Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides

ABSTRACT Bacterial microcompartments (BMCs) are organelles that encapsulate functionally linked enzymes within a proteinaceous shell. The prototypical example is the carboxysome, which functions in carbon fixation in cyanobacteria and some chemoautotrophs. It is increasingly apparent that diverse heterotrophic bacteria contain BMCs that are involved in catabolic reactions, and many of the BMCs are predicted to have novel functions. However, most of these putative organelles have not been experimentally characterized. In this study, we sought to discover the function of a conserved BMC gene cluster encoded in the majority of the sequenced planctomycete genomes. This BMC is especially notable for its relatively simple genetic composition, its remote phylogenetic position relative to characterized BMCs, and its apparent exclusivity to the enigmatic Verrucomicrobia and Planctomycetes. Members of the phylum Planctomycetes are known for their morphological dissimilarity to the rest of the bacterial domain: internal membranes, reproduction by budding, and lack of peptidoglycan. As a result, they are ripe for many discoveries, but currently the tools for genetic studies are very limited. We expanded the genetic toolbox for the planctomycetes and generated directed gene knockouts of BMC-related genes in Planctomyces limnophilus. A metabolic activity screen revealed that BMC gene products are involved in the degradation of a number of plant and algal cell wall sugars. Among these sugars, we confirmed that BMCs are formed and required for growth on l-fucose and l-rhamnose. Our results shed light on the functional diversity of BMCs as well as their ecological role in the planctomycetes, which are commonly associated with algae.
Understanding the Privacy Space

This paper reports on an ongoing research project focusing on privacy tools, and services available on the Internet. A detailed examination of 133 different privacy-related software tools and services rendered a list of 1,241 features relating to privacy. Based on the data gathered, the ongoing work is to formulate a framework to describe this "privacy space" using grounded theory and content analytic techniques. Here, we discuss some of more interesting preliminary findings garnered from a descriptive statistical analysis of the raw data. This paper discusses what can be learned from a user-centric analysis of this increasingly important class of software tools.
Coordination of Chloroplastic Metabolism in N-Limited Chlamydomonas reinhardtii by Redox Modulation (I. The Activation of Phosphoribulosekinase and Glucose-6-Phosphate Dehydrogenase Is Relative to the Photosynthetic Supply of Electrons)

Extraction of Chlamydomonas reinhardtii CW-15 cells by rapid freezing and thawing demonstrates that the in vivo activity of the algal glucose-6-phosphate dehydrogenase (G6PDH) is inhibited by the presence of light and activated in the dark, whereas phosphoribulosekinase (PRK) is light activated and inhibited in the dark. The effects of darkening are reversed by incubation with dithiothreitol (DTT) and mimicked by chemical oxidants, indicating that, as in higher plants, reduction via the ferredoxin-thioredoxin system likely regulates these enzymes. The two enzymes varied in their sensitivity to reduction; the inclusion of 0.5 mM DTT during extraction inhibited G6PDH, whereas PRK required treatment with 40 mM DTT for 1 h to reach maximum activation. The activation change for both enzymes was nearly complete within the 1st min after cells were transferred between light and dark, but the level of activation was relative to the incident light at low intensities; G6PDH activity decreased with increasing light, whereas PRK became more active. The reductive inhibition of G6PDH saturated at very low light, whereas PRK activation kinetics closely followed the increase in photosynthetic oxygen evolution. These results indicate that light-driven redox modulation of G6PDH and PRK is more than an on/off switch, but acts to optimize the reduction and oxidation of carbon in the chloroplast in accordance with the supply of electrons.
Advanced GPU-based ray casting for bricked datasets

Since the 90s, the Direct Volume Rendering shows itself as an efficient tool for the visual analysis of volumetric datasets. There are approaches that allow for the real-time Ray Casting for visualization of the datasets that can be divided into bricks and entirely loaded into the GPU memory. We describe particular details, implemented in our volume rendering engine, that significantly improve rendering quality and performance.
Hormone Use, Reproductive History, and Risk of Lung Cancer: The Women’s Health Initiative Studies

Introduction: Results from the Women’s Health Initiative clinical trials demonstrated no increase in the risk of lung cancer in postmenopausal women treated with hormone therapy (HT). We conducted a joint analysis of the Women’s Health Initiative observational study data and clinical trials data to further explore the association between estrogen and estrogen-related reproductive factors and lung cancer risk. Methods: Reproductive history, oral contraceptive use, and postmenopausal HT were evaluated in 160,855 women with known HT exposures. Follow-up for lung cancer was through September 17, 2012; 2467 incident lung cancer cases were ascertained, with median follow-up of 14 years. Results: For all lung cancers, women with previous use of estrogen plus progestin of less than 5 years (hazard ratio = 0.84; 95% confidence interval = 0.71–0.99) were at reduced risk. A limited number of reproductive factors demonstrated associations with risk. There was a trend toward decreased risk with increasing age at menopause (ptrend = 0.04) and a trend toward increased risk with increasing number of live births (ptrend = 0.03). Reduced risk of non–small-cell lung cancer was associated with age 20–29 years at first live birth. Risk estimates varied with smoking history, years of HT use and previous bilateral oophorectomy. Conclusions: Indirect measures of estrogen exposure to lung tissue, as used in this study, provide only weak evidence for an association between reproductive history or HT use and risk of lung cancer. More detailed mechanistic studies and evaluation of risk factors in conjunction with estrogen receptor expression in the lung should continue as a role for estrogen cannot be ruled out and may hold potential for prevention and treatment strategies.
Performance Characterization of a High Efficiency Gas-Fed Pulsed Plasma Thruster*

We present a characterization of the performance of a recently developed gas-fed pulsed plasma thruster (GF-PPT) at low discharge energies (•5 J). The impulsive thrust measurements were made using EPPDyL’s high-accuracy interferometric microthrust stand. The thruster is best suited for small satellite applications and is operated in an unsteady pulsed mode (3 „s/pulse). It is the result of a series of design iterations aimed at achieving the highest thrust e‐ciencies for unsteady electromagnetic acceleration at low discharge energies. The use of advanced nonlinear magnetic switching technology, which insured a total system inductance of 3-4 nH, combined with an electrode geometry and radial gas injection that favor low proflle losses, yielded a total e‐ciency of 50% at 5 J with argon (at an impulse bit of 32 „Ns and a mass bit of .2 „g/shot). This is the highest measured e‐ciency ever reported for a PPT at this low energy level. Moreover, the low mass utilization e‐ciency problem that plagued previous gas-fed pulsed
Categorical prototyping: incorporating molecular mechanisms into 3D printing

We apply the mathematical framework of category theory to articulate the precise relation between the structure and mechanics of a nanoscale system in a macroscopic domain. We maintain the chosen molecular mechanical properties from the nanoscale to the continuum scale. Therein we demonstrate a procedure to ‘protoype a model’, as category theory enables us to maintain certain information across disparate fields of study, distinct scales, or physical realizations. This process fits naturally with prototyping, as a prototype is not a complete product but rather a reduction to test a subset of properties. To illustrate this point, we use large-scale multi-material printing to examine the scaling of the elastic modulus of 2D carbon allotropes at the macroscale and validate our printed model using experimental testing. The resulting hand-held materials can be examined more readily, and yield insights beyond those available in the original digital representations. We demonstrate this concept by twisting the material, a test beyond the scope of the original model. The method developed can be extended to other methods of additive manufacturing.
Harmonization of fibrinogen assay results: study within the framework of the Dutch project ‘Calibration 2000’

In a Dutch project for harmonization of fibrinogen assays, the commutability of potential calibrators for fibrinogen was assessed by means of a twin‐study design, which is, in essence, a multicentre, split‐patient sample, between‐field‐methods protocol. The study consisted of simultaneous analysis of fresh‐frozen patient plasmas and three potential calibrators for fibrinogen by 48 Dutch laboratories forming 24 couples. The state‐of‐the‐art intralaboratory standard deviation was used to assess the commutability of the potential calibrators. The potential calibrators were commutable for the Clauss, but not for the prothrombin time (PT)‐derived assays. One potential calibrator was used in an attempt to harmonize fibrinogen assay results in a Dutch field study. The interlaboratory coefficient of variation (CV) of three out of four test samples could be reduced significantly using the common calibrator. The average overall CV for the four test samples was 10.3% using the routine measurements and 7.8% using the common calibrator. Despite the reduction in the overall CV, the bias between Clauss and PT‐derived assay results in two coumarin test samples could not be eliminated.
Parametric-primary resonance of current-carrying ferromagnetic beam in coupled magnetic-temperature fields

A differential equation is derived to analyze the current-carrying ferromagnetic beam in coupled magnetic-temperature fields by means of Galerkin method. Melnikov's function is used to get the necessary critical condition for the chaotic motion of the system in primary resonance. In this system, the phenomenon of chaotic motion couldn't be found. Based on the multiple scales method for nonlinear vibration analysis, the first approximation solutions and the stability corresponding to steady state solutions of the parametric-primary resonance system are obtained. Numerical analysis results show that the temperature can change the internal frequency and the value of amplitude obviously.
Sparse Pose Regression via Componentwise Clustering Feature Point Representation

We propose two-dimensional pose estimation from a single range image of the human body, using sparse regression with a componentwise clustering feature point representation (CCFPR) model. CCFPR includes primary feature points and secondary feature points. The primary feature points consist of the torso center and five extremal points of human body, and further serve to classify all body pixels as the points of six body components. The secondary feature points are given by the cluster centers of each of the five components other than the torso, using K-means cluster. The human pose is obtained by learning a sparse projection matrix, which maps CCFPR to the skeleton points of human body, based on the assumption that each skeleton point be represented by a combination of a few feature points of associated body components. Experimental results on both virtual data and real data show that, under the sparse regression model with a suitably selected cluster number, CCFPR outperforms the random decision forest approach and prediction results of Kinect sensor v2 .
Terlipressin therapy with and without albumin for patients with hepatorenal syndrome: Results of a prospective, nonrandomized study

Vasopressin analogues associated with albumin improve renal function in hepatorenal syndrome (HRS). The current study was aimed at assessing the efficacy of the treatment, predictive factors of response, recurrence of HRS, and survival after therapy. Twenty‐one consecutive patients with HRS (16 with type 1 HRS, 5 with type 2 HRS) received terlipressin (0.5‐2 mg/4 hours intravenously) until complete response was achieved (serum creatinine level < 1.5 mg/dL) or for 15 days; 13 patients received intravenous albumin together with terlipressin. Twelve of the 21 patients (57%) showed complete response. Albumin administration was the only predictive factor of complete response (77% in patients receiving terlipressin and albumin vs. 25% in those receiving terlipressin alone, P = .03). Treatment with terlipressin and albumin was associated with a remarkable decrease in serum creatinine level, increase in arterial pressure, and suppression of the renin‐aldosterone system. By contrast, no significant changes in these parameters were found in patients treated with terlipressin alone. Only 1 patient showed ischemic adverse effects. Recurrence of HRS occurred in 17% of patients with complete response. The occurrence of complete response was associated with an improved survival. In conclusion, terlipressin therapy reverses HRS in a high proportion of patients. Recurrence rate after treatment withdrawal is uncommon. Albumin appears to improve markedly the beneficial effects of terlipressin.
Highly Active Antiretroviral Therapy and Clinical Progression in Patients Failing Protease Predicts Phenotypic Resistance Human Immunodeficiency Virus Type 1 Longitudinal Use of a Line Probe Assay for

10.1128/AAC.46. 6.1928-1933.2002. 2002, 46(6):1928. DOI: Antimicrob. Agents Chemother. Schmit Robert Hemmer, François Schneider and Jean-Claude Staub, Elodie Fontaine, Isabelle Robert, Vic Arendt, Thérèse Jean Servais, Christine Lambert, Jean-Marc Plesséria, Highly Active Antiretroviral Therapy and Clinical Progression in Patients Failing Protease Predicts Phenotypic Resistance Human Immunodeficiency Virus Type 1 Longitudinal Use of a Line Probe Assay for
A modularly vectorized two dimensional LDA for face recognition

In this paper, a modularly vectorized 2DLDA (Mv2DLDA) is proposed for face recognition. First, the original images are divided into modular blocks. Then, each sub-block is transformed into a vector. By using column vector to represent each modular block, we can obtain a two dimensional matrix representation for image. Finally 2DLDA is applied directly on these 2D matrices. Experimental results on ORL, Yale B and PIE databases show that the proposed method can achieve better recognition performance in comparison with RLDA, 2DPCA and 2DLDA.
Mechanism by Which Fatty Acids Inhibit Insulin Activation of Insulin Receptor Substrate-1 (IRS-1)-associated Phosphatidylinositol 3-Kinase Activity in Muscle*

Recent studies have demonstrated that fatty acids induce insulin resistance in skeletal muscle by blocking insulin activation of insulin receptor substrate-1 (IRS-1)-associated phosphatidylinositol 3-kinase (PI3-kinase). To examine the mechanism by which fatty acids mediate this effect, rats were infused with either a lipid emulsion (consisting mostly of 18:2 fatty acids) or glycerol. Intracellular C18:2 CoA increased in a time-dependent fashion, reaching an ∼6-fold elevation by 5 h, whereas there was no change in the concentration of any other fatty acyl-CoAs. Diacylglycerol (DAG) also increased transiently after 3–4 h of lipid infusion. In contrast there was no increase in intracellular ceramide or triglyceride concentrations during the lipid infusion. Increases in intracellular C18:2 CoA and DAG concentration were associated with protein kinase C (PKC)-θ activation and a reduction in both insulin-stimulated IRS-1 tyrosine phosphorylation and IRS-1 associated PI3-kinase activity, which were associated with an increase in IRS-1 Ser307 phosphorylation. These data support the hypothesis that an increase in plasma fatty acid concentration results in an increase in intracellular fatty acyl-CoA and DAG concentrations, which results in activation of PKC-θ leading to increased IRS-1 Ser307 phosphorylation. This in turn leads to decreased IRS-1 tyrosine phosphorylation and decreased activation of IRS-1-associated PI3-kinase activity resulting in decreased insulin-stimulated glucose transport activity.
Inducible xylitol dehydrogenases in enteric bacteria

Morganella morganii ATCC 25829, Providencia stuartii ATCC 25827, Serratia marcescens ATCC 13880, and Erwinia sp. strain 4D2P were found to induce a xylitol dehydrogenase when grown on a xylitol-containing medium. The xylitol dehydrogenases were partially purified from the four strains, and those from M. morganii ATCC 25829, P. stuartii ATCC 25827, and S. marcescens ATCC 13880 were all found to oxidize xylitol to D-xylulose. These three enzymes had KmS for xylitol of 7.1 to 16.4 mM and molecular weights ranging from 130,000 to 155,000. In contrast, the xylitol dehydrogenase from Erwinia sp. strain 4D2P oxidized xylitol at the C-4 position to produce L-xylulose, had a Km for xylitol of 72 mM, and had a molecular weight of 102,000.
Poly[[aqua[μ3-(2,6-2H2)-isonicotinato-κ3 N:O:O′][μ2-(2,6-2H2)-isonicotinato-κ2 N:O]manganese(II)] ethanol solvate]

In the title compound, {[Mn(C6H2D2NO2)2(H2O)]·C2H6O}n, the MnII metal centre displays a slightly distorted octahedral coordination geometry, provided by three O and two N atoms of five isonicotinate ligands and one O atom of a water molecule. There are two types of isonicotinate anions, one acting as a bridging tridentate group and the other in a bridging bidentate fashion, to form a polymeric three-dimensional network. The structure is stabilized by intra- and intermolecular O—H⋯O and C—H⋯O hydrogen-bond interactions.
Stepping stones towards a new prokaryotic taxonomy

Technological developments provide new insights into prokaryotic evolution and diversity and provoke a continuous need to update taxonomy and revise classification schemes. Our present species concept and definition are being challenged by the growing amount of whole genomic information, which should allow improvements in the natural species definition. The continuous quest for an objective and stable method for sorting strains into coherent homogeneous groups is inherent to prokaryotic systematics and nomenclature. Morphological, biochemical, physiological, phenotypic and chemotaxonomic criteria have been complemented by molecular data and pragmatic, purpose built, species definitions are being replaced by more natural ones based on evolutionary insights. It is imperative to give due consideration to both fundamental and applied aspects of future species concepts and definitions. The present paper discusses the present practice in prokaryotic taxonomy of how this system developed and how it may evolve in the future.
Long‐term outcome of chronic myeloid leukaemia patients with p210 and p190 co‐expression at baseline

186–197. Pongers-Willemse, M.J., Verhagen, O.J., Tibbe, G.J., Wijkhuijs, A.J., de Haas, V. , Roovers, E. , van der Schoot, C.E. & van Dongen, J.J. (1998) Real-time quantitative PCR for the detection of minimal residual disease in acute lymphoblastic leukemia using junctional region specific TaqMan probes. Leukemia, 12, 2006–2014. Pott, C. (2011) Minimal residual disease detection in mantle cell lymphoma: technical aspects and clinical relevance. Seminars in Hematology, 48, 172–184. Pott, C. , Hoster, E. , Delfau-Larue, M.H. , Beldjord, K. , Bottcher, S. , Asnafi, V. , Plonquet, A. , Siebert, R. , Callet-Bauchu, E. , Andersen, N. , van Dongen, J.J., Klapper, W. , Berger, F. , Ribrag, V. , van Hoof, A.L. , Trneny, M. , Walewski, J., Dreger, P., Unterhalt, M. , Hiddemann, W. , Kneba, M. , Kluin-Nelemans, H.C. , Hermine, O. , Macintyre, E. & Dreyling, M. (2010) Molecular remission is an independent predictor of clinical outcome in patients with mantle cell lymphoma after combined immunochemotherapy: a European MCL intergroup study. Blood, 115, 3215–3223. Pott, C. , Bruggemann, M. , Ritgen, M. , van der Velden, V.H. , van Dongen, J.J. & Kneba, M. (2013) MRD detection in B-cell non-Hodgkin lymphomas using Ig gene rearrangements and chromosomal translocations as targets for realtime quantitative PCR. Methods in Molecular Biology, 971, 175–200. van der Velden, V.H. , Cazzaniga, G. , Schrauder, A. , Hancock, J., Bader, P., Panzer-Grumayer, E.R. , Flohr, T. , Sutton, R. , Cave, H. , Madsen, H.O. , Cayuela, J.M. , Trka, J., Eckert, C. , Foroni, L. , Zur Stadt, U. , Beldjord, K. , Raff, T. , van der Schoot, C.E. & van Dongen, J.J. European Study Group on, M.R. D.d. i.A.L.L. (2007) Analysis of minimal residual disease by Ig/TCR gene rearrangements: guidelines for interpretation of real-time quantitative PCR data. Leukemia, 21, 604–611. Verhagen, O.J., Willemse, M.J., Breunis, W.B. , Wijkhuijs, A.J., Jacobs, D.C., Joosten, S.A. , van Wering, E.R. , van Dongen, J.J. & van der Schoot, C.E. (2000) Application of germline IGH probes in real-time quantitative PCR for the detection of minimal residual disease in acute lymphoblastic leukemia. Leukemia, 14, 1426–1435.
A study of stability of large wind turbine blades

The paper extends Hodger-Dowell's partial differential equations of blade motion, by building a new blade model of large horizontal axis turbines including the effects from gravity, pitch action, pre-twist and rotor speed. New equations also build an aerodynamic model using analysis of properties of air density, blade thickness and wind speed. All partial differential equations are approximated by a second-order finite difference approximation and used to simulate the stability of blade by varying parameters.
Effect of Loteprednol Etabonate 0.5% on Initiation of Dry Eye Treatment With Topical Cyclosporine 0.05%

Objective: The purpose of this work was to evaluate the effect of loteprednol etabonate (LE) before the initiation of topical cyclosporine A (tCsA) therapy in patients with mild-to-moderate dry eye disease. Prospective, multicenter randomized double-masked parallel group clinical study (NCT00407043). Methods: Hundred and eighteen patients with dry eye disease were randomized to receive either LE and tCsA (n=61) or artificial tears (AT) and tCsA (n=57). Hundred and twelve patients completed the study (LE: n=57, AT: n=55) and are included in the data analysis. Patients self-administered either LE or AT for 2 weeks 4 times per day, followed by tCsA twice per day accompanied by either LE twice per day or AT twice per day for an additional 6 weeks of treatment. Primary outcome measures included the Ocular Surface Disease Index (OSDI) questionnaire, the Likert scale using standardized facial expressions, lissamine green staining, fluorescein staining, and the Schirmer test. Additional measures included global self-assessment, and safety outcomes included slitlamp examination, intraocular pressure, and assessment of visual acuity. Results: Loteprednol etabonate pretreatment significantly reduced tCsA stinging (P<0.05). Both groups showed significantly improved OSDI scores at the 14-, 30-, and 60-day visits. Loteprednol etabonate showed significantly more OSDI improvement than AT. Both pretreatment strategies improved global self-assessment scores, Schirmer test, fluorescein staining, lissamine staining, and adjunctive AT use. Loteprednol etabonate showed superior improvement in Schirmer test, fluorescein staining, and lissamine staining. Intraocular pressure did not increase in either group. Conclusions: Loteprednol etabonate induction therapy 2 weeks before the initiation of long-term tCsA treatment for chronic dry eye disease provides more rapid relief of dry eye signs and symptoms with greater efficacy than tCsA and AT alone.