Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales

ABSTRACT The ups operon of Sulfolobus species is highly induced upon UV stress. Previous studies showed that the pili encoded by this operon are involved in cellular aggregation, which is essential for subsequent DNA exchange between cells, resulting in homologous recombination. The presence of this pilus system increases the fitness of Sulfolobus cells under UV light-induced stress conditions, as the transfer of DNA takes place in order to repair UV-induced DNA lesions via homologous recombination. Four conserved genes (saci_1497 to saci_1500) which encode proteins with putative DNA processing functions are present downstream of the ups operon. In this study, we show that after UV treatment the cellular aggregation of strains with saci_1497, saci_1498, and saci_1500 deletions is similar to that of wild-type strains; their survival rates, however, were reduced and similar to or lower than those of the pilus deletion strains, which could not aggregate anymore. DNA recombination assays indicated that saci_1498, encoding a ParB-like protein, plays an important role in DNA transfer. Moreover, biochemical analysis showed that the endonuclease III encoded by saci_1497 nicks UV-damaged DNA. In addition, RecQ-like helicase Saci_1500 is able to unwind homologous recombination intermediates, such as Holliday junctions. Interestingly, a saci_1500 deletion mutant was more sensitive to UV light but not to the replication-stalling agents hydroxyurea and methyl methanesulfonate, suggesting that Saci_1500 functions specifically in the UV damage pathway. Together these results suggest a role of Saci_1497 to Saci_1500 in the repair or transfer of DNA that takes place after UV-induced damage to the genomic DNA of Sulfolobus acidocaldarius. IMPORTANCE Sulfolobales species increase their fitness after UV stress by a UV-inducible pilus system that enables high rates of DNA exchange between cells. Downstream of the pilus operon, three genes that seem to play a role in the repair or transfer of the DNA between Sulfolobus cells were identified, and their possible functions are discussed. Next to the previously described role of UV-inducible pili in the exchange of DNA, we have thereby increased our knowledge of DNA transfer at the level of DNA processing. This paper therefore contributes to the overall understanding of the DNA exchange mechanism among Sulfolobales cells.
Crystal Structures of Cytochrome P450 105P1 from Streptomyces avermitilis: Conformational Flexibility and Histidine Ligation State

ABSTRACT The polyene macrolide antibiotic filipin is widely used as a probe for cholesterol in biological membranes. The filipin biosynthetic pathway of Streptomyces avermitilis contains two position-specific hydroxylases, C26-specific CYP105P1 and C1′-specific CYP105D6. In this study, we describe the three X-ray crystal structures of CYP105P1: the ligand-free wild-type (WT-free), 4-phenylimidazole-bound wild-type (WT-4PI), and ligand-free H72A mutant (H72A-free) forms. The BC loop region in the WT-free structure has a unique feature; the side chain of His72 within this region is ligated to the heme iron. On the other hand, this region is highly disordered and widely open in WT-4PI and H72A-free structures, respectively. Histidine ligation of wild-type CYP105P1 was not detectable in solution, and a type II spectral change was clearly observed when 4-phenylimidazole was titrated. The H72A mutant showed spectroscopic characteristics that were almost identical to those of the wild-type protein. In the H72A-free structure, there is a large pocket that is of the same size as the filipin molecule. The highly flexible feature of the BC loop region of CYP105P1 may be required to accept a large hydrophobic substrate.
Syk Associates with Clathrin and Mediates Phosphatidylinositol 3-Kinase Activation during Human Rhinovirus Internalization1

Human rhinovirus (HRV) causes the common cold. The most common acute infection in humans, HRV is a leading cause of exacerbations of asthma and chronic obstruction pulmonary disease because of its ability to exacerbate airway inflammation by altering epithelial cell biology upon binding to its receptor, ICAM-1. ICAM-1 regulates not only viral entry and replication but also signaling pathways that lead to inflammatory mediator production. We recently demonstrated the Syk tyrosine kinase to be an important mediator of HRV-ICAM-1 signaling: Syk regulates replication-independent p38 MAPK activation and IL-8 expression. In leukocytes, Syk regulates receptor-mediated internalization via PI3K. Although PI3K has been shown to regulate HRV-induced IL-8 expression and clathrin-mediated endocytosis of HRV, the role of airway epithelial Syk in this signaling pathway is not known. We postulated that Syk regulates PI3K activation and HRV endocytosis in the airway epithelium. Using confocal microscopy and immunoprecipitation, we demonstrated recruitment of the normally cytosolic Syk to the plasma membrane upon HRV16-ICAM-1 binding, along with Syk-clathrin coassociation. Subsequent incubation at 37°C to permit internalization revealed redistribution of Syk to punctate structures resembling endosomes and colocalization with HRV16. Internalized HRV was not detected in cells overexpressing the kinase inactive SykK396R mutant, indicating that kinase activity was necessary for endocytosis. HRV-induced PI3K activation was dependent on Syk; Syk knockdown by small interfering RNA significantly decreased phosphorylation of the PI3K substrate Akt. Together, these data reveal Syk to be an important mediator of HRV endocytosis and HRV-induced PI3K activation.
Learning as a function of word-frequency.

The experimental work of Howes and Solomon has indicated a high inverse relationship between the frequency with which a word appears in the language (as indicated by the Thorndike-Lorge word count1) and the duration of time required for S to perceive it.2 In an effort to provide a more exact statement of this relationship, Solomon and Postman controlled frequency more precisely by having Ss read and pronounce different nonsense words with frequencies ranging from 1 to 25' The results indicated the same inverse relationship between the recognition thresholds and the frequency of prior usage. If the assumption is made that there is a relationship between perceptual threshold and learning as measured by a recall score (that those words perceived most rapidly are easiest to learn), words which appear with a high frequency in the language should be learned more readily than those of low frequency. Aside from this theoretical consideration, the relationship found between learning and word-frequency should be of value in the calibration, construction, and utilization of word-lists which are so frequently used in rote-learning experiments. It should be noted that an earlier study by Peters did not seem to support the existence of such a relationship.4 In one phase of a series of experiments, Peters constructed five different word lists, the words in each list being selected from the 2500 most frequently used words found in the Teacher's Word Book of 10,000 Words. ' List I contained words with frequencies of 1 to 500, List II contained words with frequencies of 501-1000, List III contained words with frequencies of 1000-1500, and so forth. The Ss were then presented with these lists in a counterbalanced order. Recall scores obtained after one presentation indicated no significant differences between lists.
Asymptotic Analysis of Cooperative Diversity Systems With Relay Selection in a Spectrum-Sharing Scenario

Three low-complexity relay-selection strategies, namely, selective amplify and forward (S-AF), selective decode and forward (S-DF), and amplify and forward with partial relay selection (PRS-AF) in a spectrum-sharing scenario are studied. First, we consider a scenario where perfect channel state information (CSI) is available. For these scenarios, the respective asymptotic outage behaviors of the secondary systems are analyzed, from which the diversity and coding gains are derived and compared. Unlike the coding gain, which is shown to be very sensitive with the position of the primary receiver, the diversity gain of the secondary system is the same as the nonspectrum-sharing system. In addition, depending on the cooperative strategy employed, an increase in the number of relays may lead to severe loss of the coding gain. Afterwards, the impacts of imperfect CSI regarding the interference and transmit channels on the outage behavior of the secondary systems are analyzed. On one hand, the imperfect CSI concerning the interference channels only affects the outage performance of the primary system, whereas it has no effect on the diversity gain of the secondary system. On the other hand, the imperfect CSI concerning the transmit channels of the secondary systems may reduce the diversity gain of the three relay-selection strategies to unity, which is validated by both theoretical and numerical results.
Chaos and Control of Chaos in Current Controlled Power Factor Corrected ACDC Boost Regulator

In these modern research areas the Nonlinear Dynamics is a very popular topic, the researchers study the nonlinear behaviour of every system which can be an industrial machine/instrument or a theoretical aspect. Prior researchers already studied the nonlinear dynamics of Current Controlled DC-DC Boost Converter. But the Power Factor Corrected Boost Converter is a circuit which is used in very practical purpose where the input is AC, the AC is rectified to DC by diode bridge rectifier and the rectified DC is to feed the boost converter i.e. conventional pure DC supply is replaced by the rectifier DC. In this converter the circuit is designed specially as input power factor can maintain unity so it is called Power Factor Corrected (PFC) Boost Converter. This paper aims to develop a circuit for PFC boost converter to observe Phase-Portrait diagrams and also discuss the control of chaos.
Sweetness, Satiation, and Satiety 1-3

Satiation and satiety are central concepts in the understanding of appetite control and both have to do with the inhibition of eating. Satiation occurs during an eating episode and brings it to an end. Satiety starts after the end of eating and prevents further eating before the return of hunger. Enhancing satiation and satiety derived from foodstuffs was perceived as a means to facilitate weight control. Many studies have examined the various sensory, cognitive, postingestive, and postabsorptive factors that can potentially contribute to the inhibition of eating. In such studies, careful attention to study design is crucial for correct interpretation of the results. Although sweetness is a potent sensory stimulus of intake, sweet-tasting products produce satiation and satiety as a result of their volume as well as their nutrient and energy content. The particular case of energy intake from fluids has generated much research and it is still debated whether energy from fluids is as satiating as energy ingested from solid foods. This review discusses the satiating power of foods and drinks containing nutritive and nonnutritive sweeteners. The brain mechanisms of food reward (in terms of “liking” and “wanting”) are also addressed. Finally, we highlight the importance of reward homeostasis, which can help prevent eating in the absence of hunger, for the control of intake. J. Nutr. 142: 1149S‐1154S, 2012.
Recovery of plant communities after ecological restoration of forestry‐drained peatlands

Abstract Ecological restoration is expected to reverse the loss of biodiversity and ecosystem services. Due to the low number of well‐replicated field studies, the extent to which restoration recovers plant communities, and the factors underlying possible shortcomings, are not well understood even in medium term. We compared the plant community composition of 38 sites comprising pristine, forestry‐drained, and 5 or 10 years ago restored peatlands in southern Finland, with special interest in understanding spatial variation within studied sites, as well as the development of the numbers and the abundances of target species. Our results indicated a recovery of community composition 5–10 years after restoration, but there was significant heterogeneity in recovery. Plant communities farthest away from ditches were very similar to their pristine reference already 10 years after restoration. In contrast, communities in the ditches were as far from the target as the drained communities. The recovery appears to be characterized by a decline in the number and abundance of species typical to degraded conditions, and increase in the abundance of characteristic peatland species. However, we found no increase above the drained state in the number of characteristic peatland species. Our results suggest that there is a risk of drawing premature conclusions on the efficiency of ecological restoration with the current practice of short‐term monitoring. Our results also illustrate fine‐scale within‐site spatial variability in the degradation and recovery of the plant communities that should be considered when evaluating the success of restoration. Overall, we find the heterogeneous outcome of restoration observed here promising. However, low recovery in the number of characteristic species demonstrates the importance of prioritizing restoration sites, and addressing the uncertainty of recovery when setting restoration targets. It appears that it is easier to eradicate unwanted species than regain characteristic species by restoration.
North Atlantic ventilation using chlorofluorocarbons and idealised-tracer simulations

ABSTRACT The simulated chlorofluorocarbon CFC-11 and 29 geographically defined CFC-11 tracers, as well as 29 geographically defined idealised tracers, are used to quantify the regional contribution to the ventilation of the North Atlantic Ocean in a global version of the Miami Isopycnal Coordinate Ocean Model (MICOM) driven by the daily NCEP/NCAR forcing. Age tracers attached to 29 idealised tracers are also used to estimate the timescales for the water masses’ transports. Our results show that the simulated overturning circulation matches the available observed data for both intensity and variability, and the simulated distribution of CFC-11 concentration in the subtropical North Atlantic Ocean is in good agreement with the observations, particularly above 800 m in depth. We found that the sandwich-like distribution of CFC-11 concentration in the subtropical North Atlantic in both the observations and simulations is mainly caused by subduction from the western and eastern subpolar North Atlantic, but the contribution of the former (56.0%) is almost four times larger than that of the latter (15.7%). We demonstrated that the ocean dynamics, instead of the source function, determine the annual and inter-annual variability in both dynamically active tracer (such as water temperature and salinity) and passive tracer (such as CFC-11 and idealised tracer) concentrations in the deep North Atlantic. The ‘apparent age’ distribution shows that the surface water in the western subpolar North Atlantic takes about 12 yr to reach the Nordic Seas and takes 20 yr from the Nordic Seas to the subtropical deep North Atlantic. The transit-time derived by ‘optimum time lag’ approach shows a 9.3–13.6 yr lag for the signals propagating from the western subpolar North Atlantic to the subtropical North Atlantic, which is generally consistent with that of about 10 yr derived from the ‘apparent age’. The study suggests that geographically defined tracers can be used as an efficient tool to investigate the source and spreading pathway of water, and to forecast the spreading and spreading time of environmental accidents such as the radioactive waste in the world's oceans.
Analysis of crop residue burning and tropospheric NO2 vertical column density retrieved from satellite remote sensing in North China.

To insure air quality during the Beijing Olympic Games, open field burning of crop residues was banned in North China from May to September in 2008. The impact of this effort was estimated through the detection of the crop residue burning from MODIS data and measurement of NO2 vertical column density retrieved from OMI data. The middle and thermal infrared channels of MODIS data were used to monitor the crop residue burning from June to August in 2007 and 2008. The number of crop residue burning pixels obviously decreased from about 250d in 2007 to less than 40d in 2008 in June and July, but there was a little increase in August. Meanwhile, the monthly averaged tropospheric NO2 vertical column density retrieved from OMI data from June to August in 2007 and 2008 were used to study the difference of the variation of NO2 in these two years, and the results indicated that NO2 concentration had been reduced due to the ban of crop residue burning to some extent, but the impact of this effort was limited.
O archiwach społecznych i ich znaczeniu dla polskiego dziedzictwa narodowego oraz tożsamości lokalnej

Community archives display notable activity, especially during last years. Due to that they have become a significant element of the system of archives in Poland. But there are still a number of basic problems, not only theoretical, concerning their activity, that must be set down: their formal status (also: their holdings status), their place in system of Polish archives (in the broad sense), and shape of their relations to other archives (especially state ones). Moreover, corresponding to problems mentioned above, their fundamental meaning to national heritage and local identity must be looked into. Taking a thesis of Jerzy Skowronek, that the archival national heritage are all archival materials produced by a particular nation and state, regardless of place of keeping, the holdings of community archives must be seen as that. But not always they are simply associated with phenomena, processes or events that are crucial from the point of view of a nation as a whole. Whereas these holdings, according to a scope of their collection, are direct and very accurate reflection of local history. This makes community archives main creators and protectors of local identity, especially with common practice among community archives, that consists in dragging local communities into cooperation in making the history and, in general, into cooperating with them. Their mission, in both of these spheres, is carried out in a condition of a dichotomy. On the one hand there is intentional using of assets: creativity, enthusiasm and a special ability to reach to sources that are unavailable to other potential rivals. On the other hand, a full success is impediment due to various limitations, especially often observed financial fragility and lack of certainty of existence in a longer time perspective. Whereas state archives, having no problems in that area, due to some formal and organizational reasons cannot impact the non-state branch of the national archival holdings effectively. That, and a number of other reasons should induce both types of archives to strengthen contacts between them and to take up or intensify collaboration in various fields. It will result in increasing efficiency of archival activity performed by them separately.
Noradrenergic Sympathetic Neural Interactions with the Immune System: Structure and Function

Histochemical studies from our (Williams & Felten 1981, Williams et al. 1981, D. Felten et al. 1981, 1984, 1985, 1987a, 1987b, Livnat et al. 1985, Ackerman et al. 1986, S. Felten et al. 1987) and other laboratories (Giron et al. 1980, Bulloch & Pomeranz, 1984, Singh 1984, Walcott & MacLean 1985) have shown the presence of autonomic nerve fibers in specific compartments of both primary and secondary lymphoid organs. These nerve fibers are associated not only with blood vessels but also with lymphocytes and macrophages. We have demonstrated that the neurotransmitter norepinephrine (NE), present in the postganglionic sympathetic fibers that richly innervate lymphoid organs, acts in the spleen as both a paracrine secretion, available to receptors on cells in the white pulp, and a localized neurotransmitter in nerve terminals that directly contact T lymphocytes in the periarteriolar lymphatic sheath (PALS) (S. Felten et al. 1986, S. Felten & Olschowka 1987). We propose that NE in lymphoid organs fulfills the criteria for neurotransmission, estabUshed in more traditional efTector tissues such as the heart, and plays a role in the modulation of immune responses. This review summarizes evidence for neurotransmission, including presence and compartmentation of NE, transmitter release, post-synaptic receptors on cells of the immune system, and functional consequences of denervation and pharmacological manipulation of NE. We also review aspects of development, aging, and plasticity of noradrenergic (NA) fibers that enhance our understanding of their role in organs of the immune system.
Design Architecture, Developer Networks and Performance of Open Source Software Projects

In this dissertation I seek to understand the factors differentiating successful from unsuccessful software projects by investigating how design architectures and developers' positions within collaborative networks affect software project outcomes. There is a growing body of evidence that a product's architecture – defined here as decisions made regarding how to decompose design tasks and the resulting design structure – is a critical issue to both researchers and managers to understand. However, prior research studies on software development tend to emphasize design without taking into account the collaborative development environment, or have little power in predicting the phenomena with which the design constructs are associated because of insufficient empirical evidence. This dissertation develops and tests a model measuring the impact on software project performance of (1) software products' design architectures and (2) developers' positions within collaborative networks. Three indicators of project success are used: product quality, the signal of market success, and project velocity. Two dimensions of design architecture—degree of decomposition and coupling—and two characteristics of developer network structures—degree centrality and structural holes—are investigated for their impact on project performance. Using data gathered from SourceForge.net and the data warehouse including its monthly dumps, empirical analysis is conducted on the top 100 ranked projects and compared to a randomly chosen 100 projects. The main findings are that (1) the degree of decomposition has an inverted U-shaped relationship with project performance, (2) When tested on the sample of top 100 projects, average degree centrality of a project team has a positive and significant effects on project performance, and (3) the effects of network metrics on some of the indicators of project performance are positive in the top 100 projects and some of them are negative in random 100 projects. We employ some control variables such as number of projects each developer works on and organizational sponsorship to provide insights into the direction of the effect of degree centrality and structural holes on project success. Theoretical and practical implications are discussed, and several future research directions will be outlined.