Miracle-dz/UniFAR-FTUs huggingface dataset:
macroH2A1 Histone Variants Are Depleted on Active Genes but Concentrated on the Inactive X Chromosome

ABSTRACT Using a novel thiol affinity chromatography approach to purify macroH2A1-containing chromatin fragments, we examined the distribution of macroH2A1 histone variants in mouse liver chromatin. We found that macroH2A1 was depleted on the transcribed regions of active genes. This depletion was observed on all of the 20 active genes that we probed, with only one site showing a small amount of enrichment. In contrast, macroH2A1 was concentrated on the inactive X chromosome, consistent with our previous immunofluorescence studies. This preferential localization was seen on genes that are active in liver, genes that are inactive in liver, and intergenic regions but was absent from four regions that escape X inactivation. These results support the hypothesis that macroH2As function as transcriptional repressors. Also consistent with this hypothesis is our finding that the heterochromatin protein HP1β copurifies with the macroH2A1-containing chromatin fragments. This study presents the first detailed examination of the distribution of macroH2A1 variants on specific sequences. Our results indicate that macroH2As have complex distribution patterns that are influenced by both local factors and long-range mechanisms.
Functions of invariant NK T cells are modulated by TLR ligands and IFN-α

Invariant NK T (iNKT) cells perform numerous immunoregulatory functions. In mice, they express a unique and invariant Vα14-Jα18 rearrangement of α chain in their TCR recognizing glycolipid Ags presented by CD1d. This recognition results in the rapid release of both Th1- and Th2-type cytokines, making them early mediators of the immune response. Owing to their rapid activation and genetic rigidity of their TCR, iNKT cells share characteristics with innate lymphocytes. Therefore, we investigated whether iNKT cells could be induced to express TLRs, a class of pathogen recognition receptor. Mouse iNKT cells were stimulated with anti-CD3 monoclonal Ab and IFN-α, resulting in an increase in the transcription of TLRs 3, 5, 7 and 9, and increased surface expression of TLR3. These cells were subsequently stimulated with TLR ligands, resulting in an increase in the production of IFN-γ, IL-4 and TNF-α. Supernatants from these cells also increased macrophage production of IL-6 and prostaglandin E2, and increased their phagocytic activity and CD80 expression. These supernatants also reduced vesicular stomatitis virus-GFP replication in fibroblasts. This study demonstrates the role of IFN-α in iNKT cell activation, as well as the direct modulatory effects of TLR ligands on iNKT cell function, including antiviral activity.
Essays on the demand for ethanol in the United States: willingness to pay for E85

This dissertation contains three studies that estimate the distribution of willingness to pay (WTP) for E85 as a substitute for E10 among flex motorists in the United States. The results are vital for estimating the demand for ethanol beyond the blend wall and for analysis of the Renewable Fuel Standard. The first study attempts to estimate the distribution of preference for E85 from data generated by a survey of E85 stations in Minnesota. The study uses an extensive sample of recent observations, but estimates of the WTP distribution vary substantially depending on model specification. The conclusion is that the data are not suitable to estimate the distribution of WTP for E85.The second and third studies collect primary data from E85 stations in different regions of the United States to more accurately estimate preferences for E85 and investigate locational differences. The studies obtain revealed-preference (RP) data from flex motorists refueling at E85 stations and stated-preference (SP) data from surveying the flex motorists and presenting hypothetical scenarios. The second study uses the RP data to estimate relative preferences for E85, and the third study incorporates the SP data to better capture the wide range of fuel-switching behavior.The estimation sample consists of about nine hundred flex motorists in six urban areas in the Midwest and California. The sample of flex motorists who refuel at E85 stations is endogenously stratified; the probability of a flex motorist appearing in the sample is correlated to the motorist's WTP for E85. The models apply corrective probability weights so estimates reflect the population and not the sample.The results show that a $0.10 increase in the E85-E10 price difference decreases the probability of motorists choosing E85 by about 2.5 percent, on average, and preferences are spread over a broad range of fuel prices. In general, motorists are willing to pay more for E85 in California than in the Midwest, and when E85 and E10 are priced equally on a cost-per-mile basis, about 25 percent of flex motorists choose E85 in the Midwest compared to 75 percent in California.
Vitamin B6 requirements of nutritionally variant Streptococcus mitior

The growth rate of three vitamin B6-dependent Streptococcus mitior (B6DS) and two non-B6DS strains in Todd-Hewitt broth, with and without vitamin B6 supplementation, was examined. Even in optimally supplemented culture media, the growth rate of the three B6DS strains was much slower than that of comparable non-B6DS strains. Uptake studies with [3H] pyridoxine suggest that these B6DS strains cannot assimilate pyridoxine. Although not transported intracellularly, pyridoxine inhibited the growth of B6DS strains in media supplemented with other vitamin B6 analogs, probably by binding to the vitamin B6 transport system and inhibiting the uptake of the other vitamin B6 analogs.
Three-dimensional surface reconstruction and fluorescent visualization of cardiac activation

Optical imaging of transmembrane potentials in cardiac tissue is a rapidly growing technique in cardiac electrophysiology. Traditional studies typically use a monocular imaging setup, thus limiting investigation to a restricted region of tissue. However, studies of large-scale wavefront dynamics, especially those during fibrillation and defibrillation, would benefit from visualization of the entire epicardial surface. To solve this problem, a panoramic cardiac visualization algorithm was developed which performs the two tasks of reconstruction of the surface geometry of the heart, and representation of the panoramic fluorescence information as a texture mapping onto the geometry that was previously created. This system permits measurement of epicardial electrodynamics over a geometrically realistic representation of the actual heart being studied. To verify the accuracy of the algorithm, the procedure was applied to synthetic images of a patterned ball; further verification was provided by application of the algorithm to a model heart placed in the experimental setup. Both sets of images produced mean registration image errors on the order of 2 pixels, corresponding to roughly 3 mm on the geometry. The authors demonstrate the algorithm by visualizing epicardial wavefronts on an isolated, perfused rabbit heart.
Can serological methods help distinguish between prophylactic and alloimmune anti‐D?

Enzyme indirect antiglobulin test (EIAT) and polyethylene glycol IAT (PIAT) were evaluated for their potential use as tests to distinguish between prophylactic and alloimmune anti‐D in plasma by comparing with a tube variation of the standard low ionic strength solution‐IAT (LISS‐IAT).
Silicon Micromachined Terahertz Bandpass Filter With Elliptic Cavities

In this paper, a 400-GHz silicon micromachined elliptic cavity waveguide filter with two transmission zeros on both sides of the passband is presented. The filter is cascaded by two elliptic cavities which are operating at quasi- TM110 mode. Each elliptic cavity can introduce a transmission zero near the passband of the filter. By adjusting the axial-ratio (AR) of the elliptic cavity, the position of the introduced transmission zero could be moved to the upper side or the lower side of the passband. The micromachining process of deep reactive ion etching (DRIE) is used for the fabrication. The measured 3-dB bandwidth of the filter is 7.52%, from 380.2 to 409.9 GHz, and the measured insertion loss is 2.84 dB, including extra waveguide of about 4.5 mm at the input and output ports. In addition, the insertion loss of straight waveguide is also measured and analyzed. Then, an analysis method for the loss property is summarized. According to the measurement, the unit length loss of the waveguide is about 0.144 dB/mm at 400 GHz.
Improved lossless compression of color-mapped images by an approximate solution of the traveling salesman problem

A color-mapped image is composed of a palette and an image of indices. The color of each pixel is the palette color referenced by the pixel's index. The indices image is usually far from being smooth. This affects its compressibility by lossless image compression methods, due to their reliance on the natural smoothness of images. The indices images can be smoothed by re-ordering the palette, ie, assigning the indices to the colors in a better way. We propose a new method for palette ordering based on an approximate solution of the traveling salesman problem. The proposed method has low complexity, dependent only on the size of the palette. It is found to significantly improve the compression ratios of color-mapped images coded with the JPEG-LS lossless compression standard. The resulting compression ratios are better than those achieved by the popular GIF image file format.
Prospective study of physical activity in different periods of life and the risk of ovarian cancer

Only few studies have assessed the role of physical activity in the etiology of ovarian cancer, and the results have been inconclusive. We studied associations between physical activity and risk of ovarian cancer in 96,541 women aged 30–49 at enrollment in a prospective study in Norway and Sweden. Participants reported physical activity level at ages 14, 30 and at enrollment, and participation in competitive sports. Complete follow‐up through 2001/2002 was achieved by linkage to national registries. The relation between physical activity and ovarian cancer incidence was assessed using multivariate Cox proportional hazard models. During an average 11.1 years of follow‐up, there were 264 ovarian cancer cases (including 81 borderline tumors) diagnosed at a mean age of 49 years. Highly physically active women at cohort enrollment had a similar risk of ovarian cancer as women reporting no activity (multivariate relative risk RR = 1.08, 95% CI 0.53–2.18). Physical activity at age 30 or at age 14 did not either afford any protection from ovarian cancer, nor did a consistently high level of activity from younger ages until enrollment. Results were similar for invasive and borderline tumors, and for different subgroups of women classified according to other known risk factors for ovarian cancer. In our study of primarily premenopausal women, physical activity at different ages did neither reduce nor increase risk of ovarian cancer. In the context of the inconsistent scientific literature, our findings probably reflect that physical activity is not causally related with ovarian cancer. © 2006 Wiley‐Liss, Inc.
THE RELATIONSHIP BETWEEN OUTPUT GAP AND EXCESS LIQUIDITY IN EUROPEAN TRANSITION ECONOMIES

The aim of this thesis is to investigate the definition and measurement of the potential output and the output gap, to examine the definition and determinants of the size and the behaviour of excess liquidity in the banking sector in transition economies and last, to explore the theoretical and empirical links between the output gap and excess liquidity. Estimating potential output and the corresponding output gap is deemed as particularly relevant for the conduct of monetary and fiscal policy as well as in providing useful insights regarding the state of the economy, especially for periods with below potential production. One of the most important factors associated with a large output gap may be the efficiency of financial systems in transition economies, in particular the behaviour of banks, as they represent the main source of finance with capital markets being in their infancy. Access to banking loans is one of the main sources of finance for a firm’s growth, while excess liquidity holdings are a feature of several European transition economies. Thus, another research question addressed in this thesis is why do banks in transition economies continuously accumulate excess reserves in the face of seemingly profitable loans to invest in, relative to developed countries, which are also costly to maintain. Criticizing the prior definitions of excess liquidity in the existing literature as imprecise, another theoretical added value of this thesis consists on clarifying the excess liquidity concept and subsequently redefining its measurement. Augmenting the model with risk, regulatory and institutional variables, the findings suggest that involuntary factors that are mainly outside of banks’ control (e.g. lack of credit demand, poor institutional framework) prevail in inducing banks to accumulate excess reserves, relative to the precautionary motive. Treating potential endogeneity issue between excess liquidity and the output gap, the last finding of this research proclaims that rather being in a causal relationship, both are actually correlated via the common observed and unobserved determinants. Due to the lack of a clear transmission mechanism from one to the other factor, rather than pushing banks to reduce excess liquidity to extend lending and consequently to reduce the output gap, a policy implication of the thesis is that other factors outside of the system that are capable of pushing both variables in the desired direction need to be identified. The avoidance of a policy where banks are pushed to reduce excess liquidity is the main policy implication of this chapter, since that may lead into a new wave of bad loans rather than impetus to economic activity.
A randomised controlled feasibility trial of alcohol consumption and the ability to appropriately use a firearm

Objective: To show the feasibility of using a controlled trial to investigate the effect of alcohol on firearm use. Methods: Randomised, blinded, placebo-controlled trial in the Firearm Usage and Safety Experiments (FUSE) Lab. Treatment subjects (male, 21–40-year-old, non-habitual drinkers, with no professional firearms training) received alcohol; control subjects received placebo alcohol. The AIS PRISim Firearm Simulator, including real pistols retrofitted to discharge compressed air cartridges that simulate firearm recoil and sound, was used to measure firearm performance. Accuracy and speed for target shooting, reaction time scenarios, and scenarios requiring judgement about when to use a gun were measured. Results: 12 subjects enrolled in the trial, completing 160 training scenarios. All subjects in the alcohol arm reached target alcohol level. 33% of placebo subjects reported alcohol consumption. Mechanical malfunction of the simulator occurred in 9 of 160 (5.6%) scenarios. Intoxicated subjects were less accurate, slower to fire in reaction time scenarios, and quicker to fire in scenarios requiring judgement relative to controls. Conclusions: The feasibility of a randomised, controlled trial exploring the relationship between alcohol consumption and firearm use was shown. The hypothesis that alcohol consumption worsens accuracy and retards judgement about when to use a gun should be tested. Larger trials could inform policies regarding firearm use while intoxicated.
CT Textural Analysis of Large Primary Renal Cell Carcinomas: Pretreatment Tumor Heterogeneity Correlates With Histologic Findings and Clinical Outcomes.

OBJECTIVE The purpose of the present study is to determine whether CT texture features of newly diagnosed primary renal cell carcinomas (RCCs) correlate with pathologic features and oncologic outcomes. MATERIALS AND METHODS CT texture analysis was performed on large (> 7 cm; mean size, 9.9 cm) untreated RCCs in 157 patients (52 women and 105 men; mean age, 60.3 years). Measures of tumor heterogeneity, including entropy, kurtosis, skewness, mean, mean of positive pixels, and SD of pixel distribution histogram were derived from multiphasic CT using various filter settings: unfiltered (spatial scaling factor, 0), fine (spatial scaling factor, 2), medium (spatial scaling factor, 3-4), or coarse (spatial scaling factor, 5-6). Texture values were correlated with histologic subtype, nuclear grade, pathologic stage, and clinical outcome. RESULTS When a coarse filter setting (spatial scaling factor, 6) was used, entropy on portal venous phase CT images was positively associated with clear cell histologic findings (odds ratio [OR], 134; 95% CI, 16-1110; p < 0.001) and was negatively associated with non-clear cell subtype findings (papillary spatial scale factor, 6; OR, 0.016; 95% CI, 0.002-0.132; p < 0.001). ROC curve analysis for entropy (on portal venous phase images obtained with a spatial scaling factor of 6) revealed an AUC of 0.943 (95% CI, 0.892-0.993) for clear cell histologic findings, with similar values noted for non-clear cell histologic findings. The mean of positive pixels and the SD of the pixel distribution histogram were statistically significantly associated with histologic cell type in a similar fashion. Entropy, the SD of the pixel distribution histogram, and the mean of positive pixels were associated with nuclear grade, most prominently when fine or medium texture filters were used (p < 0.05). There was a statistically significant association of texture features noted on unenhanced CT, including the SD of the pixel distribution histogram, the mean of positive pixels, and entropy, with the time to disease recurrence and death due to disease (e.g., for entropy noted on unenhanced CT images obtained with a spatial scaling factor of 6, the hazard ratio was 3.49 [95% CI, 1.55-7.84]; p = 0.002). CONCLUSION CT texture features (in particular, entropy, the mean of positive pixels, and the SD of the pixel distribution histogram) are associated with tumor histologic findings, nuclear grade, and outcome measures. The contrast phase does seem to affect heterogeneity measures.
DETECTION OF ANTIBODIES TO TUBERCULOSIS ANTIGENS IN FREE-RANGING LIONS (PANTHERA LEO) INFECTED WITH MYCOBACTERIUM BOVIS IN KRUGER NATIONAL PARK, SOUTH AFRICA

Abstract: Bovine tuberculosis (TB), caused by Mycobacterium bovis, has become established in Kruger National Park, South Africa, in the cape buffalo (Syncerus caffer) population and in other species. TB in prey species has resulted in infection and morbidity in the resident lion (Panthera leo) prides. The only validated live animal test currently available for lions is the intradermal tuberculin test. Because this test requires capture twice, 72 hr apart, of free-ranging lions to read results, it is logistically difficult to administer in a large ecosystem. Therefore, development of a rapid animal-side screening assay would be ideal in providing information for wildlife managers, veterinarians, and researchers working with free-living lion prides. This study reports preliminary descriptive results from an ongoing project evaluating two serologic tests for M. bovis (ElephantTB Stat-Pak and dual path platform VetTB). Disease status was determined by postmortem culture and presence of pathologic lesions in 14 free-ranging lions. Seropositivity was found to be associated with M. bovis infection. Extended field studies are underway to validate these rapid animal-side immunoassays for antemortem screening tests for TB in lions.
Right-Handers and Americans Favor Turning to the Right

We tested a finding by E. S. Robinson (1933) that people have a bias to turn right upon entering a building. We hypothesized that this bias is attributable to learning derived from traffic rules that specify driving on the right side of the road and that it also could be related to handedness. We tested participants in both the United States and England in a simple "T-maze" task in order to compare their directional preference. Handedness was the best predictor of participants' directional preference. However, U.S. participants also were statistically more likely to turn right than were English participants. The preference to turn right was not found to be significantly related to eye dominance or reading direction of the primary written language of the participant, although in the case of reading direction, the sample size of right-to-left readers was too small to be conclusive. The findings support that walking direction preference is an additive function of both learned driving patterns and genetic handedness. These findings have practical implications for the design of public spaces such as schools, businesses, and urban centers.
Cytosine methyltransferase from Escherichia coli in which active site cysteine is replaced with serine is partially active.

EcoRII methyltransferase (M.EcoRII) catalyzes the transfer of methyl groups from S-adenosyl-L-methionine (SAM) to C-5 position of second cytosine in the DNA sequence 5'-CCWGG (W = A or T). The reaction is initiated by a nucleophilic attack of the C-6 of target cytosine by a cysteine that is conserved among all cytosine methyltransferases. We have replaced this cysteine in M.EcoRII with serine or alanine and purified the proteins to homogeneity. The catalytic efficiency (kcat/Km) of the mutant enzyme with serine (C186S) for methyl transfer is about 10,000 times less than that of WT but is substantially higher than the efficiency of the C186A mutant. We show that the WT enzyme and C186S mutant are proficient in exchange of proton at C-5 and that this activity is reduced in the mutant to the same extent as the methyl transfer activity. The C186S mutant is insensitive to a cysteine-specific inhibitor, and it transfers methyl groups to the same position of cytosine as the WT enzyme. The ability of serine to act as a nucleophile in the enzyme reaction suggests that it--and probably the cysteine in the WT enzyme--is activated by a nearby base. Like the WT enzyme, C186S forms stable SDS-resistant complexes with DNA containing 5-azacytosine; but unlike the WT enzyme, the mutant reacts faster with 5-azacytosine than with normal cytosine. Apparently, greater reactivity of 5-azacytosine assists the C186S mutant in catalysis.
A systematic scheme for multiple access in ethernet passive optical access networks

While backbone networks have experienced substantial changes in the last decade, access networks have not changed much. Recently, passive optical networks (PONs) seem to be ready for commercial deployment as access networks, due to the maturity of a number of enabling technologies. Among the PON technologies, Ethernet PON (EPON) standardized by the IEEE 802.3ah Ethernet in the First Mile (EFM) Task Force is the most attractive one because of its high speed, low cost, familiarity, interoperability, and low overhead. In this paper, we consider the issue of upstream channel sharing in the EPONs. We propose a novel multiple-access control scheme to provide bandwidth-guaranteed service for high-demand customers, while providing best effort service to low-demand customers according to the service level agreement (SLA). The analytical and simulation results prove that the proposed scheme performs best in what it is designed to do compared to another well-known scheme that has not considered providing differentiated services. With business customers preferring premium services with guaranteed bandwidth and residential users preferring low-cost best effort services, our scheme could benefit both groups of subscribers, as well as the operators.