Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Analysis of the Rhodobacter sphaeroides PpsR Regulon: PpsR as a Master Regulator of Photosystem Development

ABSTRACT PpsR from the anoxygenic phototrophic bacterium Rhodobacter sphaeroides has been known as an oxygen- and light-dependent repressor of bacteriochlorophyll and carotenoid biosynthesis genes and puc operons involved in photosystem development. However, the putative PpsR-binding sites, TGTN12ACA, are also located upstream of numerous nonphotosystem genes, thus raising the possibility that the role of PpsR is broader. To characterize the PpsR regulon, transcriptome profiling was performed on the wild-type strain grown at high and low oxygen tensions, on the strain overproducing PpsR, and on the ppsR mutant. Transcriptome analysis showed that PpsR primarily regulates photosystem genes; the consensus PpsR binding sequence is TGTcN10gACA (lowercase letters indicate lesser conservation); the presence of two binding sites is required for repression in vivo. These findings explain why numerous single TGTN12ACA sequences are nonfunctional. In addition to photosystem genes, the hemC and hemE genes involved in the early steps of tetrapyrrole biosynthesis were identified as new direct targets of PpsR repression. Unexpectedly, PpsR was found to indirectly repress the puf and puhA operons encoding photosystem core proteins. The upstream regions of these operons contain no PpsR binding sites. Involvement in regulation of these operons suggests that PpsR functions as a master regulator of photosystem development. Upregulation of the puf and puhA operons that resulted from ppsR inactivation was sufficient to restore the ability to grow phototrophically to the prrA mutant. PrrA, the global redox-dependent activator, was previously considered indispensable for phototrophic growth. It is revealed that the PrrBA and AppA-PpsR systems, believed to work independently, in fact interact and coordinately regulate photosystem development.
Ruthenium Tetroxide and Perruthenate Chemistry. Recent Advances and Related Transformations Mediated by Other Transition Metal Oxo-species

In the last years ruthenium tetroxide is increasingly being used in organic synthesis. Thanks to the fine tuning of the reaction conditions, including pH control of the medium and the use of a wider range of co-oxidants, this species has proven to be a reagent able to catalyse useful synthetic transformations which are either a valuable alternative to established methods or even, in some cases, the method of choice. Protocols for oxidation of hydrocarbons, oxidative cleavage of C–C double bonds, even stopping the process at the aldehyde stage, oxidative cleavage of terminal and internal alkynes, oxidation of alcohols to carboxylic acids, dihydroxylation of alkenes, oxidative degradation of phenyl and other heteroaromatic nuclei, oxidative cyclization of dienes, have now reached a good level of improvement and are more and more included into complex synthetic sequences. The perruthenate ion is a ruthenium (VII) oxo-species. Since its introduction in the mid-eighties, tetrapropylammonium perruthenate (TPAP) has reached a great popularity among organic chemists and it is mostly employed in catalytic amounts in conjunction with N-methylmorpholine N-oxide (NMO) for the mild oxidation of primary and secondary alcohols to carbonyl compounds. Its use in the oxidation of other functionalities is known and recently, its utility in new synthetic transformations has been demonstrated. New processes, synthetic applications, theoretical studies and unusual transformations, published in the last eight years (2006–2013), in the chemistry of these two oxo-species, will be covered in this review with the aim of offering a clear picture of their reactivity. When appropriate, related oxidative transformations mediated by other metal oxo-species will be presented to highlight similarities and differences. An historical overview of some aspects of the ruthenium tetroxide chemistry will be presented as well.
Patterns and Drivers of Inner City Social Differentiation in Prague and Tallinn

During the socialist era, inner residential areas of Eastern European cities were left to decay both physically and socially, and became mostly occupied by elderly inhabitants. Drawing on 2007-2011 EU-SILC data, we have analysed processes of socio-spatial differentiation in the inner cities of Prague and Tallinn during the post-socialist era, and indicate the household-level drivers of such differentiation. We found a high preference for inner city living among young people and childless households, but also the persisting patterns of elderly population in some inner city sub-areas. A weak correlation between household socio-economic status and place of residence in the inner city, however, suggests that inner cities continued to be socially mixed in the late 2000s, although differences existed in this regard between sub-areas and between the two studied cities. To a large extent, such differentiation relates to the roots found within socialist and pre-socialist legacies, but it also contains new post-socialist features, such as those created by different social and housing policies applied during the post-socialist reforms.
An unusual red‐edge excitation and time‐dependent Stokes shift in the single tryptophan mutant protein DD‐carboxypeptidase from Streptomyces: The role of dynamics and tryptophan rotamers

The fluorescence emission of the single tryptophan (W233) of the mutant protein DD‐carboxypeptidase from streptomyces is characterized by a red‐edge excitation shift (REES), i.e., the phenomenon that the wavelength of maximum emission depends on the excitation wavelength. This phenomenon is an indication for a strongly reduced dynamic environment of the single tryptophan, which has a very low accessibility to the solvent. The REES shows, however, an unusual temperature and time dependence. This, together with the fluorescence lifetime analysis, showing three resolvable lifetimes, can be explained by the presence of three rotameric states that can be identified using the Dead‐End Elimination method. The three individual lifetimes increase with increasing emission wavelength, indicating the presence of restricted protein dynamics within the rotameric states. This is confirmed by time‐resolved anisotropy measurements that show dynamics within the rotamers but not among the rotamers. The global picture is that of a protein with a single buried tryptophan showing strongly restricted dynamics within three distinct rotameric states with different emission spectra and an anisotropic environment.
Reorganization of the Intact Somatosensory Cortex Immediately after Spinal Cord Injury

Sensory deafferentation produces extensive reorganization of the corresponding deafferented cortex. Little is known, however, about the role of the adjacent intact cortex in this reorganization. Here we show that a complete thoracic transection of the spinal cord immediately increases the responses of the intact forepaw cortex to forepaw stimuli (above the level of the lesion) in anesthetized rats. These increased forepaw responses were independent of the global changes in cortical state induced by the spinal cord transection described in our previous work (Aguilar et al., J Neurosci 2010), as the responses increased both when the cortex was in a silent state (down-state) or in an active state (up-state). The increased responses in the intact forepaw cortex correlated with increased responses in the deafferented hindpaw cortex, suggesting that they could represent different points of view of the same immediate state-independent functional reorganization of the primary somatosensory cortex after spinal cord injury. Collectively, the results of the present study and of our previous study suggest that both state-dependent and state-independent mechanisms can jointly contribute to cortical reorganization immediately after spinal cord injury.
The renormalization group and critical phenomena

1. Introduction This paper has three parts. The first part is a simplified presentation of the basic ideas of the renormalization group and the ε expansion applied to critical phenomena , following roughly a summary exposition given in 1972 1. The second part is an account of the history (as I remember it) of work leading up to the papers in I971-1972 on the renormalization group. Finally, some of the developments since 197 1 will be summarized, and an assessment for the future given.
Transverse Patterning and Human Amnesia

The transverse patterning (TP) task (A B, B C, C A) has played a central role in testing the hypothesis that medial-temporal (and, in particular, hippocampal) brain damage selectively impairs learning on at least some classes of configural (i.e., nonlinear) learning tasks. Results in the animal and human literature generally support that hypothesis. Reed and Squire [Impaired transverse patterning in human amnesia is a special case of impaired memory for two-choice discrimination tasks. Behavioral Neuroscience, 113, 39, 1999], however, advanced an alternative account in which impaired TP performance in amnesia reflects a generic scaling artifact arising from the greater difficulty of the TP task compared to the elemental (i.e., linear) control task that is typically used. We begin with a critique of Reed and Squire, countering their conceptual arguments and showing that their results, when analyzed appropriately, support the configural deficit hypothesis. We then report results from eight new amnesic patients and controls on an improved version of the TP task. Despite substantial practice, accuracy of patients with bilateral hippocampal damage due to anoxia reached and maintained an asymptote of only 54% correct, well below the maximum accuracy obtainable (67%) in the absence of configural learning. A patient with selective bilateral damage to the anterior thalamic nuclei exhibited a TP accuracy asymptote that was near 67%, a pattern of two out of three correct consecutive trials, and a pattern of nearly always answering correctly for two of the three TP item pairs. These results are consistent with a set of unique and parameter-free predictions of the configural deficit hypothesis.
Flexible Conjugate Gradients

We analyze the conjugate gradient (CG) method with preconditioning slightly variable from one iteration to the next. To maintain the optimal convergence properties, we consider a variant proposed by Axelsson that performs an explicit orthogonalization of the search directions vectors. For this method, which we refer to as flexible CG, we develop a theoretical analysis that shows that the convergence rate is essentially independent of the variations in the preconditioner as long as the latter are kept sufficiently small. We further discuss the real convergence rate on the basis of some heuristic arguments supported by numerical experiments. Depending on the eigenvalue distribution corresponding to the fixed reference preconditioner, several situations have to be distinguished. In some cases, the convergence is as fast with truncated versions of the algorithm or even with the standard CG method, whereas quite large variations are allowed without too much penalty. In other cases, the flexible variant effectively outperforms the standard method, while the need for truncation limits the size of the variations that can be reasonably allowed.
Morphology and biomechanics of the microfibrillar network of sea cucumber dermis

The principal component of the body wall of the sea cucumber Cucumaria frondosa is a dermis consisting of collagen fibrils, microfibrils, proteoglycans and other soluble and insoluble components. A major structural constituent of the dermis is a network of 10­14 nm diameter microfibrils, which surrounds and penetrates bundles of collagen fibrils. This network has been extracted and purified using guanidine and bacterial collagenase. Tensile testing of the microfibrillar network in artificial sea water demonstrates that it is reversibly extensible up to approximately 300 % of its initial length. It behaves like a viscoelastic solid, having a long-range elastic component as well as a time-dependent viscous component. Reduction and alkylation of the cysteine residues in the network do not change its breaking strain or strength, but greatly increase the compliance of the network until, near the breaking strain, the tensile resistance rapidly increases. These data suggest that the strength of the network is due to non-reducible crosslinks, while its elasticity is dependent upon disulfide bonds. In deionized water, the network becomes swollen and, although it remains elastic, is much more compliant than when tested in artificial sea water. Examination of whole tissues and purified networks with the electron microscope reveals structures similar to vertebrate fibrillin-containing microfibrils. Considering that the dermis of C. frondosa is a mechanically mutable tissue in which elongation is accompanied by the sliding of collagen fibrils past one another, the microfibrillar network may act to maintain the orientation of fibrillar components during movement and may also provide a long-range restoring force.
Paleointensity applications to timing and extent of eruptive activity, 9°–10°N East Pacific Rise

Placing accurate age constraints on near‐axis lava flows has become increasingly important given the structural and volcanic complexity of the neovolcanic zone at fast spreading ridges. Geomagnetic paleointensity of submarine basaltic glass (SBG) holds promise for placing quantitative age constraints on near‐axis flows. In one of the first extensive tests of paleointensity as a dating tool or temporal marker we present the results of over 550 successful SBG paleointensity estimates from 189 near‐axis (<4 km) sites at the East Pacific Rise, 9°–10°N. Paleointensities range from 6 to 53 μT and spatially correspond to the pattern expected from known temporal variations in the geomagnetic field. Samples within and adjacent to the axial summit trough (AST) have values approximately equal to or slightly higher than the present‐day. Samples out to 1–3 km from the AST have values higher than the present‐day, and samples farther off axis have values lower than the present‐day. The on‐axis samples (<500 m from the AST) provide a test case for using models of paleofield variation for the past few hundred years as an absolute dating technique. Results from samples collected near a well‐documented eruption in 1991–1992 suggest there may be a small negative bias in the paleointensity estimates, limiting resolution of the dating technique. Possible explanations for such a bias include local field anomalies produced by preexisting magnetic terrain; anomalously high magnetic unblocking temperatures, leading to a small cooling rate bias; and/or the possibility of a chemical remanence produced by in situ alteration of samples likely to have complicated thermal histories. Paleointensity remains useful in approximating age differences in young flows, and a clear along‐axis paleointensity contrast near 9°50′N is suggestive of a ∼150–200 year age difference. Paleointensity values of off‐axis samples are generally consistent with rough age interpretations based on side scan data. Furthermore, spatial patterns in the paleointensity suggest extensive off‐axis flow emplacement may occur infrequently, with recurrence intervals of 10–20 kyr. Results of a stochastic model of lava emplacement show that this can be achieved with a single distribution of flows, with flow size linked to time between eruptions.
Social Comparisons and Contributions to Online Communities: A Field Experiment on MovieLens

We explore the use of social comparison theory as a natural mechanism to increase contributions to an online movie recommendation community by investigating the effects of social information on user behavior in an online field experiment. We find that, after receiving behavioral information about the median user's total number of movie ratings, users below the median demonstrate a 530% increase in the number of monthly movie ratings, while those above the median decrease their monthly ratings by 62%. Movements from both ends converge towards the median, indicating conformity towards a newly-established social norm in a community where such a norm had been absent. Furthermore, the social information has a more dramatic effect on those below the median, suggesting an interaction between conformity and competitive preferences. When given outcome information about the average user's net benefit score from the system, consistent with social preference theory, users with net benefit scores above average contribute 94% of the new updates in the database. In both treatments, we find a highly significant Red Queen Effect.
Long‐term follow‐up of patients with NAFLD and elevated liver enzymes

Nonalcoholic fatty liver disease (NAFLD) is the most common cause of elevated liver enzymes in patients of developed countries. We determined the long‐term clinical and histological courses of such patients. In a cohort study, 129 consecutively enrolled patients diagnosed with biopsy‐proven NAFLD were reevaluated. Survival and causes of death were compared with a matched reference population. Living NAFLD patients were offered repeat liver biopsy and clinical and biochemical investigation. Mean follow‐up (SD) was 13.7 (1.3) years. Mortality was not increased in patients with steatosis. Survival of patients with nonalcoholic steatohepatitis (NASH) was reduced (P = .01). These subjects more often died from cardiovascular (P = .04) and liver‐related (P = .04) causes. Seven patients (5.4%) developed end‐stage liver disease, including 3 patients with hepatocellular carcinoma. The absence of periportal fibrosis at baseline had a negative predictive value of 100% in predicting liver‐related complications. At follow‐up, 69 of 88 patients had diabetes or impaired glucose tolerance. Progression of liver fibrosis occurred in 41%. These subjects more often had a weight gain exceeding 5 kg (P = .02), they were more insulin resistant (P = .04), and they exhibited more pronounced hepatic fatty infiltration (P = .03) at follow‐up. In conclusion, NAFLD with elevated liver enzymes is associated with a clinically significant risk of developing end‐stage liver disease. Survival is lower in patients with NASH. Most NAFLD patients will develop diabetes or impaired glucose tolerance in the long term. Progression of liver fibrosis is associated with more pronounced insulin resistance and significant weight gain. (HEPATOLOGY 2006;44:865–873.)
Quantification of protein transcytosis in the human colon carcinoma cell line CaCo‐2

The transepithelial absorption of food‐type proteins has been shown to proceed by endocytosis along two functional pathways: a minor direct pathway allowing transport of intact protein and a major lysosomal degradative pathway. The human colon carcinoma cell line CaCo‐2 grown on Millipore filters was used here further to characterize these pathways by measuring HRP transport across the cell monolayer in Ussing chambers. In the apical‐basal direction, this transport mainly occurred along the degradative pathway and was inhibited at 4°C (7.41 ± 1.26 pmoles/h·cm2 vs. 27.40 ± 8.91 at 37°C). The amount conveyed via the direct pathway was very small (0.89 ± 0.35 pmoles/h·cm2) and did not diminish at 4°C (1.43 ± 0.59 pmoles/h·cm2). In the basal‐apical direction, HRP transport along the degradative pathway at 37°C was similar to the apical‐basal value and was inhibited at 4°C (16.40 ± 4.50 vs. 2.72 ± 2.52 pmoles/h·cm2), but along the direct pathway, it was eight times the apical‐basal value (8.36 ± 3.11 pmoles/h·cm2) and was inhibited at 4°C (2.43 ± 0.78 pmoles/h·cm2). Intact HRP fluxes were not correlated with the eletrical resistance of the filters, indicating transport via a transcellular route. Monensin at 10−5 M did not affect direct or degradative transport in the apical‐to‐basal direction. These results suggest that in CaCo‐2 cells HRP undergoes bidirectional transcytosis by a fluid‐phase mechanism, but the extent of degradation during that transport varies according to the membrane (apical or basal) where it is presented.
Characteristics of teams, staff and patients: associations with outcomes of patients in assertive outreach

Background Little is known about what characteristics of teams, staff and patients are associated with a favourable outcome of severe mental illness managed by assertive outreach. Aims To identify predictors of voluntary and compulsory admissions in routine assertive outreach services in the UK. Method Nine features of team organisation and policy, five variables assessing staff satisfaction and burn-out and eleven patient characteristics taken from the baseline data of the Pan-London Assertive Outreach Study were tested as predictors of voluntary and compulsory admissions within a 9-month follow-up period. Results Weekend working, staff burn-out and lack of contact of the patient with other services were associated independently with a higher probability of both voluntary and compulsory admission. In addition, admissions in the past predicted further voluntary and compulsory admissions, and teams not working extended hours predicted compulsory admissions in the follow-up period. Conclusions Characteristics of team working practice, staff burn-out and patients' history are associated independently with outcome. Patient contact with other services is a positive prognostic factor.
In-Class Cycling to Augment College Student Academic Performance and Reduce Physical Inactivity: Results from an RCT

Most college students sit 14 hours per week on average, excluding sedentary study time. Researchers observing workplace and elementary school settings with active workstations to combat sedentary behavior have shown enhanced cognition without distraction. Until now, incorporating active workstations in college classroom settings remained relatively unexplored. This study’s purpose was to assess academic performance using in-class stationary cycle desks during a semester-long lecture course. Twenty-one college students (19–24 years) enrolled in a lecture course volunteered and were split into traditional sit (SIT) and stationary cycle (CYC) groups randomly, matched on a calculated factor equal to a physical activity (PA) score (0–680) multiplied by grade point average (GPA; 4.0 scale). CYC pedaled a prescribed rate of perceived exertion (RPE) of less than 2 out of 10 during a 50-min lecture, 3 × week for 12 weeks. CYC averaged 42 min, 7.9 miles, and 1.7 RPE during class throughout the semester. No significant differences (p > 0.05) were observed between CYC and SIT on in-class test scores or overall course grades. Although statistically insignificant, CYC had higher mean test scores and overall course grades vs. SIT (i.e., B+ vs. B, respectively). Low intensity cycling during a college lecture course maintained student academic performance and possibly reduced weekly sedentary behavior time.