Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of elevated ultraviolet radiation on Quercus robur and its insect and ectomycorrhizal associates

Saplings of pedunculate oak (Quercus robur L.) were exposed at an outdoor facility to modulated levels of elevated UV‐B radiation (280–315 nm) under treatment arrays of cellulose diacetate‐filtered fluorescent lamps which also produced UV‐A radiation (315–400 nm). Saplings were also exposed to UV‐A radiation alone under control arrays of polyester‐filtered lamps and to ambient levels of solar radiation under arrays of unenergized lamps. The UV‐B treatment corresponded to a 30% elevation above the ambient level of erythemally weighted UV‐B radiation. Sapling growth and the occurrence of associated organisms were examined over two years. In both years, leaves of saplings exposed to UV‐B treatment were thicker and smaller in area relative to leaves exposed to ambient and control levels of radiation. UV‐B treatment also retarded bud burst at one sampling in the first year of the study. Some responses were recorded which were common to both treatment and control arrays, implying that UV‐A radiation, or some other factor associated with energized lamps, was responsible for the observed effects. Saplings under treatment and control arrays were taller in the first year of the study, suffered greater herbivory from chewing insects, and had lower root dry weights and greater insertion heights of secondary branches than saplings exposed to ambient levels of radiation. Exposure of saplings to elevated UV‐A radiation alone under control arrays increased estimated leaf volumes in the second year of the study and reduced the number of secondary branches and the total number of branches per sapling after two years, relative to both treatment and ambient arrays. There were no effects of elevated ultraviolet radiation on shoot or total plant weight, root/shoot ratios, stem diameter, the numbers or insertion heights of primary or tertiary branches, total leaf number, timing of leaf fall or frequency of ectomycorrhizas. Our study suggests that any increases in UV‐B radiation as a result of stratospheric ozone depletion will influence the growth of Q. robur primarily through effects on leaf morphology.
Magnetic Epidermal Growth Factor Conjugate for Targeted Delivery to Grafted Tumor in Mouse Model

Magnetic nanoparticles conjugated with epidermal growth factor (MNP-EGF conjugates) were investigated by magnetic resonance (MR) relaxometry, on-chip quasielastic light scattering and magnetophoresis in aqueous dispersions and by MR imaging in phantom and in vivo models. MNP-EGF conjugates were prepared by carbodiimide EGF bonding with NH2-dextran modified iron oxide MNPs. The coefficients of magnetic relaxation efficiency (R1,R2,R2*) of MNP-EGF conjugates appeared to be close to the values obtained for nonconjugated MNPs and are correlating with those characteristic for negative contrast agents for MR imaging. MNP-EGF conjugates demonstrated ability of targeting MNPs to EGF receptors in EGF-overexpressed tumors. The feasibility of the MNP-EGF conjugates in diagnostics of certain cancer types was studied by MR imaging using mouse tumor models. It has been shown that intravenous and subcutaneous administration of MNP-EGF conjugates provided an enhancement of MR imaging contrast at the areas of accumulated cancer cells in melanoma mice model.
Exploring infection of wheat and carbohydrate metabolism in Mycosphaerella graminicola transformants with differentially regulated green fluorescent protein expression.

A Mycosphaerella graminicola strain transformed with the green fluorescent protein (GFP) downstream of either a carbon source-repressed promoter or a constitutive promoter was used to investigate in situ carbohydrate uptake during penetration of the fungus in wheat leaves. The promoter region of the acu-3 gene from Neurospora crassa encoding isocitrate lyase was used as a carbon source-repressed promoter. The promoter region of the Aspergillus nidulans gpdA gene encoding glyceraldehyde-3-phosphate dehydrogenase was used as a constitutive promoter. Fluorometric measurement of GFP gene expression in liquid cultures of acu-3-regulated transformants indicated that the N. crassa acu-3 promoter functions in M. graminicola as it does in N. crassa, i.e., acetate induced and carbon source repressed. Glucose, fructose, and saccharose triggered the repression, whereas mannitol, xylose, and cell wall polysaccharides did not. Monitoring the GFP level during fungal infection of wheat leaves revealed that acu-3 promoter repression occurred after penetration until sporulation, when newly differentiated pycnidiospores fluoresced. The use of GFP transformants also allowed clear visualization of M. graminicola pathogenesis. No appressoria were formed, but penetration at cell junctions was observed. These results give new insight into the biotrophic status of M. graminicola.
Structural, Functional, and Genetic Comparisons of Epstein-Barr Virus Nuclear Antigen 3A, 3B, and 3C Homologues Encoded by the Rhesus Lymphocryptovirus

ABSTRACT EBNA-3A, -3B, and -3C are three latent infection nuclear proteins important for Epstein-Barr virus (EBV)-induced B-cell immortalization and the immune response to EBV infection. All three are hypothesized to function as transcriptional transactivators, but little is known about their precise mechanism of action or their role in EBV pathogenesis. We have cloned and studied the three EBNA-3 homologues from a closely related lymphocryptovirus (LCV) which naturally infects rhesus monkeys. The rhesus LCV EBNA-3A, -3B, and -3C homologues have 37, 40, and 36% amino acid identity with the EBV genes, respectively. Function, as measured by in vitro assays, also appears to be conserved with the EBV genes, since the rhesus LCV EBNA-3s can interact with the transcription factor RBP-Jκ and the rhesus LCV EBNA-3C encodes a Q/P-rich domain with transcriptional activation properties. In order to better understand the relationship between these EBV and rhesus LCV latent infection genes, we asked if the rhesus LCV EBNA-3 locus could be recombined into the EBV genome and if it could substitute for the EBV EBNA-3s when assayed for human B-cell immortalization. Recombination between the EBV genome and rhesus LCV DNA was reasonably efficient. However, these studies suggest that the rhesus LCV EBNA-3 locus was not completely interchangeable with the EBV EBNA-3 locus for B-cell immortalization and that at least one determinant of the species restriction for LCV-induced B-cell immortalization maps to the EBNA-3 locus. The overall conservation of EBNA-3 structure and function between EBV and rhesus LCV indicates that rhesus LCV infection of rhesus monkeys can provide an important animal model for studying the role of the EBNA-3 genes in LCV pathogenesis.
Generalized Tag-induced Cross-Domain Collaborative Filtering

One of the most challenging problems in recommender systems based on the collaborative filtering (CF) concept is data sparseness, i.e., limited user preference data is available for making recommendations. Cross-domain collaborative filtering (CDCF) has been studied as an effective mechanism to alleviate data sparseness of one domain by transferring knowledge about user preferences from other domains. However, there are two key issues that need to be addressed to make a CDCF approach successful: (a) what common characteristics can be used to establish a link between different domains and (b) how to get each domain effectively and efficiently benefit from such a link. In this paper, we propose a novel algorithm, Generalized Tag-induced Cross-domain Collaborative Filtering (GTagCDCF), that exploits user-contributed tags as common characteristics to link different recommender domains together. Formulated from the probabilistic point of view, GTagCDCF takes into account all the user-item relations, the user-tag relations and the item-tag relations from different domains, resulting in a substantially extended collective matrix factorization framework, in which the common tags take the role of effectively transferring the knowledge between different domains. GTagCDCF is also found to be efficient, since its complexity is linear in the number of observed relations among users, items and tags from all domains. Using publicly available CF datasets to represent three cross-domain cases, i.e., two two-domain cases and one three-domain case, we experimentally demonstrate that GTagCDCF substantially outperforms several state-of-the-art single domain and cross-domain CF-based recommendation approaches. GTagCDCF is also shown to be effective for heterogeneous cross-domain cases, in which different domains are characterized by different types of user preferences. In addition, our investigation of the impact of user tagging behavior on GTagCDCF led to the conclusion that users can already benefit from GTagCDCF if they only share a few common tags. Finally, we validate the robustness of GTagCDCF with respect to the scale of datasets and the number of domains, based on a three-domain experiment.
dnaX36 Mutator of Escherichia coli: Effects of the τ Subunit of the DNA Polymerase III Holoenzyme on Chromosomal DNA Replication Fidelity

ABSTRACT The Escherichia coli dnaX36 mutant displays a mutator effect, reflecting a fidelity function of the dnaX-encoded τ subunit of the DNA polymerase III (Pol III) holoenzyme. We have shown that this fidelity function (i) applies to both leading- and lagging-strand synthesis, (ii) is independent of Pol IV, and (iii) is limited by Pol II.
Risk Adjustment for Measuring Health Outcomes: An Application in VA Long term Care

An empirically derived risk adjustment model is useful in distinguishing among facilities in their quality of care. We used Veterans Affairs (VA) administrative databases to develop and validate a risk adjustment model to predict decline in functional status, an important outcome measure in long-term care, among patients residing in VA long-term care facilities. This model was used to compare facilities on adjusted and unadjusted rates of decline. Predictors of decline included age, time between assessments, baseline functional status, terminal illness, pressure ulcers, pulmonary disease, cancer, arthritis, congestive heart failure, substance-related disorders, and various neurologic disorders. The model performed well in the development and validation databases (c statistics, 0.70 and 0.68, respectively). Risk-adjusted rates and rankings of facilities differed from unadjusted ratings. We conclude that judgments of facility performance depend on whether risk-adjusted or unadjusted decline rates are used. Valid risk adjustment models are therefore necessary when comparing facilities on outcomes.
in the

groups was the same as after the single 50 mg/kg dose, and the urine contained the same four metabolites. There were no marked differences between the groups, but there was a trend for the treated animals to excrete more of the acidic unknown metabolite and less free p-hydroxyphenobarbitone than after the acute administration. It has long been known that phenobarbitone is a powerful inducer of the drug metabolizing enzymes of the liver microsomes (Remmer, 1962), and it is therefore interesting to see that repeated phenobarbitone administration does not markedly affect its rate of excretion or pattern of metabolism, although this is the case with many other compounds. In view of this, and of the possible accumulation of phenobarbitone and its metabolites in the body on chronic administration, it provides further support for the view that the tolerance which occurs to this drug does not have its origin in altered drug disposition (see Caldwell & Sever, 1974).
Duration and fitness dependence of quasispecies memory.

The duration and fitness dependence of memory in viral quasispecies evolving in cell culture have been investigated using two genetic markers of foot-and-mouth disease virus (FMDV). In lineages of antigenic variant FMDV RED, which reverted to FMDV RGD, memory FMDV RED genomes were detected after 50 infectious cycles, and memory level was fitness dependent. In growth-competition experiments between a reference FMDV RGD and two different FMDV RED populations, a 7.6-fold higher fitness of the initial FMDV RED population resulted in 30 to 100-fold higher memory level. In lineages of low-fitness clones containing an elongated internal polyadenylate tract, revertants lacking excess adenylate residues became dominant by passage 20. However, genomes including a larger number of adenylate residues were detected as memory genomes after at least 150 infectious cycles. Thus, quasispecies memory can be durable and is fitness dependent, as predicted from the growth competition of two mutant forms of a genome. An understanding of factors influencing quasispecies memory levels and duration may have implications for the extended diagnosis of viruses based on the quantification of minority genomes.
Atg8 regulates vacuolar membrane dynamics in a lipidation-independent manner in Pichia pastoris

Atg8 is a ubiquitin-like protein that is required, along with its lipidation system, for autophagy in all eukaryotic cells. The lipidated form of Atg8 is anchored on the autophagosomal membrane during autophagy. Here, we demonstrate a previously unknown role for Atg8 in vacuolar membrane dynamics. In the methylotrophic yeast Pichia pastoris, vacuoles were found to fuse to become a single spherical vacuole during adaptation from glucose- to methanol-containing medium. Atg8 is responsible for the vacuolar fusion in P. pastoris during this adaptation to methanol. Although vacuole fusion required processing of Atg8 at the C-terminus, it did not require lipidation of Atg8 for autophagy. This is the first report of the function of any Atg8 protein family member in a process other than autophagy that is independent of lipidation.
Same but different: meta-analytically examining the uniqueness of mortality salience effects

One line of theorizing suggests considering death reminders—i.e., mortality salience (MS) inductions—unique in their effect on worldview defenses (e.g., Pyszczynski et al., 2006). Other theorizing suggests that meaning and certainty threats produce effects similar to MS and thus that these threats be considered theoretically equivalent (e.g., Proulx & Heine, 2006; McGregor, 2006). To help reconcile these discrepant perspectives, we meta-analytically examined MS effects as a function of the control condition utilized (meaning/certainty threats vs. other topics) and the length of delay between threat induction and subsequent defense. Results showed that MS and meaning/certainty threats both increased defensiveness after a short delay. But with a longer delay, MS produced even higher levels of defensiveness while meaning/certainty threats produced lower levels of defensiveness. Thus, the evidence supports a similarity between MS and meaning/certainty threat effects, but also a difference in time course that warrants their study as unique psychological threats. Copyright © 2010 John Wiley & Sons, Ltd.
On the computation of planetary boundary-layer height using the bulk Richardson number method

Abstract. Experimental data from four field campaigns are used to explore the variability of the bulk Richardson number of the entire planetary boundary layer (PBL), Ribc, which is a key parameter for calculating the PBL height (PBLH) in numerical weather and climate models with the bulk Richardson number method. First, the PBLHs of three different thermally stratified boundary layers (i.e., strongly stable boundary layers, weakly stable boundary layers, and unstable boundary layers) from the four field campaigns are determined using the turbulence method, the potential temperature gradient method, the low-level jet method, and the modified parcel method. Then for each type of boundary layer, an optimal Ribc is obtained through linear fitting and statistical error minimization methods so that the bulk Richardson method with this optimal Ribc yields similar estimates of PBLHs as the methods mentioned above. We find that the optimal Ribc increases as the PBL becomes more unstable: 0.24 for strongly stable boundary layers, 0.31 for weakly stable boundary layers, and 0.39 for unstable boundary layers. Compared with previous schemes that use a single value of Ribc in calculating the PBLH for all types of boundary layers, the new values of Ribc proposed by this study yield more accurate estimates of PBLHs.
Micrornas in prostate cancer: an overview

Prostate cancer is the second highest cause of cancer mortality after lung tumours. In USA it affects about 2.8 million men and the incidence increases with age in many countries. Therefore, early diagnosis is a very important step for patient clinical evaluation and for a selective and efficient therapy. The study of miRNAs' functions and molecular mechanisms has brought new knowledge in biological processes of cancer. In prostate cancer there is a deregulation of several miRNAs that may function as tumour suppressors or oncogenes. The aim of this review is to analyze the progress made to our understanding of the role of miRNA dysregulation in prostate cancer tumourigenesis.
Context Effects in the Processing of Phonolexical Ambiguity in L2

In order to comprehend speech, listeners have to combine low-level phonetic information about the incoming auditory signal with higher-order contextual information to make a lexical selection. This requires stable phonological categories and unambiguous representations of words in the mental lexicon. Unlike native speakers, second language (L2) speakers, who perceive nonnative sounds through the prism of their first language (L1), operate with fuzzy phonological categories, which lead to phonologically ambiguouslexicalrepresentations(e.g.,thewordsrock andlockcanbeconfusedifphonological representations for /r/ and /l/ are not sufficiently robust). The present study uses the AX discrimination task to establish the degree of sensitivity of L2 listeners to the Russian hard/soft phonological contrast. The same phonological contrasts are then used in the stimuli for the second task—listening comprehension task with word identification—to marksemantic,syntactic,andmorphologicaldistinctionsinwords.Thegoalofthestudy is to examine the contributions and relative efficiency of different contextual constraints (semantic, syntactic, and morphological) to the resolution of phonolexical ambiguity in L2 auditory sentence processing. The results suggest that when L2 phonological contrasts present a discriminability problem and create phonolexical ambiguity, L2 listeners rely on morphological constraints for disambiguation of word forms and syntactic constraints for disambiguation of words belonging to different parts of speech to a greater extent than on semantic constraints for disambiguation of nouns in the same form.
ATP does not regulate the reconstituted glucose transporter.

ATP has been reported to affect glucose transport in human erythrocytes and resealed erythrocyte ghosts [Jacquez, J. A. (1983) Biochim. Biophys. Acta 727, 367-378; Jensen, M. R. , & Brahm, J. (1987) Biochim. Biophys. Acta 900, 282-290]. In more detailed studies, effects of micromolar levels of ATP on transport in ghosts and inside-out vesicles, and on the fluorescence of ghosts and the purified glucose transporter [Carruthers, A. (1986) Biochemistry 25, 3592-3602; Hebert, D. N. , & Carruthers, A. (1986) J. Biol. Chem. 261, 10093-10099; Carruthers, A. (1986) J. Biol. Chem. 261, 11028-11037], have been interpreted as supporting a model in which ATP regulates the catalytic properties of the transporter. Both allosteric and covalent effects of ATP were proposed; among the allosteric effects was a 60% reduction in the Km for zero-trans uptake. In order to test whether allosteric ATP regulation of the transporter occurs, we reconstituted glucose transport activity into liposomes using erythrocyte membranes without detergent treatment. The effects of ATP, present either outside, inside, or both inside and outside the liposomes, on the transport activity were examined. Effects of ATP on trypsin-treated liposomes, which have only a single orientation of active transporters, were also tested. While the model predicts activation by ATP, only inhibition was observed. This was significant only at millimolar concentrations of ATP, in contrast to the previously reported effects at micromolar levels, and was primarily on the extracellular surface of the transporter. In addition, the ATP effects on reconstituted transport were nonspecific, with similar effects produced by tripolyphosphate. (ABSTRACT TRUNCATED AT 250 WORDS)
The Widened Heart

Believing belongs to experience. It does not generate itself. When men today repeat the Lord's Prayer, saying Jesus' words after Jesus, “Lead us not into trial but deliver us from evil,” they are giving voice to their believing for a reason. The reason is the experience of being diminished and enlarged in the world of death, beauty, and renewal — in the great world of action that is the “circumpressure” of God. Believing (literally, holding dear) arises in times of testing in which human faithfulness takes shape and becomes tangible as an affection. How faithfulness becomes palpable is the subject matter of the following account.
Effect of host glass on the optical absorption properties of Nd3+, Sm3+, and Dy3+ in lead borate glasses.

The effect of host glass composition on the optical absorption spectra of $Nd^{3+}$, $Sm^{3+}$, and $Dy^{3+}$ in lead borate glasses, with PbO contents varying from 30 to 70 mol %, has been analyzed using Judd-Ofelt theory and the compositional dependence has been determined for the hypersensitive bands. Judd-Ofelt intensity parameters $\Omega_t$ (t=2,4,6), and the radiative transition probabilities. The variation of $\Omega_2$ with PbO content has been attributed to changes in the asymmetry of the ligand field at the rare-earth (R) site due to the structural changes and to changes in R-O covalency, whereas the variation of $\Omega_6$ has been related to the variation in R-O covalency. The radiative transition probabilities of the rare-earth ions are large in lead borate glasses suggesting their suitability for laser applications.