Towards Defeasible Mappings for Tractable Description Logics ( Technical Report )

We present a novel approach to denote mappings between EL-based ontologies which are defeasible in the sense that such a mapping only applies to individuals if this does not cause an inconsistency. This provides the advantage of handling exceptions automatically and thereby avoiding logical inconsistencies that may be caused due to the traditional type of mappings. We consider the case where mappings from many possibly heterogeneous ontologies are one way links towards an overarching ontology. Questions can then be asked in terms of the concepts in the overarching ontology. We provide the formal semantics for the defeasible mappings and show that reasoning under such a setting is decidable even when the defeasible axioms apply to unknowns. Furthermore, we show that this semantics actually is strongly related to the idea of answer sets for logic programs.
Reproductive Long Intergenic Noncoding RNAs Exhibit Male Gamete Specificity and Polycomb Repressive Complex 2-Mediated Repression1[OPEN]

Long noncoding RNAs in rice with major reproductive and Polycomb complex 2-regulated subclasses have conserved members detected in Brachypodium and maize. Long noncoding RNAs (lncRNAs) have been characterized extensively in animals and are involved in several processes, including homeobox gene expression and X-chromosome inactivation. In comparison, there has been much less detailed characterization of plant lncRNAs, and the number of distinct lncRNAs encoded in plant genomes and their regulation by developmental and epigenetic mechanisms remain largely unknown. Here, we analyzed transcriptome data from Asian rice (Oryza sativa) and identified 6,309 long intergenic noncoding RNAs (lincRNAs), focusing on their expression in reproductive tissues and organs. Most O. sativa lincRNAs were expressed in a highly tissue-specific manner, with an unexpectedly high fraction specifically expressed in male gametes. Mutation of a component of the Polycomb Repressive Complex2 (PRC2) resulted in derepression of another large class of lincRNAs, whose expression is correlated with H3K27 trimethylation in developing panicles. Overlap with the sperm cell-specific lincRNAs suggests that epigenetic repression of lincRNAs in the panicles was partially relieved in the male germline. Expression of a subset of lincRNAs also showed modulation by drought in reproductive tissues. Comparison with other cereal genomes showed that the lincRNAs generally have low levels of conservation at both the sequence and structural levels. Use of a novelty detection support vector machine model enabled the detection of nucleotide sequence and structural homology in ∼10% and ∼4% of the lincRNAs in genomes of purple false brome (Brachypodium distachyon) and maize (Zea mays), respectively. This is the first study to report on a large number of lncRNAs that are targets of repression by PRC2 rather than mediating regulation via PRC2. That the vast majority of the lincRNAs reported here do not overlap with those of other rice studies indicates that these are a significant addition to the known lincRNAs in rice.
Pediatric Brain Development in Down Syndrome: A Field in Its Infancy

Abstract Objectives: As surprisingly little is known about the developing brain studied in vivo in youth with Down syndrome (DS), the current review summarizes the small DS pediatric structural neuroimaging literature and begins to contextualize existing research within a developmental framework. Methods: A systematic review of the literature was completed, effect sizes from published studies were reviewed, and results are presented with respect to the DS cognitive behavioral phenotype and typical brain development. Results: The majority of DS structural neuroimaging studies describe gross differences in brain morphometry and do not use advanced neuroimaging methods to provide nuanced descriptions of the brain. There is evidence for smaller total brain volume (TBV), total gray matter (GM) and white matter, cortical lobar, hippocampal, and cerebellar volumes. When reductions in TBV are accounted for, specific reductions are noted in subregions of the frontal lobe, temporal lobe, cerebellum, and hippocampus. A review of cortical lobar effect sizes reveals mostly large effect sizes from early childhood through adolescence. However, deviance is smaller in adolescence. Despite these smaller effects, frontal GM continues to be largely deviant in adolescence. An examination of age-frontal GM relations using effect sizes from published studies and data from Lee et al. (2016) reveals that while there is a strong inverse relationship between age and frontal GM volume in controls across childhood and adolescence, this is not observed in DS. Conclusions: Further developmentally focused research, ideally using longitudinal neuroimaging, is needed to elucidate the nature of the DS neuroanatomic phenotype during childhood and adolescence. (JINS, 2018, 24, 966–976)
Do We Have a Biocompatible Peritoneal Dialysis Fluid

Objective: Cardiovascular disease remains the leading cause of morbidity and mortality in patients on maintenance dialysis. Diabetes mellitus, dyslipidemia, hypertension, inflammation and hyperhomocyteinemia are major cardiovascular risk factors. Aim: to evaluate the effects of Icodextrin and amino acid peritoneal dialysis fluid (AAPDF) on these major cardiovascular risk factors looking for a more biocompatible PDF formula. Methods: 24 adult stable peritoneal dialysis patients were included in the study. 12 patients received 2L Icodextrin and other 12 patients received 2L AAPDF in their dialysis prescription for 8 weeks. Results: Icodextrin decreased fasting plasma glucose (p < 0.001), LDL-C (p = 0.03), SBP (p < 0.01), DBP (p < 0.05) and plasma homocysteine (p = 0.002), and increased HDL-C (p = 0.009), CRP (p = 0.035) and fibrinogen (p = 0.009). AAPDF did not affect fasting plasma glucose, LDL-C, HDL-C, CRP and fibrinogen but increased serum albumin (p = 0.03), SBP (p < 0.01), DBP (p < 0.05) and PHcy (p = 0.03). Conclusions: A biocompatible PDF should provide not only adequate dialysis and ultrafiltration but should also improve nutritional and metabolic status, blood pressure control and reduce inflammation and plasma homocyteine.
Clinical evaluation of the utility of a flexible 19-gauge EBUS-TBNA needle.

Background Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is an established modality for the assessment of mediastinal and hilar adenopathy. To overcome the sampling limitations of standard 21- and 22-gauge EBUS-TBNA needles, a new flexible 19-gauge (Flex 19G) needle was developed. Methods We performed a retrospective analysis of patients who underwent EBUS-TBNA sampling with the Flex 19G needle. A 22G needle was always used first for cytology, followed by a Flex 19G needle, either an early version (Oct/2014-Sep/2015) or a final version needle (May/2016-Jan/2017), for tissue sampling. The success rate of obtaining samples, specimen quantity, and safety were evaluated and compared. Results All sampling procedures in 45 patients and 82 targets were performed without complication and the overall diagnostic yield from cytology was 100%. Furthermore, 28% of Flex 19G samples were sufficient for histopathological diagnosis. Yield improved with an increased number of passes and if the target was larger. Compared to the early version evaluated in 52 targets, the final version of the Flex 19G needle evaluated in 30 targets provided significantly larger volume samples and more frequent diagnostic cores. Tissue obtained with the Flex 19G needle retained cohesiveness to a larger degree and was of higher cellularity compared to cytological samples processed as cell blocks. Conclusions The Flex 19G is safe and provides larger volumetric and cohesive tissue samples that are appropriate for histopathological processing. The final version of the Flex 19G could be a good choice in selected cases where greater tissue acquisition is required.