Miracle-dz/UniFAR-FTUs huggingface dataset:
Cigarette Smoke Extract Induces CYP2B6 through Constitutive Androstane Receptor in Hepatocytes

Smoking induces a wide range of drug-metabolizing enzymes. Among them, CYP2B6 as well as CYP1A2 is well known to be up-regulated in smokers. Although the induction of CYP1A2 is mediated by the aryl hydrocarbon receptor, the molecular mechanisms of CYP2B6 induction by smoking remain to be fully elucidated. In this study, by preparing cigarette smoke extract (CSE), we addressed the possibility that human constitutive androstane receptor (hCAR) is involved in smoking-mediated induction of CYP2B6. In HepG2 cells, CSE induced CYP1A2 but not CYP2B6, suggesting that CYP2B6 expression is differentially regulated from CYP1A2. Compared with liver in vivo, hCAR expression is dramatically reduced in cultured hepatocytes, such as HepG2. Therefore, to reconstitute hCAR signaling pathways in vitro, we generated adenovirus vector expressing hCAR. Real-time reverse transcription-polymerase chain reaction analyses revealed that the adenoviral transfection of hCAR resulted in the up-regulation of CYP2B6 mRNA, even in the absence of CSE. It is interesting to note that CSE stimulation augmented hCAR-mediated induction of CYP2B6. In contrast, the expression of CYP2B6 was not enhanced by adenovirus vector expressing β-galactosidase, a control vector, either in the presence or absence of CSE. In summary, hCAR mediated the CYP2B6 induction by CSE in Hep2G cells. These data suggest that smoking up-regulates CYP2B6 through hCAR in vivo.
A Family of Auxin-Conjugate Hydrolases That Contributes to Free Indole-3-Acetic Acid Levels during Arabidopsis Germination1

Auxins are hormones important for numerous processes throughout plant growth and development. Plants use several mechanisms to regulate levels of the auxin indole-3-acetic acid (IAA), including the formation and hydrolysis of amide-linked conjugates that act as storage or inactivation forms of the hormone. Certain members of an Arabidopsis amidohydrolase family hydrolyze these conjugates to free IAA in vitro. We examined amidohydrolase gene expression using northern and promoter-β-glucuronidase analyses and found overlapping but distinct patterns of expression. To examine the in vivo importance of auxin-conjugate hydrolysis, we generated a triple hydrolase mutant, ilr1 iar3 ill2, which is deficient in three of these hydrolases. We compared root and hypocotyl growth of the single, double, and triple hydrolase mutants on IAA-Ala, IAA-Leu, and IAA-Phe. The hydrolase mutant phenotypic profiles on different conjugates reveal the in vivo activities and relative importance of ILR1, IAR3, and ILL2 in IAA-conjugate hydrolysis. In addition to defective responses to exogenous conjugates, ilr1 iar3 ill2 roots are slightly less responsive to exogenous IAA. The triple mutant also has a shorter hypocotyl and fewer lateral roots than wild type on unsupplemented medium. As suggested by the mutant phenotypes, ilr1 iar3 ill2 imbibed seeds and seedlings have lower IAA levels than wild type and accumulate IAA-Ala and IAA-Leu, conjugates that are substrates of the absent hydrolases. These results indicate that amidohydrolases contribute free IAA to the auxin pool during germination in Arabidopsis.
Screening for Viral Hemorrhagic Septicemia Virus in Marine Fish along the Norwegian Coastal Line

Viral hemorrhagic septicemia virus (VHSV) infects a wide range of marine fish species. To study the occurrence of VHSV in wild marine fish populations in Norwegian coastal waters and fjord systems a total of 1927 fish from 39 different species were sampled through 5 research cruises conducted in 2009 to 2011. In total, VHSV was detected by rRT-PCR in twelve samples originating from Atlantic herring (Clupea harengus), haddock (Melanogrammus aeglefinus), whiting (Merlangius merlangus) and silvery pout (Gadiculus argenteus). All fish tested positive in gills while four herring and one silvery pout also tested positive in internal organs. Successful virus isolation in cell culture was only obtained from one pooled Atlantic herring sample which shows that today's PCR methodology have a much higher sensitivity than cell culture for detection of VHSV. Sequencing revealed that the positive samples belonged to VHSV genotype Ib and phylogenetic analysis shows that the isolate from Atlantic herring and silvery pout are closely related. All positive fish were sampled in the same area in the northern county of Finnmark. This is the first detection of VHSV in Atlantic herring this far north, and to our knowledge the first detection of VHSV in silvery pout. However, low prevalence of VHSV genotype Ib in Atlantic herring and other wild marine fish are well known in other parts of Europe. Earlier there have been a few reports of disease outbreaks in farmed rainbow trout with VHSV of genotype Ib, and our results show that there is a possibility of transfer of VHSV from wild to farmed fish along the Norwegian coast line. The impact of VHSV on wild fish is not well documented.
A Tradeoff Between Length and Width in Resolution

: We describe a family of CNF formulas in n variables, with small initial width, which have polynomial length resolution refutations. By a result of Ben-Sasson and Wigder-son it follows that they must also have narrow resolution refutations, of width O ( √ n log n ) . We show that, for our formulas, this decrease in width comes at the expense of an increase in size
A Comparison of Self-administered Proprioceptive Neuromuscular Facilitation to Static Stretching on Range of Motion and Flexibility

Abstract Wicke, J, Gainey, K, and Figueroa, M. A comparison of self-administered proprioceptive neuromuscular facilitation to static stretching on range of motion and flexibility. J Strength Cond Res 28(1): 168–172, 2014—Stretching is known to be an effective method for increasing range of motion. Proprioceptive neuromuscular facilitation (PNF) is a stretching technique that is often associated with a partner. The goal of this study was to examine the changes in hip range of motion (ROM) and hip, back and shoulder flexibility (HBSF) after an intervention of self-administered PNF vs. traditional static stretching. Nineteen healthy college-aged individuals (ages 19–25 years) completed the study. Participants were tested preintervention and postintervention for hip ROM and HBSF using a goniometer and sit-and-reach test, respectively. Interventions included static or self-PNF hamstring stretching 2 × 40 seconds on each leg for 6 weeks. Participants were randomly placed in a group, and upon completion of the intervention and a 1-week rest period, they repeated the process with the other intervention. Statistical analysis revealed that there was a significant difference (p < 0.01) in the change in hip ROM and HBSF between the static stretch and self-PNF group. Mean and SD changes in the hip ROM were −6.2 ± 6.6° vs. 0.6 ± 4.5° for the PNF and static groups, respectively (where a negative value indicates an increase in ROM) and 5.2 ± 3.3 cm vs. 2.0 ± 2.6 cm, respectively, for HSBF. In addition, significant improvements (using 99% confidence intervals) were found in the 2 measures after the PNF intervention but only in HBSF after the static stretching intervention. These results suggest that self-PNF can be used in place of static stretching, does not require a partner, and gives control of the stretching to the individual.
Polyamines control of cation transport across plant membranes: implications for ion homeostasis and abiotic stress signaling

Polyamines are unique polycationic metabolites, controlling a variety of vital functions in plants, including growth and stress responses. Over the last two decades a bulk of data was accumulated providing explicit evidence that polyamines play an essential role in regulating plant membrane transport. The most straightforward example is a blockage of the two major vacuolar cation channels, namely slow (SV) and fast (FV) activating ones, by the micromolar concentrations of polyamines. This effect is direct and fully reversible, with a potency descending in a sequence Spm4+ > Spd3+ > Put2+. On the contrary, effects of polyamines on the plasma membrane (PM) cation and K+-selective channels are hardly dependent on polyamine species, display a relatively low affinity, and are likely to be indirect. Polyamines also affect vacuolar and PM H+ pumps and Ca2+ pump of the PM. On the other hand, catabolization of polyamines generates H2O2 and other reactive oxygen species (ROS), including hydroxyl radicals. Export of polyamines to the apoplast and their oxidation there by available amine oxidases results in the induction of a novel ion conductance and confers Ca2+ influx across the PM. This mechanism, initially established for plant responses to pathogen attack (including a hypersensitive response), has been recently shown to mediate plant responses to a variety of abiotic stresses. In this review we summarize the effects of polyamines and their catabolites on cation transport in plants and discuss the implications of these effects for ion homeostasis, signaling, and plant adaptive responses to environment.
Perception and generation of mirror-inverted letters.

Reinvang I. R. Perception and generation of mirror-inverted letters. Scand. J. Psychol. , 1972, 13, 285–291. —-The ability to write and read mirror-inverted text was studied in two experiments. Exp. I showed no transfer of training from reading to writing, or vice versa, suggesting that separate systems with similar properties determine spatial reversals. In Exp. 2 subjects made more errors when trying to mirror-invert letters classified as left-orienting, rather than right-orienting. An explanation relating this finding to the left-to-right progression of text in English is offered.
In Vitro Comparison of Blood Pump Induced Platelet Microaggregates between a Centrifugal and Roller Pump During Cardiopulmonary Bypass

Platelets are consumed during cardiopulmonary bypass (CPB) and mechanical ventricular assistance, at least partly as a result of the formation of platelet microaggregates in the blood pump. There is no commonly accepted method currently available to detect platelet microaggregates during the use of CPB or left ventricular assist devices (LVAD). The purpose of this study was to develop a flow cytometric method for the quantification of platelet microaggregates generated in blood pumps, and to evaluate the effect of cellular fragments from hemolyzed erythrocytes on the perioperative assessment of platelet counts during CPB. Method Fresh human anticoagulated blood (1IU heparin /mL, activated clotting time 250 ± 24 sec.) was circulated for 120 minutes in an artificial circulatory system, containing either a centrifugal pump (CP) or roller pump (RP). Whole blood was used to quantify platelet consumption and to detect circulating platelet microaggregates in a flow cytometer. Platelet consumption was additionally analyzed using an automated “Coulter” blood cell counter. Hemolysis was analyzed by measurement of plasma free hemoglobin (fHb), as well a by flow cytometric detection of red blood cell (RBC) fragments. Results Flow cytometric analysis demonstrated significantly more circulating platelet aggregates and platelet consumption in the RP than in the CP (p<0.01). Quantification of RBC fragments and plasma free hemoglobin (fHb) levels also indicated significantly increased hemolysis in the RP than in the CP (p<0.01). In contrast, the Coulter count data indicated less platelet consumption in the PP compared to the CP. Conclusion Fragments from hemolyzed erythrocytes have the same size distribution as intact platelets and the number of RBC fragments correlates with the extent of pump-induced hemolysis during CPB. Our data suggest that assessment of platelets by “Coulter counting” cannot distinguish platelets from RBC fragments and may underestimate platelet consumption in the presence of hemolysis during CPB. We conclude that flow cytometry is more accurate in the perioperative assessment of platelet count and platelet aggregation during CPB and LVAD support.
Long-Term Mortality of 306,868 Patients with Multi-Vessel Coronary Artery Disease: CABG versus PCI

Background Several randomized controlled trials (RCT) have reported no difference in long-term mortality between coronary artery bypass grafting (CABG) and percutaneous coronary intervention (PCI). The purpose of this pooled observational analysis was to compare recent retrospective studies examining long-term survival of patients with multi-vessel coronary artery disease undergoing CABG and PCI. Methodology We searched Medline for observational studies comparing long-term (>1 year) survival between CABG and PCI for the treatment of multi-vessel coronary artery disease over the past 10 years. Results Eight studies met inclusion criteria. A total of 306,868 patients (155,502 CABG; 151,366 PCI) were identified. Follow-up ranged from 1 to 8 years. Mantel-Haenszel combined hazard ratios (HR) for mortality demonstrated a protective benefit of CABG compared with PCI (HR=0.77, 95%CI=0.75–0.79). Conclusion These findings suggest a long-term survival advantage for CABG compared with PCI in patients with multi-vessel coronary artery disease.
An Error Bound for L1-norm Support Vector Machine Coefficients in Ultra-high Dimension

Comparing with the standard L2-norm support vector machine (SVM), the L1-norm SVM enjoys the nice property of simultaneously preforming classification and feature selection. In this paper, we investigate the statistical performance of L1-norm SVM in ultra-high dimension, where the number of features p grows at an exponential rate of the sample size n. Different from existing theory for SVM which has been mainly focused on the generalization error rates and empirical risk, we study the asymptotic behavior of the coefficients of L1- norm SVM. Our analysis reveals that the estimated L1-norm SVM coefficients achieve near oracle rate, that is, with high probability, the L2 error bound of the estimated L1- norm SVM coefficients is of order Op(√q log p/n), where q is the number of features with nonzero coefficients. Furthermore, we show that if the L1-norm SVM is used as an initial value for a recently proposed algorithm for solving non-convex penalized SVM (Zhang et al., 2016b), then in two iterative steps it is guaranteed to produce an estimator that possesses the oracle property in ultra-high dimension, which in particular implies that with probability approaching one the zero coefficients are estimated as exactly zero. Simulation studies demonstrate the fine performance of L1-norm SVM as a sparse classifier and its effectiveness to be utilized to solve non-convex penalized SVM problems in high dimension.
A Monoclonal Antibody to O-Acetyl-GD2 Ganglioside and Not to GD2 Shows Potent Anti-Tumor Activity without Peripheral Nervous System Cross-Reactivity

Background Monoclonal antibodies (mAb) against GD2 ganglioside have been shown to be effective for the treatment of neuroblastoma. Beneficial actions are, however, associated with generalized pain due to the binding of anti- GD2 mAbs to peripheral nerve fibers followed by complement activation. Neuroblastoma cells that express GD2 also express its O-acetyl derivative, O-acetyl- GD2 ganglioside (OAcGD2). Hence, we investigated the distribution of OAcGD2 in human tissues using mAb 8B6 to study the cross-reactivity of mAb 8B6 with human tissues. Methodology/Principal Findings The distribution of OAcGD2 was performed in normal and malignant tissues using an immunoperoxydase technique. Anti-tumor properties of mAb 8B6 were studied in vitro and in vivo in a transplanted tumor model in mice. We found that OAcGD2 is not expressed by peripheral nerve fibers. Furthermore, we demonstrated that mAb 8B6 was very effective in the in vitro and in vivo suppression of the growth of tumor cells. Importantly, mAb 8B6 anti-tumor efficacy was comparable to that of mAb 14G2a specific to GD2. Conclusion/Significance Development of therapeutic antibodies specific to OAcGD2 may offer treatment options with reduced adverse side effects, thereby allowing dose escalation of antibodies.
What value covariance information in estimating vision parameters?

Many parameter estimation methods used in computer vision are able to utilise covariance information describing the uncertainty of data measurements. This paper considers the value of this information to the estimation process when applied to measured image point locations. Covariance matrices are first described and a procedure is then outlined whereby covariances may be associated with image features located via a measurement process. An empirical study is made of the conditions under which covariance information enables generation of improved parameter estimates. Also explored is the extent to which the noise should be anisotropic and inhomogeneous if improvements are to be obtained over covariance-free methods. Critical in this is the devising of synthetic experiments under which noise conditions can be precisely controlled. Given that covariance information is, in itself, subject to estimation error tests are also undertaken to determine the impact of imprecise covariance information upon the quality of parameter estimates. Finally, an experiment is carried out to assess the value of covariances in estimating the fundamental matrix from real images.
DNA Polymerases β and λ Mediate Overlapping and Independent Roles in Base Excision Repair in Mouse Embryonic Fibroblasts

Base excision repair (BER) is a DNA repair pathway designed to correct small base lesions in genomic DNA. While DNA polymerase beta (pol β) is known to be the main polymerase in the BER pathway, various studies have implicated other DNA polymerases in back-up roles. One such polymerase, DNA polymerase lambda (pol λ), was shown to be important in BER of oxidative DNA damage. To further explore roles of the X-family DNA polymerases λ and β in BER, we prepared a mouse embryonic fibroblast cell line with deletions in the genes for both pol β and pol λ. Neutral red viability assays demonstrated that pol λ and pol β double null cells were hypersensitive to alkylating and oxidizing DNA damaging agents. In vitro BER assays revealed a modest contribution of pol λ to single-nucleotide BER of base lesions. Additionally, using co-immunoprecipitation experiments with purified enzymes and whole cell extracts, we found that both pol λ and pol β interact with the upstream DNA glycosylases for repair of alkylated and oxidized DNA bases. Such interactions could be important in coordinating roles of these polymerases during BER.
Black Box Variational Inference

Variational inference has become a widely used method to approximate posteriors in complex latent variables models. However, deriving a variational inference algorithm generally requires significant model-specific analysis, and these efforts can hinder and deter us from quickly developing and exploring a variety of models for a problem at hand. In this paper, we present a "black box" variational inference algorithm, one that can be quickly applied to many models with little additional derivation. Our method is based on a stochastic optimization of the variational objective where the noisy gradient is computed from Monte Carlo samples from the variational distribution. We develop a number of methods to reduce the variance of the gradient, always maintaining the criterion that we want to avoid difficult model-based derivations. We evaluate our method against the corresponding black box sampling based methods. We find that our method reaches better predictive likelihoods much faster than sampling methods. Finally, we demonstrate that Black Box Variational Inference lets us easily explore a wide space of models by quickly constructing and evaluating several models of longitudinal healthcare data.
Novel Hardware Implementation of Adaptive Median Filters

A new FPGA implementation for adaptive median filters is proposed. Adaptive median filters exhibit better filtering properties than standard median filters; however, their implementation cost is higher. Proposed architecture was optimized for throughput allowing 300 M pixels to be filtered per second. The best performance/cost ratio exhibits the adaptive median filter which utilizes filtering window 7x7 pixels and can suppress shot noise with intensity up to 60%. In addition to filtering, adaptive median filters can be also used as detectors of corrupted pixels (detection statistics).
Detection of ochratoxin A and cis- and trans-resveratrol in red wines and their musts from Calabria (Italy)

The natural occurrence of ochratoxin A (OTA) and cis- and trans-resveratrols in red wines has been widely reported. The aim of this work was to evaluate the ochratoxin A (OTA) and both cis- and trans-resveratrol content of red wine (from must to wine) in a pilot-scale vinification process in Calabria (Italy). Eleven samples were collected at different stages of vinification and analysis was carried out by HPLC. Wine from manufacturer 3 contained the highest amount of trans-resveratrol (3.41 mg l−1). This wine was characterized by an Aglianico–Magliocco grape variety. Interestingly, data regarding OTA showed that the value of this contaminant was low in all analyzed samples and, in each case, below the legal limit (2.0 mg l−1 (ppb)). Overall, the results demonstrated the high quality of wines produced in Calabria.
Long-term outcomes following positive fecal occult blood test results in older adults: benefits and burdens.

BACKGROUND In the United States, older adults have low rates of follow-up colonoscopy after a positive fecal occult blood test (FOBT) result. The long-term outcomes of these real world practices and their associated benefits and burdens are unknown. METHODS Longitudinal cohort study of 212 patients 70 years or older with a positive FOBT result at 4 Veteran Affairs (VA) facilities in 2001 and followed up through 2008. We determined the frequency of downstream outcomes during the 7 years of follow-up, including procedures, colonoscopic findings, outcomes of treatment, complications, and mortality based on chart review and national VA and Medicare data. Net burden or benefit from screening and follow-up was determined according to each patient's life expectancy. Life expectancy was classified into 3 categories: best (age, 70-79 years and Charlson-Deyo comorbidity index [CCI], 0), average, and worst (age, 70-84 years and CCI, ≥4 or age, ≥85 years and CCI, ≥1). RESULTS Fifty-six percent of patients received follow-up colonoscopy (118 of 212), which found 34 significant adenomas and 6 cancers. Ten percent experienced complications from colonoscopy or cancer treatment (12 of 118). Forty-six percent of those without follow-up colonoscopy died of other causes within 5 years of FOBT (43 of 94), while 3 died of colorectal cancer within 5 years. Eighty-seven percent of patients with worst life expectancy experienced a net burden from screening (26 of 30) as did 70% with average life expectancy (92 of 131) and 65% with best life expectancy (35 of 51) (P = .048 for trend). CONCLUSIONS Over a 7-year period, older adults with best life expectancy were less likely to experience a net burden from current screening and follow-up practices than are those with worst life expectancy. The net burden could be decreased by better targeting FOBT screening and follow-up to healthy older adults.
Functional Skill Regression in Late-Stage Demel 1 tias

One hundred fifty-two institutionalized persons with late-stage dementia were rated with a geriatric developmental screening scale that notes cognitive, language, sensorimotor, and self-care abilities. The results showed that the loss offunctional abilities in late-stage dementias seems to occur in reverse order of their development in childhood. Developmental congruence was noted within these persons regardless ofdiagnosis. In addition, the average functional age rating correlated well with scores from the Folstein Mini Mental State examination (MMS) (Folstein, Folstein, & McHugh, 1975). The close correlation between scores indicates that the MMS is a fast and simple tool for predicting not only cognitive impairment but also the approximate stage offunctional development.