Miracle-dz/UniFAR-FTUs huggingface dataset:
A note on the recent natural gradient tracer test at the Borden Site

The variance in particle position, a measure of dispersion, is reviewed in the context of certain models of flow in random porous media. Asymptotic results for a highly stratified medium and an isotropic medium are particularly highlighted. Results of the natural gradient tracer test at the Borden site are reviewed in light of these models. This review suggests that the moments obtained for the conservative tracers at the Borden site could as well be explained by a model that more explicitly represents the three-dimensional nature of the flow field.
Glioblastoma Subclasses Can Be Defined by Activity among Signal Transduction Pathways and Associated Genomic Alterations

Background Glioblastoma multiforme (GBM) is an umbrella designation that includes a heterogeneous group of primary brain tumors. Several classification strategies of GBM have been reported, some by clinical course and others by resemblance to cell types either in the adult or during development. From a practical and therapeutic standpoint, classifying GBMs by signal transduction pathway activation and by mutation in pathway member genes may be particularly valuable for the development of targeted therapies. Methodology/Principal Findings We performed targeted proteomic analysis of 27 surgical glioma samples to identify patterns of coordinate activation among glioma-relevant signal transduction pathways, then compared these results with integrated analysis of genomic and expression data of 243 GBM samples from The Cancer Genome Atlas (TCGA). In the pattern of signaling, three subclasses of GBM emerge which appear to be associated with predominance of EGFR activation, PDGFR activation, or loss of the RAS regulator NF1. The EGFR signaling class has prominent Notch pathway activation measured by elevated expression of Notch ligands, cleaved Notch receptor, and downstream target Hes1. The PDGF class showed high levels of PDGFB ligand and phosphorylation of PDGFRβ and NFKB. NF1-loss was associated with lower overall MAPK and PI3K activation and relative overexpression of the mesenchymal marker YKL40. These three signaling classes appear to correspond with distinct transcriptomal subclasses of primary GBM samples from TCGA for which copy number aberration and mutation of EGFR, PDGFRA, and NF1 are signature events. Conclusions/Significance Proteomic analysis of GBM samples revealed three patterns of expression and activation of proteins in glioma-relevant signaling pathways. These three classes are comprised of roughly equal numbers showing either EGFR activation associated with amplification and mutation of the receptor, PDGF-pathway activation that is primarily ligand-driven, or loss of NF1 expression. The associated signaling activities correlating with these sentinel alterations provide insight into glioma biology and therapeutic strategies.
Culturing captures members of the soil rare biosphere

The ecological significance of rare microorganisms within microbial communities remains an important, unanswered question. Microorganisms of extremely low abundance (the ‘rare biosphere’) are believed to be largely inaccessible and unknown. To understand the structure of complex environmental microbial communities, including the representation of rare and prevalent community members, we coupled traditional cultivation with pyrosequencing. We compared cultured and uncultured bacterial members of the same agricultural soil, including eight locations within one apple orchard and four time points. Our analysis revealed that soil bacteria captured by culturing were in very low abundance or absent in the culture-independent community, demonstrating unexpected accessibility of the rare biosphere by culturing.
p62, Ref(2)P and ubiquitinated proteins are conserved markers of neuronal aging, aggregate formation and progressive autophagic defects

Suppression of macroautophagy, due to mutations or through processes linked to aging, results in the accumulation of cytoplasmic substrates that are normally eliminated by the pathway. This is a significant problem in long-lived cells like neurons, where pathway defects can result in the accumulation of aggregates containing ubiquitinated proteins. The p62/Ref(2)P family of proteins is involved in the autophagic clearance of cytoplasmic protein bodies or sequestosomes. These unique structures are closely associated with protein inclusions containing ubiquitin as well as key components of the autophagy pathway. In this study we show that detergent fractionation followed by western blot analysis of insoluble ubiquitinated proteins (IUP), mammalian p62 and its Drosophila homologue, Ref(2)P can be used to quantitatively assess the activity level of aggregate clearance (aggrephagy) in complex tissues. Using this technique we show that genetic or age-dependent changes that modify the long-term enhancement or suppression of aggrephagy can be identified. Moreover, using the Drosophila model system this method can be used to establish autophagy-dependent protein clearance profiles that are occurring under a wide range of physiological conditions including developmental, fasting and altered metabolic pathways. This technique can also be used to examine proteopathies that are associated with human disorders such as frontotemporal dementia, Huntington and Alzheimer disease. Our findings indicate that measuring IUP profiles together with an assessment of p62/Ref(2)P proteins can be used as a screening or diagnostic tool to characterize genetic and age-dependent factors that alter the long-term function of autophagy and the clearance of protein aggregates occurring within complex tissues and cells.
Communicating climate change: spatial analog versus color-banded isoline maps with and without accompanying text

People discount projected impacts of climate change that they see as spatially or temporally remote. To overcome this, climate change outreach must communicate impacts as local, concrete, immediate, and situated in a well-understood frame of reference. Spatial-analog mapping may meet this challenge: by drawing on people’s experience of existing climates, this technique matches a locality’s projected climates with present-day climates of other localities. However, analog maps’ effect on climate impact perceptions has not been compared with the effect on climate impact perceptions elicited by standard climate change mapping techniques. Accordingly, this study considers whether residents of Centre Region, Pennsylvania, who are shown spatial-analog maps for future Centre Region temperatures, perceive impacts as more salient than do residents shown the same temperature-change information directly using color-banded isallotherm maps. It also considers how responses differ when this information is presented using only text, only maps, or both maps and text. An online survey of 3094 members of 11 Centre Region organizations presents the maps and/or text and then assesses respondents’ impact perceptions. Based on 444 valid responses, the study finds that respondents, using spatial-analog survey forms, generally expect impacts to be less severe and disruptive than respondents using temperature-change forms. It also finds that respondents using survey forms with maps generally expect impacts to be more severe and disruptive than respondents using text-only forms. Climate change communicators who wish to improve understanding and engagement should therefore strongly consider using maps where possible, but should exercise caution before using spatial-analog approaches.
Minimizing energy consumption of secure wireless session with QoS constraints

We investigate techniques to minimize the energy consumed by a secure wireless session without compromising the security of the session. While we have shown elsewhere (see Karri, R. and Mishra, P., submitted to ACM MOBIHOC 2002; http://emme.poly.edu/Goodies/TEMP/MOBIHOC2002.pdf) that the energy consumed by a secure session is reduced by compressing the session negotiation messages, the protocol header and the data, we now show that it is important to match the block size of compression to the data cache size of the device. We also investigate the choice of a bulk encryption algorithm (3DES vs. AES) and a key exchange protocol (Diffie-Hellman vs. RSA) based on the energy consumed by a secure wireless session. These techniques yield energy savings of 1.3/spl times/ during data transmission and 1.2/spl times/ during data reception beyond those obtained by techniques given in our cited paper. These techniques complement and supplement those proposed in that paper, and when combined, yield overall energy savings of 2.1/spl times/ during data transmission and 4.35/spl times/ during data reception.
X‐ray CT and Laboratory Measurements on Glacial Till Subsoil Cores: Assessment of Inherent and Compaction‐Affected Soil Structure Characteristics

Abstract The aim of this study was to articulate the potential of medical computed tomographic (CT) scanning for analyzing soil structure (macroporosity, soil matrix density, number of macropores) and how these estimates compare with, and complement, traditional laboratory measurements (bulk density, total porosity, effective air‐filled porosity, and air permeability). Undisturbed soil cores were sampled at two depths (0.35 and 0.7 m) in a long‐term soil compaction experiment in southern Sweden 14 years after its establishment. Persistence of subsoil compaction was detectable by CT‐estimated soil matrix density, bulk density, and total porosity. Vertical distribution of CT‐estimated air‐filled macroporosity between 0.25‐ and 0.45‐m depth showed that biological activity effect on macroporosity was largest in the top of the soil columns from the compacted plots, whereas reduction of macroporosity was significant at the bottom of the same columns. This was not detectable by classical laboratory measurements. Variations in air permeability could be related to the CT‐estimated number of pores but not to the CT‐estimated air‐filled macroporosity. Despite using a coarse resolution, the combination of visualization and traditional laboratory measurements proved valuable in identifying the persistent effects of subsoil compaction and the differences in soil structure among the two investigated subsoil layers. However, we recommend to systematically perform a sensitivity analysis to the segmentation threshold before any further analysis of CT‐estimated parameters.
Role of planetary waves in the stratosphere‐troposphere coupled variability in the northern hemisphere winter

The role of planetary waves in stratosphere‐troposphere coupled variability is investigated using an extended singular value decomposition analysis of zonal‐mean zonal wind and the vertical component of the Eliassen‐Palm (E‐P) flux for the winters from 1979/80 to 1995/96. The results suggest a close relationship between anomalies of zonal‐mean zonal wind and the convergence zone of E‐P flux, which together shift poleward and downward from the stratosphere to the troposphere as time advances. Following enhanced vertical propagation of waves into the stratosphere, the Arctic Oscillation (AO) pattern is seen in the 500 hPa geopotential height field in association with an increased poleward propagation of tropospheric waves.
Towards a sustainable future for Nunavik

ABSTRACT The predominantly Inuit Arctic region of Nunavik in the Province of Québec, Canada, currently needs to address major challenges and opportunities. The region needs to develop more employment and wealth creation opportunities without sacrificing the vital land-based subsistence sector that provides food security, sustains cultural identity and provides social and economic stability. A decision about a new direction needs to be taken soon as major mining projects are developing at a rapid pace. In this paper we first assess existing socioeconomic and living conditions data to evaluate the state of social well-being in the region. In addition we report and analyse information from an economic forum in Kuujjuaq, Nunavik in April 2010. The purpose of the forum was to provide an opportunity for regional and local stakeholders to obtain information on specific economic opportunities for Nunavik and to discuss their merit for the communities. Based on our data evaluation and the outcomes at the forum we identify a possible sustainable development feedback envisioning process and discuss possible sustainable development directions for Nunavik.
The Fraunhofer IDMT at ImageCLEF 2011 Photo Annotation Task

This paper presents the participation of the Fraunhofer IDMT in the ImageCLEF 2011 Photo Annotation Task. Our approach is focused on text-based features and strategies to combine visual and textual infor- mation. First, we apply a pre-processing step on the provided Flickr tags to reduce noise. For each concept, tf-idf values per tag are computed and used to construct a text-based descriptor. Second, we extract RGB-SIFT descriptors using the codebook approach. Visual and text-based features are combined, once with early fusion and once with late fusion. The con- cepts are learned with SVM classiers. Further, a post-processing step compares tags and concept names to each other. Our submission con- sists of one text-only and four multi-modal runs. The results show, that a combination of text-based and visual-features improves the result. Best results are achieved with the late fusion approach. The post-processing step only improves the results for some concepts, while others worsen. Overall, we scored a Mean Average Precision (MAP) of 37.1% and an example-based F-Measure (F-ex) of 55.2%.
Rapid Evaluation of Trigonometric

A group of algorithms is presented generalizing the Fast Fourier Transform to the case of non-integer frequencies and non-equispaced nodes on the interval [-, The schemes of this paper are based on a combination of certain analytical considerations with the dsical Fast Fourier Transform, and generalize both the forward and backward FFTs. Each of the algorithms requires O(N -log N + N-log(1/e)) arithmetic operations, where - is the precision of computations and N is the number of nodes. The efficiency of the approach is illustrated by several numerical examples
“Living high − training low” altitude training improves sea level performance in male and female élite runners

Acclimatization to moderate high altitude accompanied by training at low altitude (living high–training low) has been shown to improve sea level endurance performance in accomplished, but not élite, runners. Whether élite athletes, who may be closer to the maximal structural and functional adaptive capacity of the respiratory (i.e. oxygen transport from environment to mitochondria) system, may achieve similar performance gains is unclear. To answer this question, we studied 14 élite men and eight élite women before and after 27 days of living at 2500 m while performing high‐intensity training at 1250 m. The altitude sojourn began 1 week after the USA Track and Field National Championships, when the athletes were close to their season's fitness peak. Sea level 3000‐m time trial performance was significantly improved by 1.1% (95% confidence limits 0.3–1.9%). One‐third of the athletes achieved personal best times for the distance after the altitude training camp. The improvement in running performance was accompanied by a 3% improvement in maximal oxygen uptake (72.1 ± 1.5–74.4 ± 1.5 ml kg− 1 min− 1). Circulating erythropoietin levels were near double initial sea level values 20 h after ascent (8.5 ± 0.5–16.2 ± 1.0 IU ml−1). Soluble transferrin receptor levels were significantly elevated on the 19th day at altitude, confirming a stimulation of erythropoiesis (2.1 ± 0.7–2.5 ± 0.6 μ g ml‐1). Hb concentration measured at sea level increased 1 g dl−1 over the course of the camp (13.3 ± 0.2–14.3 ± 0.2 g dl−1). We conclude that 4 weeks of acclimatization to moderate altitude, accompanied by high‐intensity training at low altitude, improves sea level endurance performance even in élite runners. Both the mechanism and magnitude of the effect appear similar to that observed in less accomplished runners, even for athletes who may have achieved near maximal oxygen transport capacity for humans.
Aberrant methylation of TMS1 in small cell, non small cell lung cancer and breast cancer

TMS1 (target of methylation‐induced silencing) is a CpG island‐associated gene that functions in the regulation of apoptosis and encodes a caspase recruitment domain, a recently described motif found in apoptotic signaling molecules. Recent evidence suggests that silencing of genes in the apoptotic pathway contribute to human carcinogenesis. We examined the DNA methylation status of the TMS1 promoter in lung and breast tumor tissues, tumor cell lines and nonmalignant tissues by methylation‐specific polymerase chain reaction (MSP) and its mRNA expression by reverse transcription PCR. Aberrant methylation of TMS1 was present in 70% (40 of 57) of small cell lung cancer (SCLC) cell lines and 41% (13 of 32) of SCLC tumor tissues, 48% (29 of 61) of non small cell lung cancer (NSCLC) cell lines and 40% (28 of 70) of NSCLC tumor tissues and 46% (12 of 26) of breast cancer cell lines and 32% (20 of 63) of breast tumor tissues. Methylation was absent in the peripheral blood lymphocytes and buccal epithelium from healthy volunteers, as well as in nonmalignant lung tissues and was rare in nonmalignant breast tissues 7% (2 of 30). DNA methylation was confirmed by sequence analysis and the methylation status correlated inversely with TMS1 RNA expression in 18 cell lines tested. RNA expression was restored by treatment with the demethylating agent 5‐aza‐2′‐deoxycytidine, in 4 of 4 methylated cell lines that lacked the TMS1 transcript. Our results suggest that methylation of TMS1 may play a role in the pathogenesis of small cell and non small lung and breast cancers. © 2003 Wiley‐Liss, Inc.
The Radial Consolidation of Clay Soils

Synopsis The radial consolidation theory of Barron (1948) and McKinlay (1961) has been extended to take account of smear at the drainage boundaries, a decreasing permeability and compressibility and non-linear structural viscosity for an homogeneous anisotropic clay. An engineering assessment is made of the errors likely to result in using laboratory ch values to predict field rates of settlement and pore pressure dissipation where the flow of pore water is predominantly in a lateral direction. Guidance is given as to the type of laboratory test that should be carried out and interpretation of the results in order to obtain a reliable estimate of the field behaviour. La theorie de consolidation radiale de Barron et McKinlay a ete etendue pour tenir compte des depots graisseux aux limites de drainage, et d'une permeabilite et d'une compressibilite decroissante et d'une viscosite de structure non-1ineaire dans le cas d'une argile anisotropique homogene. Une evaluation d'un point de vue de construction mecan.
Processing and presentation of type II collagen, a fibrillar autoantigen, by H‐2q antigen‐presenting cells

Native type II collagen (CII) is a high molecular‐weight fibrillar molecule which induces a chronic polyarthritis in mice expressing the H‐2q haplotype. The present study was initiated to analyze the processing and the presentation of this nonglobular protein by H‐2q antigen‐presenting cells (APC). Efficiency of presentation was assessed by the ability of antigen‐pulsed APC to activate collagenspecific CD4+ T cell hybridomas. Fixation of APC or the presence of chloroquine completely blocked the reactivity of the T cell hybrids to native, denatured and cyanogen bromide (CB) degraded CII, thus indicating the requirement of intracellular processing for adequate presentation of CII peptides to T cells. In the presence of various processing inhibitors (brefeldin A, leupeptin and Ntosyl‐L‐phenylalanine chloromethylketone) stimulation of T hybrids by CIIpulsed APC was reduced, pointing to the need of newly synthesized class II molecules, the use of several intracellular compartments and the implication of different proteases in the generation of CII peptides. Peritoneal macrophages and, to a lesser extent, total spleen cells, presented native and denatured CII with higher efficiency than purified splenic dendritic cells, naive or even immune B cells from CII‐primed mice. In contrast, these dendritic and B cells were fully competent to present intact ovalbumin to a specific T cell hybrid. The stimulation by dendritic cells and immune B cells was greater when CB peptides of CII were added instead of the native molecule. Similarly, the cleavage of CII was an absolute requirement for its presentation by epidermal cells and B cell lymphomas to the T cell hybridomas. Taken together, these findings emphasize the crucial role of intracellular processing for recognition of soluble CII, similar to most antigens. However, in contrast to ovalbumin, the size and fibrillar nature of the native CII molecule influences its capture by the APC, thus limiting the type of APC able to present this antigen.
Influence of Nitrogen Application Time on Nitrogen Absorption, Partitioning, and Yield of Pecan

ADDITIONAL INDEX WORDS. Carya illinoinensis, nitrate, total N, Kjeldahl, organic N ABSTRACT. Nitrogen was applied to mature pecan (Carya illinoinensis Wangenh. C. Koch.) trees annually as a single application at 125 kg·ha -1 N in March or as a split application with 60% (75 kg·ha -1 N) applied in March and the remaining 40% (50 kg·ha -1 N) applied during the first week of October. Nitrogen treatment did not affect yield, and had little effect on the amount of N absorbed. Nitrogen absorption was greater between budbreak and the end of shoot expansion than at other times of the year. Substantial amounts of N were also absorbed between leaf fall and budbreak. Little N was absorbed between the end of shoot expansion and leaf fall, or tree N losses met or exceeded N absorption. Pistillate flowers and fruit accounted for a small portion of the tree's N; ≈0.6% at anthesis and 4% at harvest. The leaves contained ≈25% of the tree's N in May and ≈17% when killed by freezing temperatures in November. Leaves appeared to contribute little to the tree's stored N reserves. Roots ≥1 cm diameter were the largest site of N storage during the winter. Stored N reserves in the perennial parts of the tree averaged 13% of the tree's total N over a three year period. Current year's N absorption was inversely related to the amount of stored N, but was not related to the current or previous year's crop load.
Environmental fate of the antifouling compound zinc pyrithione in seawater

To perform a thorough risk assessment of the new antifouling compound zinc pyrithione (ZnPT2), additional information regarding the fate of the compound is needed. The present study examined the recovery and transchelation of ZnPT2 in controlled laboratory experiments, photodegradation experiments, and a fate study in a large‐scale field experiment. Chemical analyses were performed using a newly developed method for simultaneous analyses of ZnPT2 and copper pyrithione (CuPT2). Furthermore, two antifouling paints containing ZnPT2 were examined for the fate of leaching biocide. Naturally occurring ligands and metals in seawater influence the stability of ZnPT2. The presence of free Cu2+, which is present naturally in the seawater or is released from copper‐containing paints, results in a partial transchelation of ZnPT2 into CuPT2. A complete transchelation of ZnPT2 into CuPT2 was observed when Cu2+ was present at an equimolar concentration in the absence of interfering ligands. When ZnPT2 was leached from antifouling paints containing both ZnPT2 and Cu2O, CuPT2 was found, with no trace of ZnPT2. Photodegradation was low in natural waters and absent from 1 m or more below the surface. The results show that ZnPT2 has a low persistence in seawater when leached from antifouling paints. However, the more stable and toxic transchelation product CuPT2 is formed, which has the potential to accumulate in the sediments and, therefore, should be included in both chemical analysis and risk assessment of ZPT2.