Miracle-dz/UniFAR-FTUs huggingface dataset:
Individual activator and repressor transcription factors induce global changes in chromatin mobility

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. Yet how nucleus-wide chromatin structures respond dynamically to the activity of specific TFs remains unclear. Here we asked how TFs with opposite effects on modulating local chromatin accessibility impact nucleus-wide chromatin dynamics in living cells. We combine High-resolution Diffusion mapping (Hi-D) and Dense Flow reConstruction and Correlation (DFCC) to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs in live cells. We show that expression of individual activator and repressor TFs increases nucleus-wide chromatin mobility and induces opposite coherent chromatin motions at the micron scale. Our quantitative analysis thus reveals the broad and differential impact of TFs opening and closing chromatin in nucleus-wide chromatin dynamics. Single-particle tracking (SPT) methods have been used to study dynamic TF-DNA interactions and to assess the role of TFs in shaping the chromatin mobility landscape in living eukaryotic cells ( 19 – 25 ). Most of these studies showed that the residence time of DNA-bound TFs affects the temporal expression patterns of transcription ( 19 , 23 , 24 ) and the spatial organization of chromatin in live cells ( 20 , 22 ). This shows the importance of residence times as a biophysical characteristic for regulating transcriptional activity and genome organization. A new analytical approach allowing to study the dynamic pioneer TF-chromatin interactions showed that chromatin mobility itself can directly influence the impact of pioneer TFs on gene expression ( 26 ). So far, the high spatio-temporal mobility analysis of local chromatin organization in living cells has mostly relied on fluorescent labelling of specific genomic sites, which can be spatially resolved and tracked over time using SPT ( 27 , 28 ). As an alternative approach for imaging sparsely-labelled nucleosomes over the whole nucleus, super-resolution imaging of the H2B histone was combined with SPT to visualize and track chromatin domains in living cells ( 26 , 29 ). These methods, however, apply one motion model for diffusion characterization that results in an incomplete understanding of the physical mechanisms underlying chromatin motions ( 30 ). In addition, these are limited to sparse single loci analysis, and thus lack information about neighboring chromatin sequences and long-range correlations of chromatin movements.
Uncertainties in future ozone and PM10 projections over Europe from a regional climate multiphysics ensemble

Due to the computational time required for modeling air quality climatologies, the characterization of processes introducing the largest uncertainty in air quality‐climate projections is a sound field of research. Here an air quality ensemble is assessed over Europe for present (1971–2000) and future (2071–2100, SRES A2) periods to characterize the sensitivity of regional air quality projections to the physics of the regional climate model driving the simulations. The ensemble comprises eight members resulting from combining two options of parameterization schemes for the planetary boundary layer, cumulus, and microphysics. The differences in the ensemble members (spread) for the concentration of tropospheric ozone and particulate matter (PM10) are strongly affected by the physics selected and could be considered as a matter of uncertainty in the change signals. Also, the leading processes causing the largest uncertainties in air quality projections have been identified and are mainly related to the election of the cumulus schemes.
A Qualitative Evaluation Of The Information, Education And Communication (IEC) Component Of The Tuberculosis Control Programme In Delhi, India

TB control programs have recognized that knowledge and behavior of the patient, as well as of the general population have a profound influence on the treatment seeking behavior and completion of course of treatment. The ongoing IEC efforts against tuberculosis in Delhi were intensified in the form of a multi-pronged media campaign. Objectives of this study were to evaluate (i) the impact of the campaign on awareness generation (ii) their opinion for making the campaign more effective (ii) perceptions of health personnel regarding the Campaign. The following qualitative methods were used(I) Focus Group Discussion ,(ii) key informant interviews (iii) In-depth interviews. Results and Conclusion: The study observed that (i) Different segments of the population varied their observations of IEC messages(ii) Stigma associated with tuberculosis is widely prevalent. (iii) Television voted as the most effective IEC medium. Therefore IEC strategies should be tailor-made and suited according to the needs of a sub-population. Funded by Delhi Tapedic Unmulan Samiti
THE SENSITWITY OF NORTHERN SIERRA NEVADA STREAMFLOW TO CLIMATE CHANGE

ABSTRACT: The sensitivity of streamflow to climate change was investigated in the American, Carson, and Truckee River Basins, California and Nevada. Nine gaging stations were used to represent streamflow in the basins. Annual models were developed by regressing 1961–1991 streamflow data on temperature and precipitation. Climate-change scenarios were used as inputs to the models to determine streamflow sensitivities. Climate-change scenarios were generated from historical time series by modifying mean temperatures by a range of +4°C to—4°C and total precipitation by a range of +25 percent to -25 percent. Results show that streamflow on the warmer, lower west side of the Sierra Nevada generally is more sensitive to temperature and precipitation changes than is streamflow on the colder, higher east side. A 2°C rise in temperature and a 25-percent decrease in precipitation results in stream-flow decreases of 56 percent on the American River and 25 percent on the Carson River. A 2°C decline in temperature and a 25-percent increase in precipitation results in streamflow increases of 102 percent on the American River and 22 percent on the Carson River.
Arrhythmia Management Devices

172 Almost 4 decades after its conception the implantable cardioverter–defibrillator (ICD) has emerged as a widely accepted treatment modality for the prevention of sudden cardiac death (SCD). The indications for ICD therapy have rapidly expanded over the past 10 years, and, today, >100 000 ICDs are implanted annually in the United States. More recently, however, some have raised words of caution as to the potential overestimation of ICD-associated benefits and hazards in individual patients. Therefore, this review summarizes the current scientific basis for ICD indications, puts it in context with recent guidelines, and discusses areas where additional trial evidence is needed to clarify pending issues regarding the optimal use of device therapy.
Hubungan Efesiensi Operasional dengan Kinerja Profitabilitas pada Sektor Perbankan yang Go Public di Bursa Efek Indonesia

Tujuan penelitian ini adalah untuk dapat mengetahui pentingnya hubungan antara tingakat efisiensi operasional dan kinerja profitabilitas perbankan di Bursa Efek Indonesia (BEI) dan untuk mejelaskan sejauh mana tingkat operasional efisiensi memberikan informasi tentang profitabilitas kinerja perbankan di Bursa Efek Indonesia (BEI). Objek penelitian ini adalah perusahaan perbankan go public yang terdaftar di Bursa Efek Indonesia (BEI) dengan jumlah populasi sebanyak 25 bank dimana populasi ini adalah juga menjadi sampel, serta periode penelitian dari tahun 2005 sampai dengan tahun 2008. Metode analisis yang digunakan adalah Regresi Linier Berganda ( Multiple Linier Regression ). Hasil pengujian membuktikan bahwa variable bebas memiliki pengaruh terhadap variable terikat. Variabel CAR mempengaruhi ROA secara signifikan sedangkap MSDN dan LDR tidak berpengaruh signifikan terhadap ROA pada perusahaan perbankan go public di Bursa Efek Indonesia. Kata Kunci : Capital Adequacy Ratio (CAR), Dana Pihak Ketiga (DPK/MSDN), Loan to deposit Ratio (LDR), Return on Assets (ROA)
Commentary: On Causes, Causal Inference, and Potential Outcomes

I would like to structure my remarks on the papers by Vandenbroucke et al. and by Krieger and Davey Smith around a series of propositions that articulate my views concerning causes, causation, and potential outcomes. I will then relate each of the propositions to the material discussed by Vandenbroucke et al. and by Krieger and Davey Smith and discuss where I agree and disagree with their comments. Certain claims about the potential outcomes framework made by Vandenbroucke et al. have also been clarified in a recent letter. See also related discussion on another recent similar article by Schwartz et al.
Surficial bitumen in the Athabasca oil sands region, Alberta, Canada

The Athabasca Oil Sands of Northeastern Alberta, Canada, are primarily recovered by surface mining operations. These areas are required by regulation to be reclaimed at mine closure. Recent cuts in the proposed borrow areas for cover material have revealed unusual deposits of hydrocarbons at quantities exceeding clean soil guidelines in the surficial materials. This article outlines recent work in characterising the hydrocarbon composition and groundwater leaching potential of this surficial bitumen. Characterisation consisted of field sampling with analysis by standard Canadian chromatographic methods. An initial investigation of contaminant mobility and biodegradability was conducted using a custom unsaturated soil column leaching experiment. Hydrocarbons were found to be primarily above C30. Concentrations greater than C60 were approximately 10 times those below C60. As expected, minimal leaching occurred, suggesting a minimal risk to groundwater. This result provides meaningful evidence that the material can be directly placed for reclamation. This option in turn represents a meaningful saving in terms of cost, effort and energy for the mine operators.
Observations of the geopause at the equatorial magnetopause: Density and temperature

Magnetic flux tubes containing plasmaspheric ion density and composition have been observed in the region between the classical plasmapause and the magnetopause. New observations show that these ion distributions exist at the equatorial, post‐noon magnetopause. Comparison to observations of similar distributions at geosynchronous orbit and to simulations leads to the conclusion that these ions are convected from these regions to the magnetopause. This represents an extension of the geopause to the outer edge of the magnetosphere on the dayside. The presence of ion densities >10cm−3 in this region must have profound impact on the nature of plasma processes that occur there.
Impact of MR based attenuation correction on neurological PET studies

Hybrid positron emission tomography (PET) and magnetic resonance (MR) scanners have become a reality in recent years with the benefits of reduced radiation exposure, reduction of imaging time, and potential advantages in quantification. Appropriate attenuation correction remains a challenge. Biases in PET activity measurements were demonstrated using the current MR based attenuation correction technique. We aim to investigate the impact of using standard MRAC technique on the clinical and research utility of PET/MR hybrid scanner for amyloid imaging. Methods: Florbetapir scans were obtained on 40 participants on a Biograph mMR hybrid scanner with simultaneous MR acquisition. PET images were reconstructed using both MR and CT derived attenuation map. Quantitative analysis was performed for both datasets to assess the impact of MR based attenuation correction to absolute PET activity measurements as well as target to reference ratio (SUVR). Clinical assessment was also performed by a nuclear medicine physician to determine amyloid status based on the criteria in the FDA prescribing information for florbetapir. Results: MR based attenuation correction led to underestimation of PET activity for most part of the brain with a small overestimation for deep brain regions. There is also an overestimation of SUVR values with cerebellar reference. SUVR measurements obtained from the two attenuation correction methods were strongly correlated. Clinical assessment of amyloid status resulted in identical classification as positive or negative regardless of the attenuation correction methods. Conclusions: MR based attenuation correction cause biases in quantitative measurements. The biases may be accounted for by a linear model, although the spatial within CT field of view (FOV), attenuation coefficients were estimated by converting CT Hounsfield values into attenuation coefficients for 511 keV photons using a bilinear function defined by three control points: (–1,000 HU, 0 cm –1 ), (0 HU, 0.093 cm –1 ), and (1,326 HU, 0.172 cm –1 ) ( 15 ). For voxels outside of CT FOV, the attenuation coefficients derived from the Dixon sequence were used. For each participant dataset, two reconstructed PET images were generated, one based on Dixon MRAC and the other based on CTAC. It should be emphasized that exactly the same reconstruction algorithm was used for both MRAC and CTAC, the only difference is the source of the attenuation map.
The influence of air‐sea exchange on the isotopic composition of oceanic carbon: Observations and modeling

Although the carbon isotropic composition of ocean waters after they leave the surface ocean is determined by biological cycling, air-sea exchange affects the carbon isotopic composition of surface waters in two ways. The equilibrium fractionation between oceanic and atmospheric carbon increases with decreasing temperature. In Southern Ocean Surface Waters this isotopic equilibrium enriches {delta}{sup 13}C relative to the {delta}{sup 13}C expected from uptake and release of carbon by biological processes alone. Similarly, surface waters in the subtropical gyres are depleted in {delta}{sup 13}C due to extensive air-sea exchange at warm temperatures. Countering the tendency toward isotopic equilibration with the atmosphere (a relatively slow process), are the effects of the equilibration of CO{sub 2} itself (a much faster process). In regions where there is a net transfer of isotopically light CO{sub 2} from the ocean to the atmosphere (e.g., the equator) surface waters become enriched in {sup 13}C, whereas in regions where isotopically light CO{sub 2} is entering the ocean (e.g., the North Atlantic) surface waters become depleted in {sup 13}C. A compilation of high quality oceanic {delta}{sup 13}C measurements along with experiments performed using a zonally averaged three-basin dynamic ocean model are used to explore these processes. 40 refs., 14more » figs., 1 tab. « less
A TREE‐RING RECONSTRUCTION OF STREAMFLOW FOR THE COLORADO FRONT RANGE 1

ABSTRACT: Water resource planning is based primarily on 20th century instrumental records of climate and streamflow. These records are limited in length to approximately 100 years, in the best cases, and can reflect only a portion of the range of natural variability. The instrumental record neither can be used to gage the unusualness of 20th Century extreme low flow events, nor does it allow the detection of low‐frequency variability that may underlie short‐term variations in flow. In this study, tree rings are used to reconstruct mean annual streamflow for Middle Boulder Creek in the Colorado Front Range, a semi‐arid region of rapid growth and development. The reconstruction is based on a stepwise regression equation that accounts for 70 percent of the variance in the instrumental record, and extends from 1703–1987. The reconstruction suggests that the instrumental record of streamflow for Middle Boulder Creek is not representative of flow in past centuries and that several low flow events in the 19th century were more persistent than any in the 20th century. The 1840s to early 1850s period of low flow is a particularly notable event and may have coincided with a period of low flow in the Upper Colorado River Basin.
Probe Permeametry: An Overview and Bibliography

Applications of probe permeameters in both laboratory and outcrop studies of permeability heterogeneity are common. We present an overview of the current status of probe permeameter data acquisition, analysis, and application. The multidisciplinary nature of probe permeameter studies has led to their publication in diverse scientific journals. We present a bibliography that includes literature covering both the technology and the application of probe permeametry.
Exploring the climate change refugia potential of equatorial Pacific coral reefs

Global climate models project a 21st century strengthening of the Pacific Equatorial Undercurrent (EUC). The consequent increase in topographic upwelling of cool waters onto equatorial coral reef islands would mitigate warming locally and modulate the intensity of coral bleaching. However, EUC water is potentially more acidic and richer in dissolved inorganic nutrients (DIN), both widely considered detrimental to coral reef health. My analysis of the Simple Ocean Data Assimilation product indicates that the EUC has indeed strengthened over the past 130 years. This result provides an historical baseline and dynamical reference for future intensification. Additionally, I reared corals in laboratory experiments, co-manipulating food, light and CO2 (acidity) to test the role of nutrition in coral response to elevate CO2 conditions. Heterotrophy yields larger corals but CO2 sensitivity is independent of feeding. Conversely, factors that enhance zooxanthellate photosynthesis (light and DIN) reduce CO2 sensitivity. Corals under higher light also store more lipid but these reserves are not utilized to maintain calcification under elevated CO2 My results suggest that while mitigation of CO2 effects on calcification is not linked to energetic reserve, EUC fueled increases in DIN and productivity could reduce effects of elevated CO2 on coral calcification.
Temporal SNR characteristics in segmented 3D‐EPI at 7T

Three‐dimensional segmented echo planar imaging (3D‐EPI) is a promising approach for high‐resolution functional magnetic resonance imaging, as it provides an increased signal‐to‐noise ratio (SNR) at similar temporal resolution to traditional multislice 2D‐EPI readouts. Recently, the 3D‐EPI technique has become more frequently used and it is important to better understand its implications for fMRI. In this study, the temporal SNR characteristics of 3D‐EPI with varying numbers of segments are studied. It is shown that, in humans, the temporal variance increases with the number of segments used to form the EPI acquisition and that for segmented acquisitions, the maximum available temporal SNR is reduced compared to single shot acquisitions. This reduction with increased segmentation is not found in phantom data and thus likely due to physiological processes. When operating in the thermal noise dominated regime, fMRI experiments with a motor task revealed that the 3D variant outperforms the 2D‐EPI in terms of temporal SNR and sensitivity to detect activated brain regions. Thus, the theoretical SNR advantage of a segmented 3D‐EPI sequence for fMRI only exists in a low SNR situation. However, other advantages of 3D‐EPI, such as the application of parallel imaging techniques in two dimensions and the low specific absorption rate requirements, may encourage the use of the 3D‐EPI sequence for fMRI in situations with higher SNR. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
Diurnal variations in convective storm activity over contiguous North China during the warm season based on radar mosaic climatology

[1] Diurnal variations in the formation and development of convective storms over contiguous North China during the warm season were studied using reflectivity from six China Next Generation Weather Radars between 2008 and 2011. Our results, including temporal and spatial analysis of hourly storm frequency through the warm season, and inter-month comparisons during June, July and August, indicate that most storms initiate over the northwestern mountains in the afternoon as a result of solar heating, with the highest frequency in June, and the lowest in August. Storms propagate from the mountains to the southeastern foothills and plains, with the highest rates occurring in June, and the lowest in August. In the late afternoon, there is a remarkably high storm frequency over the foothills and plains, which indicates a significant topographic control on the southeastward propagation and intensification of storms during the warm season. Storm activity occurs mainly on the plains through the night, with the highest frequency in July and the lowest in June, as a result of a favorable nocturnal convection mechanism. The region-averaged hourly storm frequencies for the warm season, and also for each month in JJA, are all bimodally distributed, with peak frequencies occurring in late afternoon and during the night, with the highest frequency recorded in the late afternoon during June and July, but at night in August. In general, the mean storm frequency is highest during the day and night in July, and lowest from afternoon to evening in August, but from nighttime to the next morning in June.
Mathematical Models of Distribution of Sediment Concentration

Mathematical models have been developed that can completely describe the distribution of sediment concentration from the channel bed to the water surface. These models can be used to estimate the mean (depth-averaged) sediment concentration by a quick, point sampling in river engineering practice. The developed models are products of a combined application of the deterministic and probabilistic concepts. The complementary nature of the two concepts strengthens the methodology of describing the various features of sediment transport. The models incorporate a velocity distribution equation that corresponds to a probability distribution derived by maximizing the information entropy. The probability distribution is a compact description of the system at a channel section, and its resilience or stability explains the applicability of the developed models of velocity and sediment distributions in a wide range of flows, steady or unsteady.