Miracle-dz/UniFAR-FTUs huggingface dataset:
13C‐metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites

Since most bio‐production processes are conducted in a batch or fed‐batch manner, the evaluation of metabolism with respect to time is highly desirable. Toward this aim, we applied 13C‐metabolic flux analysis to nonstationary conditions by measuring the mass isotopomer distribution of intracellular metabolites. We performed our analysis on batch cultures of wild‐type Escherichia coli, as well as on Pyk and Pgi mutants, obtained the fluxes and metabolite concentrations as a function of time. Our results for the wild‐type indicated that the TCA cycle flux tended to increase during growth on glucose. Following glucose exhaustion, cells controlled the branch ratio between the glyoxylate pathway and the TCA cycle, depending on the availability of acetate. In the Pyk mutant, the concentrations of glycolytic intermediates changed drastically over time due to the dumping and feedback inhibition caused by PEP accumulation. Nevertheless, the flux distribution and free amino acid concentrations changed little. The growth rate and the fluxes remained constant in the Pgi mutant and the glucose‐6‐phosphate dehydrogenase reaction was the rate‐limiting step. The measured fluxes were compared with those predicted by flux balance analysis using maximization of biomass yield or ATP production. Our findings indicate that the objective function of biosynthesis became less important as time proceeds on glucose in the wild‐type, while it remained highly important in the Pyk mutant. Furthermore, ATP production was the primary objective function in the Pgi mutant. This study demonstrates how cells adjust their metabolism in response to environmental changes and/or genetic perturbations in the batch cultivation. © 2010 American Institute of Chemical Engineers Biotechnol. Prog. , 2010
Topography-guided laser in situ keratomileusis (TOPOLINK) to correct irregular astigmatism after previous refractive surgery.

PURPOSE To assess whether topography-driven laser in situ keratomileusis (LASIK) can correct induced corneal irregular astigmatism. METHODS A prospective non-comparative case series of 41 eyes (38 patients) with irregular astigmatism following corneal refractive surgery, included two groups: Group 1 (26 eyes) with a defined topographic pattern and Group 2 (15 eyes) with no pattern. Ablation was performed using the Technolas 217C excimer laser with a software ablation program (TOPOLINK) based on corneal topography. Uncorrected and best spectacle-corrected visual acuity, manifest and cycloplegic refraction, corneal topography, superficial corneal surface quality, and image distortion were measured. RESULTS At 6 months follow-up in Group 1 eyes (defined topographic pattern) mean preoperative BSCVA improved from 0.16 +/- 0.11 LogMAR (0.4 to 0) to 0.09 +/- 0.10 LogMAR (0.2 to 0) (P = .001) (safety index of 1.1). In Group 2 eyes (no pattern), mean preoperative BSCVA was 0.18 +/- 0.11 LogMAR (0.4 to 0), similar to the postoperative BSCVA of 0.17 +/- 0.10 LogMAR (0.3 to 0) (safety index of 0.98). Mean postoperative UCVA was > or = 0.3 LogMAR in 25 eyes (96.2%) in Group 1 (efficacy index of 0.8) and 7 eyes (46.6%) in Group 2 (efficacy index of 0.5). Both superficial corneal surface quality and image distortion significantly improved in Group 1; there were no significant changes in Group 2. We reoperated nine eyes (21.9%). CONCLUSIONS Topographic-assisted LASIK was helpful in selected cases where irregular astigmatism showed a pattern. It was ineffective in undefined irregular astigmatism. Partial correction of the irregularity and regression of the obtained effect was common.
Creating a virtual archery experience

In this paper we describe the design of a virtual reality simulator for traditional intuitive archery. Traditional archers aim without a target figure. Good shooting results require an excellent body-eye coordination that allows the user to perform identical movements when drawing the bow. Our simulator provides a virtual archery experience and supports the user to learn and to practice the motion sequence of traditional archery in a virtual environment. We use a low-cost tracking system to capture the user's motion in order to correct his movement. To provide a realistic haptic feedback a real bow is used as interaction device. Our system should provide a believable user experience and support the user to learn how to shoot in the traditional way. Following a user-centered iterative design approach we developed a number of prototypes and evaluated them for refinement in sequent iteration cycles.
Modeling Human Antitumor Responses In Vivo Using Umbilical Cord Blood-Engrafted Mice

Mice engrafted with human immune cells offer powerful in vivo model systems to investigate molecular and cellular processes of tumorigenesis, as well as to test therapeutic approaches to treat the resulting cancer. The use of umbilical cord blood mononuclear cells as a source of human immune cells for engraftment is technically straightforward, and provides T lymphocytes and autologous antigen-presenting cells (including B cells, monocytes, and DCs) that bear cognate antigen presenting molecules. By using a human-specific oncogenic virus, such as Epstein-Barr virus, de novo neoplastic transformation of the human B cells can be induced in vivo in a manner that models progressive stages of tumorigenesis from nascent neoplasia to the establishment of vascularized tumor masses with an immunosuppressive environment. Moreover, since tumorigenesis occurs in the presence of autologous T cells, this type of system can be used to investigate how T cells become suppressed during tumorigenesis, and how immunotherapies counteract immunosuppression. This minireview will provide a brief overview of the use of human umbilical cord blood transplanted into immunodeficient murine hosts to model antitumor responses.
World Equity Premium Based Risk Aversion Estimates

The equity premium puzzle holds that the coefficient of relative risk aversion estimated from the consumption based CAPM under power utility is excessively high. Moreover, estimates in the literature vary considerably across countries. We gauge the uncertainty pertaining to the country risk aversion estimates by means of jackknife resampling and pooling. The confidence band for the world risk aversion estimate from the pooled country data is much tighter and the pooled point estimate presents less of a puzzle than the individual country estimates.
5α‐Reduced glucocorticoids exhibit dissociated anti‐inflammatory and metabolic effects

BACKGROUND AND PURPOSE Dissociating anti‐inflammatory efficacy from the metabolic side effects of glucocorticoids is an attractive therapeutic goal. 5α‐Tetrahydro‐corticosterone (5αTHB), produced from corticosterone by 5α‐reductases, activates glucocorticoid receptors. This study compares the effects of 5αTHB on inflammation and metabolism in vitro and in vivo.
FaceForge: Markerless Non-Rigid Face Multi-Projection Mapping

Recent publications and art performances demonstrate amazing results using projection mapping. To our knowledge, there exists no multi-projection system that can project onto non-rigid target geometries. This constrains the applicability and quality for live performances with multiple spectators. Given the cost and complexity of current systems, we present a low-cost easy-to-use markerless non-rigid face multi-projection system. It is based on a non-rigid, dense face tracker and a real-time multi-projection solver adapted to imprecise tracking, geometry and calibration. Using this novel system we produce compelling results with only consumer-grade hardware.
Extensive Cross-Reactivity of CD4+ Adenovirus-Specific T Cells: Implications for Immunotherapy and Gene Therapy

ABSTRACT Adenovirus (Ad)-specific T-cell responses in healthy adult donors were investigated. Ad5, inactivated by methylene blue plus visible light, induced proliferation and gamma interferon (IFN-γ) production in peripheral blood mononuclear cells of the majority of donors. Responding T cells were CD4+ and produced IFN-γ upon restimulation with infectious Ad5 and Ads of different subgroups. T-cell clones showed distinct cross-reactivity patterns recognizing Ad serotypes from either one subgroup (C), two subgroups (B and C), or three subgroups (A, B, and C). This cross-reactivity of Ad-specific T cells has relevance both for Ad-based gene therapy protocols, as well as for the feasibility of T-cell-mediated adoptive immunotherapy in recipients of an allogeneic stem cell transplantation.
Using learning theory, interprofessional facilitation competencies, and behavioral indicators to evaluate facilitator training

Abstract Despite the increasing need for faculty and preceptors skilled in interprofessional facilitation (IPF), the relative novelty of the field poses a challenge to the development and evaluation of IPF programs. We use learning theory and IPF competencies with associated behavioral indicators to develop and evaluate six key messages in IPF training and experience. Our mixed methods approach included two phases: quantitative data collection with embedded qualitative data, followed by qualitative data collection in explanatory sequential fashion. This enabled triangulated analyses of both data types and of facilitation behaviors from facilitator and student perspectives. Results indicate the competency-based training was effective. Facilitators felt comfortable performing behaviors associated with IPF competencies; student observations of those behaviors supported facilitator self-reported performance. Overall, students perceived more facilitation opportunities than facilitators. Findings corroborate the importance of recruiting seasoned facilitators and establishing IPF guidelines that acknowledge variable team dynamics and help facilitators recognize teachable moments.
Homogeneity analysis of high yield manufacturing process of mems-based pzt thick film vibrational energy harvesters

: This work presents a high yield wafer scale fabrication of MEMS-based unimorph silicon/PZT thick film vibrational energy harvesters aimed towards vibration sources with peak frequencies in the range of a few hundred Hz. By combining KOH etching with mechanical front side protection, SOI wafer to accurately define the thickness of the silicon part of the harvester and a silicon compatible PZT thick film screen-printing technique, we are able to fabricate energy harvesters on wafer scale with a yield higher than 90%. The characterization of the fabricated harvesters is focused towards the full wafer/mass-production aspect; hence the analysis of uniformity in harvested power and resonant frequency.
Antimutagenicity of green tea polyphenols in the liver of transgenic medaka

We examined the ability of a mixture of the predominant green tea polyphenolic compounds (GTP) to reduce benzo[a]pyrene (B[a]P)‐induced mutations in the cII gene of the λ transgenic medaka. Fish were treated with 50 ppb B[a]P for 24 hr, followed by exposure to 2 ppm or 10 ppm GTP for 28 days. cII mutations in livers of fish exposed to B[a]P were increased significantly, 2.6‐fold above controls. In contrast, the addition of GTP significantly reduced the frequency of cII mutants by 84%, comparable to that of controls. The frequencies of mutations at G:C basepairs, mutations that are highly characteristic of B[a]P exposure, were elevated significantly in treated fish. By comparison, B[a]P‐exposed fish also treated with GTP showed reductions in these mutations, demonstrating a protective effect of GTP against B[a]P‐induced mutagenesis. The antioxidant mechanism of GTP possibly played an important role in the reduction of B[a]P mutagenicity. These results corroborate findings from rodent models, showing that the protective effects of green tea extend to different species, and suggesting that similar mechanisms of B[a]P mutagenesis and GTP antimutagenesis are shared among the models. These studies illustrate the utility of λ transgenic medaka for in vivo mutation analyses and suggest that this fish may be a valuable model in chemoprevention studies. Environ. Mol. Mutagen. , 2005. © 2005 Wiley‐Liss, Inc.
LEFT TO RIGHT PARSING OF LEXICALIZED TREE‐ADJOINING GRAMMARS 1

This paper presents an algorithm (a parser) for analyzing sentences according to grammatical constraints expressed in the framework of lexicalized tree‐adjoining grammar. For the current grammars of English, the algorithm behaves much better and requires much less time than its worst‐case complexity. The main objective of this work is to design a practical parser whose average‐case complexity is much superior to its worst case. Most of the previous methods always required the worst‐case complexity. The algorithm can be used in two modes. As a recognizer it outputs whether the input sentence is grammatically correct or not. As a parser it outputs a detailed analysis of the grammatically correct sentences. As sentences are read from left to right, information about possible continuations of the sentence is computed. In this sense, the algorithm is called a predictive left to right parser. This feature reduces the average time required to process a given sentence. In the worst case, the parser requires an amount of time proportional to G2n6 for a sentence of n words and for a lexicalized tree‐adjoining grammar of size G. The worst‐case complexity is only reached with pathological (not naturally occurring) grammars and inputs.
The importance of maternal diet quality during pregnancy on cognitive and behavioural outcomes in children: a systematic review and meta-analysis

Objectives This systematic review and meta-analysis provides a quantitative summary of the literature exploring the relationship between maternal diet quality during pregnancy and child cognitive and affective outcomes. We investigate whether there are indications for robust associations and aim to identify methodological strengths and challenges of the current research to provide suggestions of improvement for future research. Design and participants Relevant studies were identified through a systematic literature search in relevant databases. All studies investigating maternal diet quality during pregnancy in relation to child cognitive or affective functioning in children of elementary school age or younger were assessed for inclusion. Results 18 relevant studies, comprising 63 861 participants were identified. The results indicated a small positive association between better maternal diet quality during pregnancy and child functioning. We observed publication bias and significant heterogeneity between studies, where type of diet classification, publication year and outcome domain together accounted for about 30% of this heterogeneity. Trim and fill analysis substantiated the presence of publication bias for studies in the affective domain and showed an adjusted effect size of Hedge’s g=0.088 (p=0.0018) (unadjusted g=0.093 (p=0.03)). We observed no publication bias in the cognitive domain, where results indicated a slightly larger effect size (g=0.14 (p<0.0001)) compared with that of the affective domain. The overall summary effect size was g=0.075 (p<0.0001) adjusted for publication bias (unadjusted g=0.112 (p=0.0001)). Child diet was not systematically controlled for in the majority of the studies. Conclusion The results indicated that a better maternal diet quality during pregnancy has a small positive association with child neurodevelopment, with more reliable results seen for cognitive development. These results warrant further research on the association between maternal diet quality during pregnancy and cognitive and affective aspects of child neurodevelopment, whereby it is crucial that future studies account for child diet in the analysis.
The polio eradication effort: should vaccine eradication be next?

The World Health Organization (WHO) has implemented a plan to eradicate poliovirus that is widely viewed as having made enormous progress. If all goes as planned, polio will be eradicated on this planet by the year 2003. However, there is a debate, as highlighted in a pair of Policy Forums in this issue, over when vaccination against polio can be stopped. Dove and Racaniello believe that the reliance of the WHO on the live Sabin oral poliovirus vaccine (OPV) means that there will be a continuing threat of release of potentially pathogenic virus into the environment. They are also concerned that the planned destruction of all wild-type polio stocks will not be possible. They therefore recommend a switch to the inactivated polio vaccine (IPV). In response, Hull and Aylward explain why a switch from OPV is not necessary and describe the studies being sponsored by the WHO to determine how and when immunization can safely be ended.
Antibiotic Exposure as a Risk Factor for Fluconazole-Resistant Candida Bloodstream Infection

ABSTRACT Recent exposure to azoles is an important risk factor for infection with fluconazole-resistant Candida spp. , but little is known about the role of antibacterial drug exposure in the emergence of drug-resistant Candida. We did a prospective nationwide surveillance study of candidemia in Israel and analyzed the propensity score-adjusted association between antifungal and antibacterial drug exposure and bloodstream infection with C. glabrata and fluconazole-resistant Candida isolates. Four hundred forty-four episodes of candidemia (450 Candida isolates, 69 [15%] C. glabrata isolates, and 38 [8.5%] fluconazole-resistant isolates) from 18 medical centers in Israel were included. C. glabrata bloodstream infection was strongly associated with recent metronidazole exposure (odds ratio [OR], 3.2; P < 0.001). Infection with a fluconazole-resistant isolate was associated with exposure to carbapenems, trimethoprim-sulfamethoxazole, clindamycin, and colistin (odds ratio, 2.8; P = 0.01). The inclusion of antibacterial drug exposure in a multivariable model significantly enhanced the model's predictive accuracy for fluconazole-resistant Candida bloodstream infection. Our findings may be relevant to the selection of empirical antifungal treatment and broaden the scope of antibiotic-associated collateral damage.
Magnetosome size distribution in uncultured rod‐shaped bacteria as determined by electron microscopy and electron spectroscopic imaging

We report uncultured rod‐shaped magnetotactic bacteria from natural waters that biomineralize magnetic crystals in two different size ranges. Electron spectroscopic imaging of whole bacteria deposited over formvar‐coated grids permitted a better visualization and measurement of the magnetosomes. All magnetosomes of individual bacteria could be observed by this technique. The magnetosomes formed one large chain, composed of three to four columns of crystals, disposed in parallel to the main axis of the bacteria. The magnetosomes ranged from 19 to 136 nm in length and 14 to 112 nm width. Smaller magnetosomes (less than 80 nm in length) localized mostly in extremities of the bacterial body while larger preferentially localized in the middle part of the cell. Electron spectroscopic diffraction and X‐ray microanalysis indicate that both types of magnetosomes contain magnetite (Fe3O4). In projection, most magnetosomes seem to present pseudo‐hexagonal morphologies described for magnetite. As the aspect ratios for smaller and larger magnetosomes are different, we suggest that different levels of control on biomineralization of magnetosomes may exist. Microsc. Res. Tech. 42:459–464, 1998. © 1998 Wiley‐Liss, Inc.
Flywheel energy storage advances using HTS bearings

High-temperature-superconducting (HTS) bearings have the potential to reduce rotor idling losses and make flywheel energy storage economical. Demonstration of large, high-speed flywheels is key to market penetration, Toward this goal, we have developed and tested a flywheel system with 5- to 15-kg disk-shaped rotors. Rim speeds exceeded 400 m/s, and stored energies were >80 Wh. Test implementation required technological advances in nearly all aspects of the flywheel system, Features and limitations of the design and tests are discussed, especially those related to achieving greater energy storage levels.
Calibration-Based Auto White Balance Method for Digital Still Camera

This paper introduces a calibration-based auto white balance method for digital still camera. The main idea is to detect white-points in an image accurately. White-Point Color Temperature Curve (WPCTC) is constructed from sensor calibration and is utilized to estimate white-point locations in a scene. Minimum Color Temperature Distance (MCTD) with a luminance threshold is defined to further locate white-points of an image exactly. Our proposed method is performed in RGB color space so it is suitable for digital still camera pipeline design. In our experiments, our approach is compared with other white balance methods and performs better in color consistency.
Attacks and Counter Measures in BST Overlay Structure of Peer-To-Peer System

There are various overlay structures that provide efficient and scalable solutions for point and range query in a peer-topeer network. Overlay structure based on m-Binary Search Tree (BST) is one such popular technique. It deals with the division of the tree into different key intervals and then assigning the key intervals to a BST. The popularity of the BST makes this overlay structure vulnerable to different kinds of attacks. Here we present four such possible attacks namely index poisoning attack, eclipse attack, pollution attack and syn flooding attack. The functionality of BST is affected by these attacks. We also provide different security techniques that can be applied against these attacks. Keywords—BST, eclipse attack, index poisoning attack, pollution attack, syn flooding attack.
Overexpression of wild-type and mutant ARF1 and ARF6: distinct perturbations of nonoverlapping membrane compartments

The ARF GTP binding proteins are believed to function as regulators of membrane traffic in the secretory pathway. While the ARF1 protein has been shown in vitro to mediate the membrane interaction of the cytosolic coat proteins coatomer (COP1) and gamma-adaptin with the Golgi complex, the functions of the other ARF proteins have not been defined. Here, we show by transient transfection with epitope-tagged ARFs, that whereas ARF1 is localized to the Golgi complex and can be shown to affect predictably the assembly of COP1 and gamma-adaptin with Golgi membranes in cells, ARF6 is localized to the endosomal/plasma membrane system and has no effect on these Golgi-associated coat proteins. By immuno-electron microscopy, the wild-type ARF6 protein is observed along the plasma membrane and associated with endosomes, and overexpression of ARF6 does not appear to alter the morphology of the peripheral membrane system. In contrast, overexpression of ARF6 mutants predicted either to hydrolyze or bind GTP poorly shifts the distribution of ARF6 and affects the structure of the endocytic pathway. The GTP hydrolysis-defective mutant is localized to the plasma membrane and its overexpression results in a profound induction of extensive plasma membrane vaginations and a depletion of endosomes. Conversely, the GTP binding-defective ARF6 mutant is present exclusively in endosomal structures, and its overexpression results in a massive accumulation of coated endocytic structures.