Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical Disclosure of the Mycolate Outer Membrane of Corynebacterium glutamicum

ABSTRACT Corynebacterineae is a specific suborder of Gram-positive bacteria that includes Mycobacterium tuberculosis and Corynebacterium glutamicum. The cell wall of these bacteria is composed of a heteropolymer of peptidoglycan (PG) linked to arabinogalactan (AG), which in turn is covalently associated with an atypical outer membrane, here called mycomembrane (M). The latter structure has been visualized by cryo-electron microscopy of vitreous sections, but its biochemical composition is still poorly defined, thereby hampering the elucidation of its physiological function. In this report, we show for the first time that the mycomembrane-linked heteropolymer of PG and AG (M-AG-PG) of C. glutamicum can be physically separated from the inner membrane on a flotation density gradient. Analysis of purified M-AG-PG showed that the lipids that composed the mycomembrane consisted almost exclusively of mycolic acid derivatives, with only a tiny amount, if any, of phospholipids and lipomannans, which were found with the characteristic lipoarabinomannans in the plasma membrane. Proteins associated with or inserted in the mycomembrane were extracted from M-AG-PG with lauryl-dimethylamine-oxide (LDAO), loaded on an SDS-PAGE gel, and analyzed by tandem mass spectrometry or by Western blotting. Sixty-eight different proteins were identified, 19 of which were also found in mycomembrane fragments released by the terminal-arabinosyl-transferase-defective ΔAftB strain. Almost all of them are predicted to contain a signal sequence and to adopt the characteristic β-barrel structure of Gram-negative outer membrane proteins. These presumed mycomembrane proteins include the already-known pore-forming proteins (PorA and PorB), 5 mycoloyltransferases (cMytA, cMytB, cMytC, cMytD, and cMytF), several lipoproteins, and unknown proteins typified by a putative C-terminal hydrophobic anchor.
Identity of the Growth-Limiting Nutrient Strongly Affects Storage Carbohydrate Accumulation in Anaerobic Chemostat Cultures of Saccharomyces cerevisiae

ABSTRACT Accumulation of glycogen and trehalose in nutrient-limited cultures of Saccharomyces cerevisiae is negatively correlated with the specific growth rate. Additionally, glucose-excess conditions (i.e., growth limitation by nutrients other than glucose) are often implicated in high-level accumulation of these storage carbohydrates. The present study investigates how the identity of the growth-limiting nutrient affects accumulation of storage carbohydrates in cultures grown at a fixed specific growth rate. In anaerobic chemostat cultures (dilution rate, 0.10 h−1) of S. cerevisiae, the identity of the growth-limiting nutrient (glucose, ammonia, sulfate, phosphate, or zinc) strongly affected storage carbohydrate accumulation. The glycogen contents of the biomass from glucose- and ammonia-limited cultures were 10- to 14-fold higher than those of the biomass from cultures grown under the other three glucose-excess regimens. Trehalose levels were specifically higher under nitrogen-limited conditions. These results demonstrate that storage carbohydrate accumulation in nutrient-limited cultures of S. cerevisiae is not a generic response to excess glucose but instead is strongly dependent on the identity of the growth-limiting nutrient. While transcriptome analysis of wild-type and msn2Δ msn4Δ strains confirmed that transcriptional upregulation of glycogen and trehalose biosynthesis genes is mediated by Msn2p/Msn4p, transcriptional regulation could not quantitatively account for the drastic changes in storage carbohydrate accumulation. The results of assays of glycogen synthase and glycogen phosphorylase activities supported involvement of posttranscriptional regulation. Consistent with the high glycogen levels in ammonia-limited cultures, the ratio of glycogen synthase to glycogen phosphorylase in these cultures was up to eightfold higher than the ratio in the other glucose-excess cultures.
Topic Model Stability for Hierarchical Summarization

We envisioned responsive generic hierarchical text summarization with summaries organized by section and paragraph based on hierarchical structure topic models. But we had to be sure that topic models were stable for the sampled corpora. To that end we developed a methodology for aligning multiple hierarchical structure topic models run over the same corpus under similar conditions, calculating a representative centroid model, and reporting stability of the centroid model. We ran stability experiments for standard corpora and a development corpus of Global Warming articles. We found flat and hierarchical structures of two levels plus the root offer stable centroid models, but hierarchical structures of three levels plus the root didn’t seem stable enough for use in hierarchical summarization.
Possibility of prenatal diagnosis of hereditary triose phosphate isomerase deficiency

Prenatal diagnosis has been performed on umbilical cord blood of an 18 weeks fetus of heterozygous triosephosphate isomerase (TPI) deficient parents. After excluding maternal blood contamination, TPI activity was measured and found to be 60 per cent of the normal mean whereas the value of glucose‐6‐phosphate dehydrogenase activity was in the normal range of fetal blood. In addition, the analysis of the characteristics of fetal TPI, i.e. Km measurements for glyceraldehyde‐3‐phosphate, heat stability tests and electrophoretic studies, did not show any evidence of a special form of TPI in fetal blood. These results were consistent with the heterozygous state and were confirmed at birth.
Let's play!: mobile health games for adults

Researchers have designed a variety of systems that promote wellness. However, little work has been done to examine how casual mobile games can help adults learn how to live healthfully. To explore this design space, we created OrderUP! , a game in which players learn how to make healthier meal choices. Through our field study, we found that playing OrderUP! helped participants engage in four processes of change identified by a well-established health behavior theory, the Transtheoretical Model: they improved their understanding of how to eat healthfully and engaged in nutrition-related analytical thinking, reevaluated the healthiness of their real life habits, formed helping relationships by discussing nutrition with others and started replacing unhealthy meals with more nutritious foods. Our research shows the promise of using casual mobile games to encourage adults to live healthier lifestyles.
A Full-duplex WDM Millimeter-Wave-Band Radio-on-Fiber System Using A Supercontinuum Light Source

We demonstrate a full-duplex WDM millimeter-wave-band radio-on-fiber (RoF) system using a supercontinuum (SC) light source. For downlink transmission, the periodic nature of arrayed waveguide grating, where the period is free spectral range, is used for utilizing the full bandwidth of the SC light source. Half of the SC output modes are used for uplink transmission with photonic downconversion. These techniques are effective to use a wealth of optical frequency resources from the SC light source. Two-channel downlink and one-channel uplink 60-GHz band RoF signals were simultaneously transmitted over 25-km standard single-mode fiber with error-free and no noticeable power penalty.
Mutation-driven Test Case Generation Using Short-lived Concurrent Mutants - First Results

In the context of black-box testing, generating test cases through model mutation is known to produce powerful test suites but usually has the drawback of being prohibitively expensive. This paper presents a new version of the tool MoMuT::UML (www.momut.org), which implements a scalable version of mutation-driven test case generation (MDTCG). It is able to handle industrial-sized UML models comprising networks of, e.g., 2800 interacting state machines. To achieve the required scalability, the implemented algorithm exploits the concurrency in MDTCG and combines it with a search based generation strategy. For evaluation, we use seven case studies of different application domains with an increasing level of difficulty, stopping at a model of a railway station in Austria's national rail network.
Changes in career satisfaction among primary care and specialist physicians, 1997-2001.

CONTEXT A number of forces have changed the practice of medicine in the past decade. Evidence suggests that physicians are becoming less satisfied in this environment. OBJECTIVES To describe changes in career satisfaction in a large, nationally representative sample of physicians and to examine market and practice factors associated with changes in physician satisfaction. DESIGN AND SETTING Data were collected from the first 3 rounds of the Community Tracking Study (CTS) Physician Survey, a series of nationally representative telephone surveys of physicians in 60 US sites conducted in 1996-1997 (round 1: 12 385 respondents; 65% response rate), 1998-1999 (round 2: 12 280 respondents; 61% response rate), and 2000-2001 (round 3: 12 389 respondents; 59% response rate) for the Center for Studying Health System Change. The second and third rounds of the survey included physicians sampled in the previous round, as well as new physicians. PARTICIPANTS Primary care and specialist physicians who spent at least 20 hours per week in direct patient care activities. MAIN OUTCOME MEASURES Changes in physicians' overall satisfaction with their career and the proportion of dissatisfied physicians in particular sites. RESULTS Physician satisfaction levels declined marginally between 1997 and 2001, with most of the decline occurring between 1997 and 1999. Among primary care physicians, 42.4% were very satisfied in 1997, as were 43.3% of specialists, compared with 38.5% and 41.4%, respectively, in 2001. There were nearly equal increases in those who reported that they were somewhat satisfied. Overall means mask significant differences across the 60 sites. Among 12 sites randomly selected for more intensive study, the proportion of respondents who were somewhat or very dissatisfied ranged from 8.8% of physicians in Lansing, Mich (1999), to 34.2% in Miami, Fla (1997). Between 1997 and 1999, 25.6% of primary care physicians reported decreased satisfaction and 18.1% reported improved satisfaction, while approximately equal percentages reported increased (19.8%) and decreased (20.4%) satisfaction between 1999-2001. Findings were similar for specialist physicians. In multivariable models, the strongest and most consistent predictors of change in satisfaction were changes in measures of clinical autonomy, including increases in hours worked and physicians' ability to obtain services for their patients. Changes in exposure to managed care were weakly related to changes in satisfaction. CONCLUSIONS Our findings demonstrate that overall physician satisfaction levels over this time period did not change dramatically. In addition, satisfaction and changes in satisfaction vary greatly among sites. Rather than declining income, threats to physicians' autonomy, to their ability to manage their day-to-day patient interactions and their time, and to their ability to provide high-quality care are most strongly associated with changes in satisfaction.
Novel glimepiride derivatives with potential as double-edged swords against type II diabetes

Sulphonylurea drugs have been widely used in the safe and efficacous therapy of type II diabetes during the past five decades. They lower blood glucose predominantly via the stimulation of insulin release from pancreatic β-cells. However, a moderate insulin-independent regulation of fatty acid esterification and release in adipose tissue cells has been reported for certain sulphonylureas, in particular for glimepiride. On basis of the known pleiotropic pathogenesis of type II diabetes with a combination of β-cell failure and peripheral, including adipocyte, insulin resistance, anti-diabetic drugs exerting both insulin releasing- and fatty acid-metabolizing activities in a more balanced and potent fashion may be of advantage. However, the completely different molecular mechanisms underlying the insulin-releasing and fatty acid-metabolizing activities, as have been delineated so far for glimepiride, may hamper their optimization within a single sulphonylurea molecule. By analyzing conventional sulphonylureas and novel glimepiride derivatives for their activities at the primary targets and downstream steps in both β-cells and adipocytes in vitro we demonstrate here that the insulin-releasing and fatty acid-metabolizing activities are critically dependent on both overlapping and independent structural determinants. These were unravelled by the parallel losses of these two activities in a subset of glimepiride derivatives and the impairment in the insulin-releasing activity in parallel with elevation in the fatty acid-metabolizing activity in a different subset. Together these findings may provide a basis for the design of novel sulphonylureas with blood glucose-lowering activity relying on less pronounced stimulation of insulin release from pancreatic β-cells and more pronounced insulin-independent stimulation of esterification as well as inhibition of release of fatty acids by adipocytes than provoked by the sulphonylureas currently used in therapy.
Integrating building information modelling (BIM) into engineering education: an exploratory study of industry perceptions using social network data

An exploratory analysis was conducted by using a qualitative analysis of the data obtained from a popular online social network platform for professionals – LinkedIn. Data in the form of discussion posts and comments associated with BIM in education were captured from a BIM-specific discussion group using NVivo 10 software. To carry out the analysis, discussion posts and comments were coded to identify important themes emerging from the data. These themes were then examined, interpreted and discussed. OUTCOMES The results showed that the themes emerged from the selected discussion posts were concentrated on the recommendations on how BIM can be integrated into a curriculum and the barriers to the integration. The need to teach BIM as a collaborative process rather just a software tool was highlighted, with the difficulty in bridging educational silos identified as one of the main barriers. CONCLUSIONS BIM is an innovative concept that can help improve the efficiency of the AEC industry. To successfully integrate BIM into education, the industry perceived that there is the need for universities to be more innovative in developing a collaborative curriculum that requires integration across different educational disciplines. This represents a major challenge to be overcome not only for engineering education, but also other related disciplines within the AEC context.
An Avatar-Based System for Identifying Individuals Likely to Develop Dementia

This paper presents work on developing an automatic dementia screening test based on patients’ ability to interact and communicate — a highly cognitively demanding process where early signs of dementia can often be detected. Such a test would help general practitioners, with no specialist knowledge, make better diagnostic decisions as current tests lack specificity and sensitivity. We investigate the feasibility of basing the test on conversations between a ‘talking head’ (avatar) and a patient and we present a system for analysing such conversations for signs of dementia in the patient’s speech and language. Previously we proposed a semi-automatic system that transcribed conversations between patients and neurologists and extracted conversation analysis style features in order to differentiate between patients with progressive neurodegenerative dementia (ND) and functional memory disorders (FMD). Determining who talks when in the conversations was performed manually. In this study, we investigate a fully automatic system including speaker diarisation, and the use of additional acoustic and lexical features. Initial results from a pilot study are presented which shows that the avatar conversations can successfully classify ND/FMD with around 91% accuracy, which is in line with previous results for conversations that were led by a neurologist.
A new mathematical framework for optimal choice of actions

Optimal choice of actions is a fundamental problem relevant to (cid:133)elds as diverse as neuroscience, psychology, economics, computer science, control engineering. Despite this broad relevance the abstract setting is similar: we have an agent choosing actions over time, an uncertain dynamical system whose state is a⁄ected by those actions, and a performance criterion which the agent seeks to optimize. Solving problems of this kind remains hard, partly because of overly generic formulations. Here we propose a more structured formulation which greatly simpli(cid:133)es the construction of optimal control laws. An exhaustive search over actions is avoided and the problem is reduced to a linear one: computing a statistical expectation. This gives rise to unique theoretical properties and yields original algorithms that outperform Dynamic Programming and Reinforcement Learning. The new framework makes it possible to reformulate or approximate existing problems, as well as quantify intuitive performance criteria which have been di¢ cult to capture in previous formulations. Development of a general class of easily solvable problems tends to accelerate progress (cid:150)as linear systems theory has done for example. Our framework may have similar impact, in multiple (cid:133)elds of science and engineering where optimal choice of actions is relevant. Acknowledgements
Acute nonlymphocytic leukemia, preleukemia, and acute myeloproliferative syndrome secondary to treatment of other malignant diseases. Clinical and cytogenetic characteristics and results of in vitro culture of bone marrow and HLA typing.

Thirty-one patients were studied with a clinical picture of preleukemia, acute myeloproliferative syndrome. or overt acute nonlymphocytic leukemia following irradiation and/ or chemotherapy for lymphoproliferative disorders, multipIe myeloma, or solid tumors. In 28 patients the original tumor was in complete remission. All patients had developed leukocytosis or unexplained cytopenia. The initial examinations disclosed overt acute nonlymphocytic leukemia in 5, acute myeloproliferative syndrome in 5, and preleukemia in 21 patients. During the follow-up period. acute myeloproliferation or overt leukemia developed in 1 6/21 preleukemic patients. Clonal cytogenetic abnormalities in the bone marrow were observed in 26/31 patients. 21 were hypodiploid. and all abnormal clones apparently were lacking a B or C group chromosome. Banding technique disclosed the abnormality as 5q in four. 5 in one.
Enzyme immunoassay in which a myeloma protein is used for detection of salmonellae

An enzyme immunoassay (EIA) in which an immunoglobulin A monoclonal antibody from a myeloma (MOPC 467) is used was developed to detect the presence of Salmonella organisms. This myeloma protein binds to a flagellar determinant of the organisms but is not directed toward the H antigens. Of 100 strains tested, 94% were detectable with this antibody. The EIA, used with MOPC 467, is quick, sensitive, and specific, showing virtually no cross-reactivity to other enteric organisms. Initial screening of antibody reactivity was performed by Ouchterlony gel diffusion with the supernatants of heat-treated Salmonella cultures. After this, an EIA was performed on the heat extracts with the myeloma protein, which had been directly coupled to alkaline phosphatase. A positive reaction was indicated by the production of a yellow color after the addition of a substrate (p-nitrophenylphosphate), and this was quantitated by determining the absorbance at 405 nm. The EIA proved to be slightly more sensitive than the Ouchterlony analysis. The sensitivity of the EIA is such that as few as 10(6) Salmonella organisms per ml were detected. This concentration was easily obtained after a 24-h preenrichment incubation of the sample. Mixtures of Salmonella strains with a 10 x concentration of Escherichia coli did not prevent detection of the Salmonella strains. This EIA can be successfully used to detect contamination of foods, as it was used to detect the intentional contamination of infant formula in these studies. Indications are that the EIA is sensitive enough to detect Salmonella strains in M broth subcultures taken directly from a preenrichment culture. Testing of samples could thus be completed 36 h after culture initiation, rather than after 96 h, the time currently needed.
Strong gravitational lensing and dynamical dark energy

We study the strong gravitational lensing properties of galaxy clusters obtained from N-body simulations with different kinds of dark energy (DE). We consider both dynamical DE, due to a scalar field self-interacting through Ratra–Peebles (RP) or supergravity (SUGRA) potentials, and DE with constant negative w=p/ρ=−1 (ΛCDM). We have 12 high-resolution lensing systems for each cosmological model with mass greater than 5.0 × 1014 h−1 M⊙. Using a ray shooting technique, we make a detailed analysis of the lensing properties of these clusters, paying particular attention to the number of arcs and their properties (magnification, length and width). We find that the number of giant arcs produced by galaxy clusters changes in a considerable way from ΛCDM models to dynamical dark energy models with an RP or SUGRA potential. These differences originate from the different epochs of cluster formation and from the non-linearity of the strong lensing effect. We suggest that strong lensing is one of the best tools to discriminate among different kinds of dark energy.
Type I interferon correlates with serological and clinical manifestations of SLE

Background: Systemic lupus erythematosus (SLE) is an autoimmune disease affecting multiple organ systems triggered by the production of autoantibodies. Previous clinical studies in humans and murine models suggest that type I interferons (IFNs) are important for the initiation and potentiation of SLE activity. Methods: 65 consecutive patients with SLE were identified from the University of California, San Francisco Lupus Clinic with moderate-severe disease activity. 94 serological samples were collected. Type I IFN levels and the ability of plasma to induce expression of several surface markers of dendritic cell maturation were measured. Results: Type I IFN levels correlated with the presence of cutaneous manifestations, and there was a trend towards correlation with renal disease. No correlation was found between type I IFN levels and neurological disease. Type I IFN levels correlated positively with the SLEDAI score and anti-dsDNA levels and inversely with C3 levels. Interestingly, type I IFN levels were highest in African American patients. SLE plasma also induced the expression of MHC class I, CD38, and CD123 on monocytes, and was blocked by the addition of a monoclonal antibody to IFNAR1. Conclusions: The pathogenic role of type I IFN is suggested by the induction of cell surface markers for dendritic cell maturation. The potential therapeutic utility of antibodies directed to either type I IFN or IFNAR1/IFNAR2 may be of interest in further studies.
Mars Observer Camera

A camera designed to operate under the extreme constraints of the Mars Observer Mission was selected by NASA in April, 1986. Contingent upon final confirmation in mid-November, the Mars Observer Camera (MOC) will begin acquiring images of the surface and atmosphere of Mars in September-October 1991. The MOC incorporates both a wide angle system for low resolution global monitoring and intermediate resolution regional targeting, and a narrow angle system for high resolution selective surveys. Camera electronics provide control of image clocking and on-board, internal editing and buffering to match whatever spacecraft data system capabilities are allocated to the experiment. The objectives of the MOC experiment follow.