Miracle-dz/UniFAR-FTUs huggingface dataset:
Amino terminus of outer membrane PhoE protein: localization by use of a bla-phoE hybrid gene

Expression of a recently constructed bla-phoE hybrid gene results in synthesis and incorporation into the outer membrane of PhoE protein containing an amino-terminal extension of 158 amino acid residues of beta-lactamase (Tommassen et al., EMBO J. 2:1275-1279, 1983). As the PhoE protein part of this hybrid protein is apparently normally incorporated into the outer membrane, the beta-lactamase part of the protein can be considered as a label of the amino terminus of PhoE protein. By using trypsin accessibility experiments, this beta-lactamase part was shown to be located at the periplasmic side of the membrane. Therefore, the amino terminus of PhoE protein most likely faces the periplasm.
Stripped gas as fuel for newly formed H ii regions in the encounter between VCC 1249 and M 49: a unified picture from NGVS and GUViCS

Context. We study the peculiar interacting galaxy system of VCC 1249/M 49 located in the core of the Virgo B subcluster. Owing to a recent interaction between the dwarf galaxy VCC 1249 and the halo gas of the elliptical galaxy M 49, neutral hydrogen has been displaced from the interstellar medium of this dwarf into the Virgo intracluster medium. Observations also reveal multiple compact star-forming regions (aka H II regions) that are embedded in this H I cloud, with a projected separation up to 13 kpc from VCC 1249 in the northwest direction. Aims. Motivated by recent near-ultraviolet imaging from the GALEX Ultraviolet Virgo Cluster Survey (GUViCS) of the VCC 1249/M 49 system that shows significant ongoing/recent star formation in the compact regions, we aim to constrain the origin of these outlying H II regions with a multi-wavelength approach. Methods. Using deep optical (u,g,i,z) imaging from the Next Generation Virgo Cluster Survey (NGVS) and new Hα imaging obtained at the San Pedro Martir observatory together with Keck long-slit spectroscopy, we characterize the star formation rates, ages, and metallicity of VCC 1249 and its outlying compact regions. Moreover, we analyze the color and luminosity profile of the galaxy to investigate its recent interaction with M 49. Results. Our new observations indicate that VCC 1249 underwent a recent interaction with M 49 in which both ram-pressure stripping and tidal interaction occured. The joint action of the two mechanisms led to the removal of the H I gas from the interstellar medium of VCC 1249, while the gravitational tides triggered the stellar tail and counter-tail of VCC 1249. Our stellar population synthesis analysis reveals that the star formation in this galaxy was truncated around 200 Myr ago and that the outlying H II regions were born in situ ≈10 Myr ago out of pre-enriched gas removed from the dwarf galaxy. These observations also reveal that interactions between central and satellite galaxies similar to those between VCC 1249/M 49 may be an effective way of dispersing metals into the halos of massive galaxies.
Nonstatistical 13C Distribution during Carbon Transfer from Glucose to Ethanol during Fermentation Is Determined by the Catabolic Pathway Exploited*

Background: Different fermentation pathways should lead to distinctive isotope patterns in the products. Results: Three pathways for glucose catabolism show discrete isotope patterns in ethanol. Conclusion: Catabolism by different enzyme sequences leads to differential isotope redistribution patterns. Significance: Learning how isotope fractionation occurs in nature is crucial for interpreting fractionation during biochemical and physical processes for traceability. During the anaerobic fermentation of glucose to ethanol, the three micro-organisms Saccharomyces cerevisiae, Zymomonas mobilis, and Leuconostoc mesenteroides exploit, respectively, the Embden-Meyerhof-Parnas, the Entner-Doudoroff, and the reductive pentose phosphate pathways. Thus, the atoms incorporated into ethanol do not have the same affiliation to the atomic positions in glucose. The isotopic fractionation occurring in each pathway at both the methylene and methyl positions of ethanol has been investigated by isotopic quantitative 13C NMR spectrometry with the aim of observing whether an isotope redistribution characteristic of the enzymes active in each pathway can be measured. First, it is found that each pathway has a unique isotope redistribution signature. Second, for the methylene group, a significant apparent kinetic isotope effect is only found in the reductive pentose phosphate pathway. Third, the apparent kinetic isotope effects related to the methyl group are more pronounced than for the methylene group. These findings can (i) be related to known kinetic isotope effects of some of the enzymes concerned and (ii) give indicators as to which steps in the pathways are likely to be influencing the final isotopic composition in the ethanol.
Honor and harmed social-image. Muslims’ anger and shame about the cartoon controversy

ABSTRACT Two studies examined anger and shame, and their associated appraisals and behavioral intentions, in response to harm to an in-group's social-image. In Study 1, 37 British Muslims (18 men, 19 women) reported incidents in which they were devalued as Muslims. In Study 2, 108 British Muslims (57 females, 50 males, 1 undisclosed) were presented with objective evidence of their in-group's devaluation: the controversial cartoons about Prophet Muhammad The appraisal of harm to social-image predicted anger and shame (Studies 1 and 2), whereas the appraisal of offense only predicted anger (Study 2). Anger was a more empowering response than shame, as anger predicted willingness for public confrontation (Studies 1 & 2), institutional punishment (Study 2), and written disapproval (Study 2). In contrast, shame only predicted written disapproval (Study 2). Furthermore, independent of individual differences in identification as Muslim, a mediation model showed that individual differences in honor orientation predicted anger and shame via the appraisals (Study 2). Implications for theory and research are discussed.
Sugar-induced plant growth is dependent on brassinosteroids

Sugars, the end products of photosynthesis, not only fuel growth and development of plants as carbon and energy sources, but also function as signaling molecules to modulate a range of important processes during plant growth and development. We recently found that sugar can promote hypocotyl elongation in Arabidopsis in darkness and this is largely dependent on brassinosteroids (BRs), a group of essential phytohormones involved in mediation of plant cell elongation. Sugars not only positively regulate the transcription of BZR1, the gene encoding the BR-activated transcription factor BRASSINAZOLE RESISTANT1 (BRZ1), but also stabilize the BZR1 protein. Based on these results, we proposed that BZR1 may act as a converging node for crosstalk between BR and sugar signaling in regulating plant growth in darkness. In this short communication, we present some new data showing that HEXOKINASE1 (HXK1), the first identified glucose (Glc) sensor in plants, was positively involved in Glc promotion of hypocotyl elongation in Arabidopsis in the dark. It appears that the function of HXK1 is dependent on the presence of BR, suggesting that BR may act downstream of HXK1 to positively regulate Glc-induced hypocotyl elongation in Arabidopsis in darkness.
Abdominal aortic aneurysm: a 6-year comparison of endovascular versus transabdominal repair.

OBJECTIVE To test the hypothesis that endovascular repair of abdominal aortic aneurysm (AAA) will result in a significant reduction in mortality and morbidity rates and cost when compared with open transabdominal repair. SUMMARY BACKGROUND DATA Since the introduction of endovascular repair of AAA this decade, multiple groups have evaluated different endovascular grafts. Despite the excellent results reported initially, there has been a paucity of well-controlled, comparative studies looking at long-term outcome. METHODS From 1992 to 1998, the first 100 consecutive patients undergoing endovascular AAA repair (mean age 74.7, AAA size 5.6 cm) were compared to 100 patients undergoing transabdominal repair (mean age 72.9, AAA size 5.9 cm). All patients undergoing endovascular repair received a device manufactured by Endovascular Technologies, Inc. (Menlo Park, CA) and were prospectively followed with periodic examination, contrast-enhanced computed tomography, and duplex scanning. Of the 200 patients, 198 have been available for long-term follow-up. RESULTS The two groups had similar preoperative risk factors. Surgical time (211 vs. 256 minutes, p < 0.005), blood loss (326 vs. 1010 ml, p < 0.005), and blood replacement (0.4 vs. 1.6 units, p < 0.005) were all decreased in the endovascular group. Median intensive care unit stay (0 vs. 2 days) and hospital stay (2 vs. 7 days) were significantly reduced in the endovascular group. Insignificant trends in lower morbidity rates (myocardial infarction 1 % vs. 5%, respiratory failure 1 % vs. 5%, colon ischemia 0% vs. 2%) were present in patients undergoing endovascular repair. This led to decreased hospital cost and increased hospital profit. The surgical mortality rate (2% vs. 3%) and 5-year survival rate (65% vs. 72%) have been equivalent between the two groups. CONCLUSIONS The surgical mortality rate is low for both groups and not statistically different. Endovascular repair significantly reduces resource utilization (surgical time, blood replacement, intensive care unit and hospital stay) and cost when compared to transabdominal aneurysm repair. Long-term survival is equivalent in patients undergoing AAA repair regardless of technique. Although endovascular repair appears durable for up to 6 years, longer follow-up studies are warranted.
Increasingly Sensitive Assays for Cardiac Troponins: A Review

Cardiac troponins are the preferred biomarkers for diagnosis of myocardial infarction because of their high sensitivity and specificity for myocardial injury. However, acute and chronic conditions distinct from acute coronary syndromes (ACS) commonly lead to small elevations in troponin levels, with few data available regarding management of care for patients with such conditions. Recently developed highly sensitive troponin assays will likely lead to a substantial increase in the proportion of detectable troponin levels attributable to non-ACS conditions. Novel algorithms with highly sensitive assays, incorporating baseline troponin values and changes in values over 1 to 2 hours, may allow rapid exclusion of myocardial infarction and help to address specificity concerns but must be validated in appropriate target populations. Enhanced detection of very low troponin levels with highly sensitive assays has made feasible several potential new indications for troponin testing, including in the ambulatory setting, where assessment for low-level chronic myocardial injury may enhance risk stratification for heart failure and cardiac death.
Designing modular robotic playware

In this paper, we explore the design of modular robotic objects that may enhance playful experiences. The approach builds upon the development of modular robotics to create a kind of playware, which is flexible in both set-up and activity building for the end-user to allow easy creation of games. Key features of this design approach are modularity, flexibility, and construction, immediate feedback to stimulate engagement, activity design by end-users, and creative exploration of play activities. These features permit the use of such modular playware by a vast array of users, including disabled children who often could be prevented from using and taking benefits from modern technologies. The objective is to get any children moving, exchanging, experimenting and having fun, regardless of their cognitive or physical ability levels. The paper describes two prototype systems developed as modular robotic tiles, and discusses the challenges and opportunities of this modular playware when used by children with different cognitive abilities.
Epstein-Barr virus EBNA3C represses Cp, the major promoter for EBNA expression, but has no effect on the promoter of the cell gene CD21

EBNA3C is a potent repressor of transcription when bound to DNA as a fusion with the DNA binding domain (DBD) of GALA. A survey of promoters has revealed that the wild-type, unfused EBNA3C can specifically repress expression from reporter plasmids containing the Epstein-Barr virus Cp latency-associated promoter. Repression of Cp activity required amino acids 207 to 368, which encompasses a region resembling a basic DBD adjacent to a leucine zipper DNA binding motif and a site which binds to the cellular factor CBF1/RBP-Jkappa. However, amino acids 207 to 368 are dispensable when the protein is bound to DNA as a fusion with the GAL4 DBD, thus implicating this region in DNA binding. Mutation of the CBF1/RBP-Jkappa binding site in EBNA3C abrogated repression, strongly suggesting that CBF1/RBP-Jkappa is necessary for targeting the viral protein to Cp. Consistent with this result, mutation of the EBNA2 response element (a CBF1/RBP-Jkappa binding site) in Cp also prevented significant repression. In addition, amino acids 346 to 543, which were previously defined as important for the repressor activity of the GAL4-EBNA3C fusion proteins, also appear to be necessary for the repression of Cp. Since repression by these fusions was not observed in all cell types, it seems likely that EBNA3C either depends on a corepressor which may interact with amino acids 346 to 543 or is modified in a cell-specific manner in order to repress. These data are consistent with EBNA3C contributing to the regulation of EBNA expression in latently infected B cells through CBF1/RBP-Jkappa and another factor, but this need not directly involve EBNA2. Finally, although it has been reported that EBNA3C can upregulate CD21 in some B cells, we were unable to demonstrate any effect of EBNA3C on reporter plasmids which contain the CD21 promoter.
Making greed work in networks: a game-theoretic analysis of switch service disciplines

This paper discusses congestion control from a game-theoretic perspective. There are two basic premises: 1) Users are assumed to be independent and selfish. 2) Central administrative control is exercised only at the network switches. The operating points resulting from selfish user behavior depend crucially on the service disciplines implemented in network switches. This effect is investigated in a simple model consisting of a single exponential server shared by many Poisson sources. We discuss the extent to which one can guarantee, through the choice of switch service disciplines, that these selfish operating points will be efficient and fair. We also discuss to what extent the choice of switch service disciplines can ensure that these selfish operating points are unique and are easily and rapidly accessible by simple self optimization techniques. We show that no service discipline can guarantee optimal efficiency. As for the other properties, we show that the traditional FIFO service discipline guarantees none of these properties, but that a service discipline called fair share guarantees all of them. While the treatment utilizes game-theoretic concepts, no previous knowledge of game theory is assumed.
Structure–function analysis of the filamentous actin binding domain of the neuronal scaffolding protein spinophilin

Spinophilin, a neuronal scaffolding protein, is essential for synaptic transmission, and functions to target protein phosphatase‐1 to distinct subcellular locations in dendritic spines. It is vital for the regulation of dendritic spine formation and motility, and functions by regulating glutamatergic receptors and binding to filamentous actin. To investigate its role in regulating actin cytoskeletal structure, we initiated structural studies of the actin binding domain of spinophilin. We demonstrate that the spinophilin actin binding domain is intrinsically unstructured, and that, with increasing C‐terminal length, the domain shows augmented secondary structure content. Further characterization confirmed the previously known crosslinking activity and uncovered a novel filamentous actin pointed‐end capping activity. Both of these functions seem to be fully contained within residues 1–154 of spinophilin.
Protease Imaging of Human Atheromata Captures Molecular Information of Atherosclerosis, Complementing Anatomic Imaging

Objective—There is hope that molecular imaging can identify vulnerable atherosclerotic plaques. However, there is a paucity of clinical translational data to guide the future development of this field. Here, we cross-correlate cathepsin-B or matrix metalloproteinase-2/-9 molecular optical imaging data of human atheromata or emboli with conventional imaging data, clinical data, and histopathologic data. Methods and Results—Fifty-two patients undergoing carotid endarterectomy (41 atheromata) or carotid stenting (15 captured emboli) were studied with protease-activatable imaging probes. We show that protease-related fluorescent signal in carotid atheromata or in emboli closely reflects the pathophysiologic alterations of plaque inflammation and statin-mediated therapeutic effects on plaque inflammation. Inflammation-related fluorescent signal was observed in the carotid bifurcation area and around ulcero-hemorrhagic lesions. Pathologically proven unstable plaques had high cathepsin-B–related fluorescent signal. The distribution patterns of the mean cathepsin-B imaging signals showed a difference between the symptomatic vs asymptomatic plaque groups. However, the degree of carotid stenosis or ultrasonographic echodensity was weakly correlated with the inflammatory proteolytic enzyme-related signal, suggesting that molecular imaging yields complimentary new information not available to conventional imaging. Conclusion—These results could justify and facilitate clinical trials to evaluate the use of protease-sensing molecular optical imaging in human atherosclerosis patients.
Dephasing of interference in Landau-Zener transitions.

We study the effect of dephasing on the Landau-Zener transition. Our approach is based on the interpretation of the transition as an interference process. We derive a phase-uncertainty factor for a general coupling to an environment, and demonstrate the enhancement of the asymptotic transition probability due to this phase uncertainty. We discuss the dependence of this enhancement on the properties of a specific environment at hand, the form of the coupling term, and the coupling strength. Given a certain type of coupling to the environment, we find the characteristic dephasing time (τ O ) corresponding to the crossover from weak to strong dephasing
High Potential for Methodical Improvements of Fish-Based Translocation Analysis for Retrospective Radiation Biodosimetry

Abstract Due to their high stability and accumulation over time, translocations are currently the cytogenetic marker of choice for radiation dose estimation following protracted radiation overexposures or overexposures that occurred up to several decades in the past (environmental/occupational/medical exposures). In the course of this, particular intention is focused on the quantification of low doses (≪ 1.0 Gy) for the purpose of evaluating potential associations between different radiation-induced chromosomal aberrations and future health impairments, usually cancer. However, existing limitations of FISH-based translocation analysis give occasion to further optimize this method. In particular, the practical and technical aspects of the method offer a great scope for potential improvements considerably facilitating the performance of extensive studies. On the one hand, huge studies encompassing a considerable number of different collectives aiming at the determination of spontaneous translocation frequencies due to several already determined and potentially not yet known confounders are essential for improved individual dosimetry in the very low dose range. An accurate and reliable individual dosimetry and the methodical feasibility of extensive FISH-based studies are prerequisites to further elucidate the characteristics of radiation induced cancer; e.g., radiation and radiation quality specificity or total dose and dose rate dependencies. This paper focuses on the practical and technical limitations of FISH-based translocation analysis, in fact the tremendous workload and costs of huge approaches, and points out how this could be overcome by method optimization, namely standardizing and automating translocation scoring to allow sharing of future work and planning of more extensive studies. Health Phys. 103(2):127Y132; 2012
Glycaemic index, breast and colorectal cancer.

Glycaemic index (GI) is an extension of the fibre hypothesis [1] and a ranking of carbohydrates based on their postprandial blood glucose response [2]. The basic concept is that a higher rate of carbohydrate absorption leads to higher blood glucose and insulin rise, and hence a higher GI index. GI has been linked to non-insulin-dependent diabetes mellitus [3, 4], coronary heart disease, and also to excess risk of colorectal [5] and breast [6] cancer. Refined cereal intake has also been related to elevated risk of oral, oesophageal and laryngeal [7], and other digestive tract neoplasms [8]. The possible link is related to mutagenic and perhaps promotional effects of insulin and insulin-like growth factor (IGF) on the process of carcinogenesis [9–11]. Available data on GI and cancer risk are, however, extremely scanty. A multicentre case–control study from Italy found an odds ratio (OR) of 1.7 for colorectal cancer [5] and 1.4 for breast cancer [6] in the highest GI quintile, with significant trends in risk. To provide further information on the issue, we considered data from two case–control studies on colorectal and breast cancer conducted between 1992 and 2001 in the Swiss Canton of Vaud [12, 13]. Cases were 323 patients (192 males, 131 females) with incident, histologically confirmed colon (n = 169) or rectal (n = 154) cancer (median age 65 years), and 331 women with breast cancer (median age 58 years) admitted to the University Hospital of Lausanne, Switzerland. Controls were 1145 subjects (330 males, 815 females) aged <75 years (median age 59 years) residing in the same geographical area and admitted to the same hospital as cases for acute, non-neoplastic diseases (33% traumas, 31% nontraumatic orthopaedic conditions, 19% surgical conditions and 17% miscellaneous other disorders). Sixteen percent of subjects (17% of cases, 15% of controls) who were approached for interview refused. The structured questionnaire included information on socio-demographic characteristics and lifestyle habits, and menstrual and hormonal factors for women. A food-frequency questionnaire (FFQ) was used to assess subjects’ habitual diet, including information on weekly frequency of consumption of specific foods, as well as complex recipes (79 items) during the 2 years prior to cancer diagnosis or hospital admission (for controls). GI was expressed as a percentage of the glycaemic response elicited using white bread as a standard food. For each subject, average daily GI was calculated by summing the products of the carbohydrate content per serving, for each food or recipe, times the average number of servings per week, times its GI, all divided by the total amount of available weekly carbohydrate intake. A score of the daily average glycaemic load (GL) was computed as the GI, but without dividing by the total amount of carbohydrates [14, 15]. ORs and the corresponding 95% confidence intervals (CI) were computed by tertile (of the control distribution) of daily GI and GL score, using