Miracle-dz/UniFAR-FTUs huggingface dataset:
Lactogenic Hormonal Induction of Long Distance Interactions between β-Casein Gene Regulatory Elements*

Lactogenic hormone regulation of β-casein gene expression in mammary epithelial cells provides an excellent model in which to study the mechanisms by which steroid and peptide hormone signaling control gene expression. Prolactin- and glucocorticoid-mediated induction of β-casein gene expression involves two principal regulatory regions, a proximal promoter and a distal enhancer located in the mouse approximately −6 kb upstream of the transcription start site. Using a chromosome conformation capture assay and quantitative real time PCR, we demonstrate that a chromatin loop is created in conjunction with the recruitment of specific transcription factors and p300 in HC11 mammary epithelial cells. Stimulation with both prolactin and hydrocortisone is required for the induction of these long range interactions between the promoter and enhancer, and no DNA looping was observed in nontreated cells or cells treated with each of the hormones separately. The lactogenic hormone-induced interaction between the proximal promoter and distal enhancer was confirmed in hormone-treated primary three-dimensional mammary acini cultures. In addition, the developmental regulation of DNA looping between the β-casein regulatory regions was observed in lactating but not in virgin mouse mammary glands. Furthermore, β-casein mRNA induction and long range interactions between these regulatory regions were inhibited in a progestin-dependent manner following stimulation with prolactin and hydrocortisone in HC11 cells expressing human PR-B. Collectively, these data suggest that the communication between these regulatory regions with intervening DNA looping is a crucial step required to both create and maintain active chromatin domains and regulate transcription.
Scale dependent drivers of wild bee diversity in tropical heterogeneous agricultural landscapes

Summary Factors associated with agricultural intensification, for example, loss of seminatural vegetation and pesticide use has been shown to adversely affect the bee community. These factors may impact the bee community differently at different landscape scales. The scale dependency is expected to be more pronounced in heterogeneous landscapes. However, the scale‐dependent response of the bee community to drivers of its decline is relatively understudied, especially in the tropics where the agricultural landscape is often heterogeneous. This study looked at effects of agricultural intensification on bee diversity at patch and landscape scales in a tropical agricultural landscape. Wild bees were sampled using 12 permanent pan trap stations. Patch and landscape characteristics were measured within a 100 m (patch scale) and a 500 m (landscape scale) radius of pan trap stations. Information on pesticide input was obtained from farmer surveys. Data on vegetation cover, productivity, and percentage of agricultural and fallow land (FL) were collected using satellite imagery. Intensive areas in a bee‐site network were less specialized in terms of resources to attract rare bee species while the less intensive areas, which supported more rare species, were more vulnerable to disturbance. A combination of patch quality and diversity as well as pesticide use regulates species diversity at the landscape scale (500 m), whereas pesticide quantity drove diversity at the patch scale (100 m). At the landscape scale, specialization of each site in terms of resources for bees increased with increasing patch diversity and FL while at the patch scale specialization declined with increased pesticide use. Bee functional groups responded differentially to landscape characteristics as well as pesticide use. Wood nesting bees were negatively affected by the number of pesticides used but other bee functional groups were not sensitive to pesticides. Synthesis and Applications: Different factors affect wild bee diversity at the scale of landscape and patch in heterogeneous tropical agricultural systems. The differential response of bee functional groups to agricultural intensification underpins the need for guild‐specific management strategies for wild bee conservation. Less intensively farmed areas support more rare species and are vulnerable to disturbance; consequently, these areas should be prioritized for conservation to maintain heterogeneity in the landscape. It is important to conserve and restore seminatural habitats to maintain complexity in the landscapes through participatory processes and to regulate synthetic chemical pesticides in farm operations to conserve the species and functional diversity of wild bees.
Phenazines and Other Redox-Active Antibiotics Promote Microbial Mineral Reduction

ABSTRACT Natural products with important therapeutic properties are known to be produced by a variety of soil bacteria, yet the ecological function of these compounds is not well understood. Here we show that phenazines and other redox-active antibiotics can promote microbial mineral reduction. Pseudomonas chlororaphis PCL1391, a root isolate that produces phenazine-1-carboxamide (PCN), is able to reductively dissolve poorly crystalline iron and manganese oxides, whereas a strain carrying a mutation in one of the phenazine-biosynthetic genes (phzB) is not; the addition of purified PCN restores this ability to the mutant strain. The small amount of PCN produced relative to the large amount of ferric iron reduced in cultures of P. chlororaphis implies that PCN is recycled multiple times; moreover, poorly crystalline iron (hydr)oxide can be reduced abiotically by reduced PCN. This ability suggests that PCN functions as an electron shuttle rather than an iron chelator, a finding that is consistent with the observation that dissolved ferric iron is undetectable in culture fluids. Multiple phenazines and the glycopeptidic antibiotic bleomycin can also stimulate mineral reduction by the dissimilatory iron-reducing bacterium Shewanella oneidensis MR1. Because diverse bacterial strains that cannot grow on iron can reduce phenazines, and because thermodynamic calculations suggest that phenazines have lower redox potentials than those of poorly crystalline iron (hydr)oxides in a range of relevant environmental pH (5 to 9), we suggest that natural products like phenazines may promote microbial mineral reduction in the environment.
Perfluoropolyether Boundary Lubricants Based on the Star Architecture

Star PFPE (perfluoropolyether) polymers based on an aromatic benzene core and a non-aromatic cyclotriphosphazene (CTP) core are investigated as boundary lubricant films on rigid magnetic media. The effect of the benzene and CTP cores on head-disk spacing are measured by the changes in the acoustic emission signal as a function of head-disk spacing at similar lubricant film thicknesses. The earlier head-disk contact observed with the CTP core is attributed in part to its larger size perpendicular to the plane of the disk surface. The adhesion of the benzene and CTP cores to the underlying carbon film is investigated by ab initio quantum chemistry. The nonaromatic nature of the CTP ring and the lack of steric accessibility to the CTP core nitrogen atoms prevent good adhesive interactions with the underlying carbon film. Conversely, the π-electrons of aromatic benzene create a quadrupole moment in the direction perpendicular to the plane of the benzene that can interact with the underlying carbon surface and hence provide weak adhesion. Electron-withdrawing and -donating substituents on the benzene ring can be used to exert a “push-pull” effect on the π-electrons to alter the strength of the intermolecular interactions to specific functional groups of the underlying carbon surface. These effects are visualized by mapping the electrostatic potential of the benzene core as a function of electron-withdrawing and -donating substituents and computing model dimer optimized geometries and intermolecular interaction energies. Finally, the thermal stability of the star PFPE polymers are quantified by measuring the evaporation rate of thin films (11 Å) as a function of time at the HDD temperature (~ 60°C). Thermogravimetric analyses (TGA) of the neat polymers also provide direction for improvement of the synthetic lubricants.
Combined use of nitroglycerin and N-acetylcysteine in the management of unstable angina pectoris.

The vasodilator effects of nitroglycerin (NTG) are mediated via activation of guanylate cyclase; this process is believed to require the availability of free sulfhydryl groups. Previous studies in man have shown that the sulfhydryl donor N-acetylcysteine (NAC) potentiates the systemic and coronary vasodilator effects of NTG. Furthermore, interaction of NTG and NAC may lead to the formation of S-nitroso-NAC, which strongly inhibits platelet aggregation. The effects of intravenous NTG combined with intravenous NAC (5 g 6 hourly) were compared with those of intravenous NTG alone in a double-blind trial in 46 patients with severe unstable angina pectoris unresponsive to conventional treatment, which included calcium antagonists and cutaneous nitrates in all but one patient. Treatment with NTG/NAC (24 patients) and that with NTG alone (22 patients) was associated with a similar frequency of episodes of chest pain and of increments in NTG infusion rate for pain control (10 vs 17; p = NS). The NTG/NAC group had a significantly lower incidence of acute myocardial infarction than the NTG/placebo group (three vs 10 patients; p = .013). Symptomatic hypotension occurred frequently in the NTG/NAC group (seven vs 0 patients; p = .006). Lactate-pyruvate ratios and venous NTG concentrations were not significantly affected by NAC. Subsequently, another 20 consecutive patients were treated with intravenous NTG and continuously infused NAC (10 g/day). Seven remained pain free during the first 24 hr of NTG infusion; 11 required increments in NTG infusion rate for pain control. Acute myocardial infarction occurred in one patient, while none developed symptomatic hypotension. (ABSTRACT TRUNCATED AT 250 WORDS)
Metabolic engineering of a thermophilic bacterium to produce ethanol at high yield

We report engineering Thermoanaerobacterium saccharolyticum, a thermophilic anaerobic bacterium that ferments xylan and biomass-derived sugars, to produce ethanol at high yield. Knockout of genes involved in organic acid formation (acetate kinase, phosphate acetyltransferase, and L-lactate dehydrogenase) resulted in a strain able to produce ethanol as the only detectable organic product and substantial changes in electron flow relative to the wild type. Ethanol formation in the engineered strain (ALK2) utilizes pyruvate:ferredoxin oxidoreductase with electrons transferred from ferredoxin to NAD(P), a pathway different from that in previously described microbes with a homoethanol fermentation. The homoethanologenic phenotype was stable for >150 generations in continuous culture. The growth rate of strain ALK2 was similar to the wild-type strain, with a reduction in cell yield proportional to the decreased ATP availability resulting from acetate kinase inactivation. Glucose and xylose are co-utilized and utilization of mannose and arabinose commences before glucose and xylose are exhausted. Using strain ALK2 in simultaneous hydrolysis and fermentation experiments at 50°C allows a 2.5-fold reduction in cellulase loading compared with using Saccharomyces cerevisiae at 37°C. The maximum ethanol titer produced by strain ALK2, 37 g/liter, is the highest reported thus far for a thermophilic anaerobe, although further improvements are desired and likely possible. Our results extend the frontier of metabolic engineering in thermophilic hosts, have the potential to significantly lower the cost of cellulosic ethanol production, and support the feasibility of further cost reductions through engineering a diversity of host organisms.
Reproductive success of planktivorous seabirds in the North Pacific is related to ocean climate on decadal scales

Growing evidence indicates relationships between seabird demography and both large- and small-scale variation in climate and oceanography, yet few studies have examined multiple species and locations simultaneously. As secondary consumers, least, whiskered, and crested auklets (Aethia pusilla, A. pygmaea, and A. cristatella, respectively), congeneric planktivorous seabirds endemic to the Bering and Okhotsk seas, are expected to respond to changes in ocean climate due to their low trophic positioning. From 1990 to 2008, we measured reproductive success (productivity) and breeding phenology (mean hatching date) of auklets on Buldir, Kiska, and Kasatochi, 3 islands spanning 585 km across the Aleutian Islands, Alaska, USA. A model including Island, Species, and Winter Aleutian Low Pressure Index (ALPI) best explained productivity, with reproductive success decreasing among all species with increasing ALPI (β = -0.273 ± 0.0263 (SE)), likely through control of water temperature and prey (zooplankton) availability. Auklet productivity also increased with increasing winter sea surface temperature (SST) in the western North Pacific and western Bering Sea (and correspondingly decreased with increasing SST in the Gulf of Alaska), and was correlated negatively with spring sea-level air pressure in the North Pacific. These responses are reflective of positive values of the Aleutian low pressure system. Though our datasets cover only 19 yr or less, we found similar correlations between climate and auklet productivity among all species and islands. Together, our results suggest that ocean climatic conditions and reproductive success of plankti- vorous auklets are significantly related.
Characterization of Salmonella enterica Subspecies I Genovars by Use of Microarrays

ABSTRACT Subspecies 1 of Salmonella enterica is responsible for almost all Salmonella infections of warm-blooded animals. Within subspecies 1 there are over 2,300 known serovars that differ in their prevalence and the diseases that they cause in different hosts. Only a few of these serovars are responsible for most Salmonella infections in humans and domestic animals. The gene contents of 79 strains from the most prevalent serovars were profiled by microarray analysis. Strains within the same serovar often differed by the presence and absence of hundreds of genes. Gene contents sometimes differed more within a serovar than between serovars. Groups of strains that share a distinct profile of gene content can be referred to as “genovars” to distinguish them from serovars. Several misassignments within the Salmonella reference B collection were detected by genovar typing and were subsequently confirmed serologically. Just as serology has proved useful for understanding the host range and pathogenic manifestations of Salmonella, genovars are likely to further define previously unrecognized specific features of Salmonella infections.
Toward High-Quality Gradient Estimation on Regular Lattices

In this paper, we present two methods for accurate gradient estimation from scalar field data sampled on regular lattices. The first method is based on the multidimensional Taylor series expansion of the convolution sum and allows us to specify design criteria such as compactness and approximation power. The second method is based on a Hilbert space framework and provides a minimum error solution in the form of an orthogonal projection operating between two approximation spaces. Both methods lead to discrete filters, which can be combined with continuous reconstruction kernels to yield highly accurate estimators as compared to the current state of the art. We demonstrate the advantages of our methods in the context of volume rendering of data sampled on Cartesian and Body-Centered Cubic lattices. Our results show significant qualitative and quantitative improvements for both synthetic and real data, while incurring a moderate preprocessing and storage overhead.
Population‐density estimation using regression and area‐to‐point residual kriging

Census population data are associated with several analytical and cartographic problems. Regression models using remote‐sensing covariates have been examined to estimate urban population density, but the performance may not be satisfactory. This paper describes a kriging‐based areal interpolation method, namely area‐to‐point residual kriging, which can be used to disaggregate the residuals remaining from regression. Compared with conventional cokriging, the area‐to‐point residual kriging is much simpler in that only a semivariogram model for the point residuals is required, as opposed to a set of auto‐ and cross‐semivariogram models involving the dependent variable and all the covariates. In addition, area‐to‐point residual kriging explicitly accounts for any scale differences between source data and target values. The method is illustrated by disaggregating population from census units to the land‐use zones within them. Comparative results for regression with and without area‐to‐point residual kriging show that area‐to‐point residual kriging can substantially improve interpolation accuracy.
DNA vaccines against human immunodeficiency virus type 1

Summary: Development of a vaccine against human immunodeficiency virus type 1 (HIV‐1) is the main hope for controlling the acquired immunodeficiency syndrome pandemic. An ideal HIV vaccine should induce neutralizing antibodies, CD4+ helper T cells, and CD8+ cytotoxic T cells. While the induction of broadly neutralizing antibodies remains a highly challenging goal, there are a number of technologies capable of inducing potent cell‐mediated responses in animal models, which are now starting to be tested in humans. Naked DNA immunization is one of them. This review focuses on the stimulation of HIV‐specific T cells and discusses in the context of the current ‘state‐of‐art’ of DNA vaccines, the areas where this technology might assist either alone or as a part of more complex vaccine formulations in the HIV vaccine development.
L‐glutamate as an excitatory transmitter at the Drosophila larval neuromuscular junction.

The possibility that L‐glutamate is the excitatory transmitter at the Drosophila larval neuromuscular junction and the ionic basis of its action on the muscle membrane are examined. 2. Iontophoretically applied L‐glutamate causes muscle depolarization (L‐glutamate potential) if and only if the L‐glutamate pipette is within a few mum of the nerve ending. D‐glutamate, substance P, ACh and GABA are ineffective. 3. Bath‐applied L‐glutamate produces similar changes in the time course and amplitude of miniature excitatory junctional potential (m.e.j.p.), excitatory junctional potential (e.j.p.) and the L‐glutamate potential. 4. Neuromuscular transmission and excitation‐contraction coupling are operative in a haemolymph‐like solution containing 1 mM L‐glutamate. 5. The reversal potentials of the e.j.p. and the L‐glutamate potential are identical to each other, changing similarly with changes in the ionic compositions of the external medium (twelve solutions). 6. The ionic dependence of the reversal potentials is predicted from an extended constant‐field equation using a ratio of sodium:potassium permeabilities of PNa/PK=1‐3, and a ratio of magnesium:potassium permeabilities of PMg/PK=4‐7. 7. It is concluded that L‐glutamate is, or is an agonist of, the excitatory transmitter at certain Drosophila larval neuromuscular junctions.
Coarsening Massive Influence Networks for Scalable Diffusion Analysis

Fueled by the increasing popularity of online social networks, social influence analysis has attracted a great deal of research attention in the past decade. The diffusion process is often modeled using influence graphs, and there has been a line of research that involves algorithmic problems in influence graphs. However, the vast size of today's real-world networks raises a serious issue with regard to computational efficiency. In this paper, we propose a new algorithm for reducing influence graphs. Given an input influence graph, the proposed algorithm produces a vertex-weighted influence graph, which is compact and approximates the diffusion properties of the input graph. The central strategy of influence graph reduction is coarsening, which has the potential to greatly reduce the number of edges by merging a vertex set into a single weighted vertex. We provide two implementations; a speed-oriented implementation which runs in linear time with linear space and a scalability-oriented implementation which runs in practically linear time with sublinear space. Further, we present general frameworks using our compact graphs that accelerate existing algorithms for influence maximization and influence estimation problems, which are motivated by practical applications, such as viral marketing. Using these frameworks, we can quickly obtain solutions that have accuracy guarantees under a reasonable assumption. Experiments with real-world networks demonstrate that the proposed algorithm can scale to billion-edge graphs and reduce the graph size to up to 4%. In addition, our influence maximization framework achieves four times speed-up of a state-of-the-art D-SSA algorithm, and our influence estimation framework cuts down the computation time of a simulation-based method to 3.5%.
Breakthrough in Xenon Capture and Purification Using Adsorbent-Supported Silver Nanoparticles.

Rare gas capture and purification is a major challenge for energy, environment, and health applications. Of utmost importance for the nuclear industry, novel separation processes for Xe are urgently needed for spent nuclear fuel reprocessing and nuclear activity monitoring. The recovered, non-radioactive Xe is also of high economic value for lighting, surgical anesthetic, etc. Here, using adsorption and breakthrough experiments and statistical mechanics molecular simulation, we show the outstanding performance of zeolite-supported silver nanoparticles to capture/separate Xe at low concentrations (0.087-100 ppm). We also establish the efficiency of temperature swing adsorption based on such adsorbents for Xe separation from Kr/Xe mixtures and air streams corresponding to off-gases generated by nuclear reprocessing. This study paves the way for the development of novel, cost-efficient technologies relying on the large selectivity/capacity of adsorbent-supported silver nanoparticles which surpass all materials ever tested.
Weaving the Pedantic Web

Over a decade after RDF has been published as a W3C recommendation, publishing open and machine-readable content on the Web has recently received a lot more attention, including from corporate and governmental bodies; notably thanks to the Linked Open Data community, there now exists a rich vein of heterogeneous RDF data published on the Web (the so-called \Web of Data") accessible to all. However, RDF publishers are prone to making errors which compromise the e ectiveness of applications leveraging the resulting data. In this paper, we discuss common errors in RDF publishing, their consequences for applications, along with possible publisher-oriented approaches to improve the quality of structured, machine-readable and open data on the Web.
Incremental Process Mining

The problem of synthesis of Petri nets from transition sys- tems or languages has many applications, ranging from CAD for VLSI to medical applications, among others. The most common algorithms to accomplish this task are based on the theory of regions. However, one of the problems of such algorithms is its space requirements: for real-life or industrial instances, some of the region-based algorithms cannot handle in memory the internal representation of the input or the exploration lattice required. In this paper, the incremental derivation of a basis of regions and the later partitioned basis exploration is presented, which allows the splitting of large inputs.