Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of Juniperus virginiana on plant species composition in an Oklahoma grassland

We established transects under twenty Juniperus virginiana trees that invaded an unburned central Oklahoma grassland within the last 20 years to determine their effects on plant species composition. Species richness and stem density increased as distance from the trunk increased. Stem density was also higher towards the south side of trees. Graminoid, forb and total cover were related to distance from the trunk and transect direction. Ordination revealed weak compositional gradients related to “openness” and compass direction. Woody species tended to be most abundant underneath J. virginiana canopies whereas grass and forb species were most abundant in the prairie. Woody and shade-tolerant species preferentially occurred in north transects and quadrats underneath the tree. Conversely, forbs had highest abundance on edge quadrats whereas graminoids dominated south transects and prairie quadrats. Thus, invasion of grasslands by J. virginiana influences species composition in a spatially complex manner.
Receptor-selective agonists and modes of a 7 receptor activation

Ž . Ž . Ž The a7-selective agonists 32,4-dimethoxybenzylidene -anabaseine GTS-21 , also known as DMXB, and 34-hydroxy,2-methoxy. Ž . benzylidene anabaseine 4OH-GTS-21 produce a variety of behavioral and cytoprotective effects that may be related to the activation of either large transient currents at high concentrations or small sustained currents at lower agonist concentrations. We are using acutely Ž . dissociated hypothalamic neurons, which express a central nervous system CNS a7-type receptor, to test a model for the concentrationdependent desensitization of a7-mediated responses. Our results confirm that 4OH-GTS-21 is a potent activator of neuronal a7 nicotinic-acetylcholine receptor. The rapid application of agonist leads to a brief period of maximal receptor-activation followed by desensitization. Rise rates, decay rates, and the degree to which current was desensitized were all concentration-dependent. Following the initial peak response to a 300-mM 4OH-GTS-21 application, current is reduced to baseline values within about 100 ms. Application of 30 mM 4OH-GTS-21 produced both a transient peak current and a sustained current that decayed only slowly after the removal of agonist. In the case of a 300-mM 4OH-GTS-21 application, after agonist was removed, we saw a rebound response up to the level of the 30-mM sustained current. The data, therefore, suggest that a sufficient level of agonist occupation can be retained on the receptor to promote activation for up to several hundred milliseconds. q 2000 Elsevier Science B.V. All rights reserved.
Estrogen deprivation and excess energy supply accelerate 7,12-dimethylbenz(a)anthracene-induced mammary tumor growth in C3H/HeN mice

BACKGROUND/OBJECTIVES Obesity is a risk factor of breast cancer in postmenopausal women. Estrogen deprivation has been suggested to cause alteration of lipid metabolism thereby creating a cellular microenvironment favoring tumor growth. The aim of this study is to investigate the effects of estrogen depletion in combination with excess energy supply on breast tumor development. MATERIALS/METHODS Ovariectomized (OVX) or sham-operated C3H/HeN mice at 4 wks were provided with either a normal diet or a high-fat diet (HD) for 16 weeks. Breast tumors were induced by administration of 7,12-dimethylbenz(a)anthracene once a week for six consecutive weeks. RESULTS Study results showed higher serum concentrations of free fatty acids and insulin in the OVX+HD group compared to other groups. The average tumor volume was significantly larger in OVX+HD animals than in other groups. Expressions of mammary tumor insulin receptor and mammalian target of rapamycin proteins as well as the ratio of pAKT/AKT were significantly increased, while pAMPK/AMPK was decreased in OVX+HD animals compared to the sham-operated groups. Higher relative expression of liver fatty acid synthase mRNA was observed in OVX+HD mice compared with other groups. CONCLUSIONS These results suggest that excess energy supply affects the accelerated mammary tumor growth in estrogen deprived mice.
Ensembles of probabilistic principal surfaces and competitive evolution on data: two different approaches to data classification

Probabilistic Principal Surfaces (PPS) offer very powerful visualization and classification capabilities and overcome most of the shortcomings of other neural tools such as SOM, GTM, etc. More specifically PPS build a probability density function of a given data set of patterns lying in a D-dimensional space (with D ≫ 3) which can be expressed in terms of a limited number of latent variables laying in a Q-dimensional space (Q is usually 2-3) which can be used to visualize the data in the latent space. PPS may also be arranged in ensembles to tackle very complex classification tasks. Competitive Evolution on Data (CED) is instead an evolutionary system in which the possible solutions (cluster centroids) compete to conquer the largest possible number of resources (data) and thus partition the input data set in clusters. We discuss the application of Spherical-PPS to two data sets coming, respectively, from astronomy (Great Observatory Origins Deep Survey) and from genetics (microarray data from yeast genoma) and of CED to the genetics data only.
Characterization and rescue of telomeric abnormalities in ICF syndrome type I fibroblasts

Mutations in the human DNA methyltransferase 3B (DNMT3B) gene lead to ICF (immunodeficiency, centromeric region instability, and facial anomalies) syndrome type I. We have previously described a telomere-related phenotype in cells from these patients, involving severe hypomethylation of subtelomeric regions, abnormally short telomeres and high levels of telomeric-repeat-containing RNA (TERRA). Here we demonstrate that ICF-patient fibroblasts carry abnormally short telomeres at a low population doubling (PD) and enter senescence prematurely. Accordingly, we attempted to rescue the senescence phenotype by ectopic expression of human telomerase, which led to elongated telomeres with hypomethylated subtelomeres. The senescence phenotype was overcome under these conditions, thus dissociating subtelomeric-DNA hypomethylation per se from the senescence phenotype. In addition, we examined whether the subtelomeric methylation could be restored by expression of a normal copy of full length DNMT3B1 in ICF fibroblasts. Ectopic expression of DNMT3B1 failed to rescue the abnormal hypomethylation at subtelomeres. However, partial rescue of subtelomeric-hypomethylation was achieved by co-expression of DNMT3B1 together with DNA methyltransferase 3-like (DNMT3L), encoding a protein that functions as a stimulator of DNMT3A and DNMT3B. DNMT3B1 and DNMT3L are predominantly expressed during early embryonic development, suggesting that de novo subtelomeric DNA methylation during crucial stages of human embryonic development may be necessary for setting and maintaining normal telomere length.
Learning Concept Classification Rules Using Genetic Algorithms

In this paper we explore the use of an adaptive search technique (genetic algorithms) to construct a system GABEL which continually learns and refines concept classification rules from its interaction with the environment. The performance of the system is measured on a set of concept learning problems and compared with the performance of two existing systems: ID5R and C4.5. Preliminary results support that, despite minimal system bias, GABIL is an effective concept learner and is quite competitive with ID5R and C4.5 as the target concept increases in complexity.
Selectivity and tolerance for visual texture in macaque V2

Significance The brain generates increasingly complex representations of the visual world to recognize objects, to form new memories, and to organize visual behavior. Relatively simple signals in the retina are transformed through a cascade of neural computations into highly complex responses in visual cortical areas deep in the temporal lobe. The representations of visual signals in areas that lie in the middle of this cascade remain poorly understood, yet they are critical to understanding how the cascade operates. Here, we demonstrate changes in the representation of visual information from area V1 to V2, and show how these changes extract and represent information about the local statistical features of visual images. As information propagates along the ventral visual hierarchy, neuronal responses become both more specific for particular image features and more tolerant of image transformations that preserve those features. Here, we present evidence that neurons in area V2 are selective for local statistics that occur in natural visual textures, and tolerant of manipulations that preserve these statistics. Texture stimuli were generated by sampling from a statistical model, with parameters chosen to match the parameters of a set of visually distinct natural texture images. Stimuli generated with the same statistics are perceptually similar to each other despite differences, arising from the sampling process, in the precise spatial location of features. We assessed the accuracy with which these textures could be classified based on the responses of V1 and V2 neurons recorded individually in anesthetized macaque monkeys. We also assessed the accuracy with which particular samples could be identified, relative to other statistically matched samples. For populations of up to 100 cells, V1 neurons supported better performance in the sample identification task, whereas V2 neurons exhibited better performance in texture classification. Relative to V1, the responses of V2 show greater selectivity and tolerance for the representation of texture statistics.
Evolution of Open Source Software Networks

The work presented in this paper is focused on the Open Source Software (OSS) community structure, with particular emphasis on the Concurrent Versions System (CVS) and Subversion (SVN) datasets used to produce the network structure. The theme of the work in this paper is the dynamics of these networks over time. Much research has been done analyzing the network structure at some particular point in time or the network formed by conflating connections made over a specific time span. We present a review of OSS research using CVS/SVN data. We provide an introduction to complex networks as it relates to the open source software community and the numerous studies analyzing networks formed by different software communities, such as SourceForge and GNU Savannah. We also present an initial analysis of the developer and project networks for BerliOS Developer, SourceForge, and GNU Savannah. We also present the results of a study on the importance of social network structure as an indicator of longterm project success. We propose work relating to the evolution of open source software networks as well as the importance of the dynamic network structure.
Scaling Up Antiretroviral Treatment Services in Karnataka, India: Impact on CD4 Counts of HIV-Infected People

Setting Twelve antiretroviral treatment centres under National AIDS Control Programme (NACP), Karnataka State, India. Objective For the period 2004-2011, to describe the trends in the numbers of people living with HIV (PLHIV) registered for care and their median baseline CD4 counts, disaggregated by age and sex. Design Descriptive study involving analysis of routinely captured data (year of registration, age, sex, baseline CD4 count) under NACP. Results 34,882 (97% of total eligible) PLHIV were included in analysis. The number registered for care has increased by over 12 times during 2004-11; with increasing numbers among females. The median baseline CD4 cell count rose from 125 in 2004 to 235 in 2011 – the increase was greater among females as compared to males. However, about two-thirds still presented at CD4 cell counts less than 350. Conclusion We found an increasing trend of median CD4 counts among PLHIV presenting to ART centres in Karnataka, an indicator of enhanced and early access to HIV care. Equal proportion of females and higher baseline CD4 counts among them allays any fear of differential access by gender. Despite this relative success, a substantial proportion still presented at low CD4 cell counts indicating possibly delayed HIV diagnosis and delayed linkage to HIV care. Universal HIV testing at health care facilities and strengthening early access to care are required to bridge the gap.
Peak flow rate and death due to coronary heart disease: 30-year results from the Northwick Park Heart cohort study

Objective Numerous studies have reported that chronic obstructive pulmonary disease or impaired lung function are associated with later coronary heart disease (CHD). However, it is unclear if lung function is an independent risk factor, as many of these studies have included only limited measures of other factors associated with CHD. Methods In total 2167 men of all ages in the first Northwick Park Heart Study were followed for a median of 30 years. Cox regression models were used to assess the relationship between peak flow rate (PFR) and CHD mortality adjusted for potential confounders measured at baseline. Analyses allowed for missing data, and secondary analyses for repeat measures on some men and competing risks of CHD death. Results There were 254 CHD deaths with some evidence of an association between PFR and CHD mortality. The adjusted HRs (95% CIs) from the lowest to the highest of four PFR quartiles were 1.53 (1.04 to 2.25), <430 L/min; 1.43 (0.99 to 2.08), 430 – <490 L/min; and 1.31 (0.93 to 1.86), 490 – <550 L/min; compared with the reference group of ≥550 L/min (trend test p=0.025). Other associations with CHD mortality were observed for systolic blood pressure (p<0.0001), body mass index (p=0.0002), smoking status (p=0.015), blood cholesterol (p=0.005), plasma fibrinogen (p=0.001) and high-risk ECG (p=0.021). There were no strong associations for factors V and VIII or platelet count. Conclusions After allowing for a range of other risk factors associated with CHD, there was only limited evidence of a relation between PFR and CHD mortality.
Cortical plasticity, dynamic neural fields and self-organization. (Plasticité corticale, champs neuronaux dynamiques et auto-organisation)

The aim of the present work is the modeling of the formation, maintenance and reorganization of somatosensory cortical maps using the theory of dynamic neural fields. A dynamic neural field is a partial integro-differential equation that is used to model the cortical activity of a part of the cortex. Such a neural field is used in this work in order to model a part of the area 3b of the primary somatosensory cortex. In addition a skin model is used in order to provide input to the cortical model. From a computational point of view the model is able to perform distributed, numerical and adaptive computations. The model is able to explain the formation of topographic maps and their reorganization in the presence of a cortical lesion or a sensory deprivation, where balance between excitation and inhibition plays a crucial role. In addition, the model is consistent with neurophysiological data of area 3b. Finally, it has been shown that attention plays a key role in the organization of receptive fields of neurons of the somatosensory cortex. Therefore, in this work has been proposed a definition of somatosensory attention and a potential explanation of its influence on somatotopic organization through a number of experimental results. By changing the gains of lateral connections, it is possible to control the shape of the solution of the neural field. This leads to significant alterations of receptive fields sizes, resulting to a better performance during the execution of demanding haptic tasks.
Causal Models: The Representational Infrastructure for Moral Judgment

This chapter has three objectives. First, we formulate a coarse model of the process of moral judgment to locate the role of causal analysis. We propose that causal analysis occurs in the very earliest stages of interpreting an event and that early moral appraisals depend on it as do emotional responses and deliberative reasoning. Second, we argue that causal models offer the best representation for formulating psychological principles of moral appraisal. Causal models directly represent causes, consequences, and the structural relations among them. In other words, they represent mechanisms. Finally, we speculate that moral appraisals reflect the similarity between an idealized causal model of moral behavior and a causal model of the event being judged. Psychology of Learning and Motivation, Volume 50 # 2009 Elsevier Inc. ISSN 0079-7421, DOI: 10.1016/S0079-7421(08)00401-5 All rights reserved. 1 Author's personal copy
Beta 2-adrenergic receptor and angiotensin II receptor modulation of sympathetic neurotransmission in human atria.

The aim of the present study was to investigate beta-adrenergic receptor and angiotensin II (Ang II) receptor modulation of norepinephrine release in human atria. Slices of human atrial appendages were incubated with [3H]norepinephrine, superfused with Krebs-Henseleit solution, and electrically stimulated in superfusion chambers. Pretreatment of the tissue with 6-hydroxydopamine (1.2 mmol/L) before the [3H]norepinephrine incubation to destroy sympathetic nerves reduced the uptake of radioactivity and abolished the stimulation-induced (S-I) outflow of radioactivity. Furthermore, S-I outflow of radioactivity was prevented by the addition of tetrodotoxin (1 mumol/L) to and omission of extracellular Ca2+ from the superfusion solution. Separation of [3H]norepinephrine from its metabolites revealed that the S-I outflow of radioactivity was mainly composed of intact [3H]norepinephrine. Thus, the S-I outflow of radioactivity was taken as an index of norepinephrine release. Isoproterenol (0.001 to 0.1 mumol/L) dose-dependently enhanced the S-I outflow of radioactivity. The concentration-response curve of isoproterenol was shifted to the right by the selective beta 2-adrenergic receptor antagonist ICI 118551 (0.01 and 0.1 mumol/L) but not by the beta 1-adrenergic receptor-selective antagonist atenolol (0.3 and 30 mumol/L). Ang II (0.001 to 1.0 mumol/L) also dose-dependently enhanced S-I outflow of radioactivity. The facilitatory effect of Ang II was blocked by either the peptide Ang II receptor antagonist saralasin (1.0 mumol/L) or EXP 3174 (0.1 mumol/L), the in vitro active form of the nonpeptide Ang II receptor antagonist losartan. The cell-permeable cAMP analogue 8-bromo-cAMP (30 to 300 mumol/L) dose-dependently enhanced S-I outflow of radioactivity. (ABSTRACT TRUNCATED AT 250 WORDS)
Age of First Breeding Interacts with Pre- and Post-Recruitment Experience in Shaping Breeding Phenology in a Long-Lived Gull

Individual variation in timing of breeding is a key factor affecting adaptation to environmental change, yet our basic understanding of the causes of such individual variation is incomplete. This study tests several hypotheses for age-related variation in the breeding timing of Lesser Black-backed Gulls, based on a 13 year longitudinal data set that allows to decouple effects of age, previous prospecting behavior, and years of breeding experience on arrival timing at the colony. At the population level, age of first breeding was significantly associated with timing of arrival and survival, i.e. individuals tended to arrive later if they postponed their recruitment, and individuals recruiting at the age of 4 years survived best. However, up to 81% of the temporal variation in arrival dates was explained by within-individual effects. When excluding the pre-recruitment period, the effect of increasing age on advanced arrival was estimated at 11 days, with prior breeding experience accounting for a 7 days advance and postponed breeding for a 4 days delay. Overall, results of this study show that delayed age of first breeding can serve to advance arrival date (days after December 1st) in successive breeding seasons throughout an individual’s lifetime, in large part due to the benefits of learning or experience gained during prospecting. However, prospecting and the associated delay in breeding also bear a survival cost, possibly because prospectors have been forced to delay through competition with breeders. More generally, results of this study set the stage for exploring integrated temporal shifts in phenology, resource allocation and reproductive strategies during individual lifecycles of long-lived migratory species.
Effect of Silver Diamine Fluoride and Potassium Iodide Treatment on Secondary Caries Prevention and Tooth Discolouration in Cervical Glass Ionomer Cement Restoration

This study investigated the effect of silver diamine fluoride (SDF) and potassium iodide (KI) treatment on secondary caries prevention and tooth discolouration in glass ionomer cement (GIC) restoration. Cervical GIC restorations were done on 30 premolars with: Group 1, SDF + KI; Group 2, SDF (positive control); Group 3, no treatment (negative control). After cariogenic biofilm challenge, the demineralisation of dentine adjacent to the restoration was evaluated using micro-computed tomography (micro-CT) and Fourier transform infrared (FTIR) spectroscopy. The colour of dentine adjacent to the restoration was assessed using CIELAB system at different time points. Total colour change (∆E) was calculated and was visible if ∆E > 3.7. Micro-CT showed the outer lesion depths for Groups 1, 2 and 3 were 91 ± 7 µm, 80 ± 7 µm and 119 ± 8 µm, respectively (p < 0.001; Group 2 < Group 1 < Group 3). FTIR found that there was a significant difference in amide I-to-hydrogen phosphate ratio among the three groups (p < 0.001; Group 2 < Group 1 < Group 3). ∆E of Groups 1, 2 and 3 after biofilm challenge were 22.5 ± 4.9, 70.2 ± 8.3 and 2.9 ± 0.9, respectively (p < 0.001; Group 3 < Group 1 < Group 2). SDF + KI treatment reduced secondary caries formation on GIC restoration, but it was not as effective as SDF treatment alone. Moreover, a perceptible staining on the restoration margin was observed, but the intensity of discolouration was less than that with solely SDF treatment.
Dispersion map optimization in hybrid Raman/erbium-doped fiber amplifier-based 40-Gb/s link

We report on dispersion map optimization in hybrid Raman/erbium-doped fiber amplifier-based links with different types of in-line fibers and dispersion-compensating fibers. The results show that the linear relationship between precompensation and in-line cumulated dispersion depends on Raman gain and can be explained by the power profile approach.