gebhart/patrepeval huggingface dataset:
Constraint‐based modeling of heterologous pathways: Application and experimental demonstration for overproduction of fatty acids in Escherichia coli (2014)

ABSTRACT Constraint‐based modeling has been shown, in many instances, to be useful for metabolic engineering by allowing the prediction of the metabolic phenotype resulting from genetic manipulations. But the basic premise of constraint‐based modeling—that of applying constraints to preclude certain behaviors—only makes sense for certain genetic manipulations (such as knockouts and knockdowns). In particular, when genes (such as those associated with a heterologous pathway) are introduced under artificial control, it is unclear how to predict the correct behavior. In this paper, we introduce a modeling method that we call proportional flux forcing (PFF) to model artificially induced enzymatic genes. The model modifications introduced by PFF can be transformed into a set of simple mass balance constraints, which allows computational methods for strain optimization based on flux balance analysis (FBA) to be utilized. We applied PFF to the metabolic engineering of Escherichia coli ( E. coli ) for free fatty acid (FFA) production—a metabolic engineering problem that has attracted significant attention because FFAs are a precursor to liquid transportation fuels such as biodiesel and biogasoline. We show that PFF used in conjunction with FBA‐based computational strain optimization methods can yield non‐obvious genetic manipulation strategies that significantly increase FFA production in E. coli . The two mutant strains constructed and successfully tested in this work had peak fatty acid (FA) yields of 0.050 g FA/g carbon source (17.4% theoretical yield) and 0.035 g FA/g carbon source (12.3% theoretical yield) when they were grown using a mixed carbon source of glucose and casamino acids in a ratio of 2‐to‐1. These yields represent increases of 5.4‐ and 3.8‐fold, respectively, over the baseline strain. Biotechnol. Bioeng. 2014;111: 2056–2066. © 2014 Wiley Periodicals, Inc.
Development, Progression, and Regression of Microalbuminuria in Japanese Patients With Type 2 Diabetes Under Tight Glycemic and Blood Pressure Control (2005)

Development and progression were low and regression was high with SBP of 120 mmHg, provided A1C was maintained at 6.5%.
"Open" systems relaying (1994)

This paper describes a development in relaying hardware and philosophy which has been made possible by DSPs and industrial grade PCs. Details are given of a prototype design capable of being assembled and configured by a utility and results of tests on this prototype using the RTDS at the Manitoba HVDC Research Centre are presented. The project is a joint effort between the University of Manitoba and Manitoba Hydro.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ADAR1 regulates melanoma cell invasiveness by controlling beta3-integrin via microRNA-30 family members. (2020)

Melanoma cells utilize multiple mechanisms to exit the primary tumor mass, invade the surroundings and subsequently distant tissues. We have previously reported that the expression of the RNA editing enzyme ADAR1 (adenosine deaminase acting on RNA) is downregulated in metastatic melanoma, which facilitates proliferation and invasion. Here we show that ADAR1 controls melanoma invasiveness by regulating ITGB3 expression via miR-30a and miR-30d. ADAR1 overexpression or knockdown leads to an increase or decrease, respectively, in the expression of both microRNAs. The effect is independent of RNA-editing. Dual luciferase assays show that both microRNAs directly regulate the expression of the ITGB3 integrin. Overexpression of the miR-30a or miR-30d lead to a decrease in ITGB3 and a resultant decreased invasive and metastatic capacities. Neutralization of the endogenous miR-30a or miR-30d leads to the opposite effect. The microRNAs regulate ITGB3 levels probably through a post-transcriptional effect, as both mRNA and protein levels of ITGB3 are affected. These results further expand our knowledge on the ADAR1-ITGB3 network and its central role in acquisition of the invasive phenotype of metastatic melanoma.
The Floppy Nissen Fundoplication (1985)

In 1976 we defined a technique of "floppy" Nissen fundoplication (FNF) that prevented experimental pathologic reflux without preventing gaseous eructations or vomiting (normal reflux) when appropriate. This report describes the one- to eight-year follow-up of the 77 patients operated on since that time. The FNF has been completely effective in preventing pathologic reflux in 75 of 77 patients and has been partially effective in two others who are now subjectively asymptomatic. Adverse side effects were reported by two patients, one with gas-bloat and one with inability to belch or vomit. The lower esophageal sphincter pressure of patients postoperatively was increased to low normal values from a mean of 8.94 +/- 1.66 to 14.31 +/- 0.7 mm Hg (normal, 21.2 +/- 4.2 mm Hg). Since FNF does not cause greatly increased lower esophageal sphincter pressure, the inference that the FNF prevents reflux by altering the physiology of a reflux event is supported. In conclusion, the floppy fundoplication has been an effective operation with a low incidence of adverse side effects and without a tendency for late failure.
HYDROXYAPATITE: A PLATFORM FOR RECRUITING SYSTEMICALLY ADMINISTERED DRUGS (2021)

Targeted delivery of drugs is a major challenge in diseases such as infections and tumors. The aim of this study was to demonstrate that hydroxyapatite (HA) particles can act as a recruiting moiety...
Molecular genetics of polyunsaturated fatty acid biosynthesis in marine bacteria (2002)

No description available
Monitoring and assessment of aqueous/perfluorocarbon fermentation systems (1988)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1989.
Optimal Placement of Wireless Chargers in Rechargeable Sensor Networks (2018)

Energy scarcity is the serious issue for the lifetime of a sensor network. The promising solution for this issue is to utilize the wireless chargers to replenish the batteries of sensor nodes. Wireless chargers transmit the power source to sensor nodes through the air without any interconnecting cables. The crucial issue is to identify the optimal position for each charger to minimize the number of chargers required to recharge the entire sensors. In this paper, enhanced sensor coverage with the Daubechies wavelet algorithm is proposed to identify the optimal position for the wireless chargers. Daubechies wavelets have dilation and translation functions for horizontal or vertical movement of the chargers in the region. Furthermore, the proposed algorithm mobilizes the redundant chargers in the optimal position. The series of simulation results confirms that the proposed method performs better to identify the optimal solution compared with other techniques.
Magnetoresistive Switch Effect and Its Application to Magnetic Field Sensors (2005)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
High-accuracy electron tomography of semiconductor devices (2015)

As semiconductor industries have implemented three dimensional (3-D) structures in order to improve device performance, i.e., to decrease power requirement and to lower current leakage, a conventional 2-D TEM cross-section is no longer sufficient to visualize the structure of a device. Electron Tomography (ET) provides more comprehensive representation in comparison to conventional 2-D cross section TEM images. Electron tomography allows for object visualization of practical interest at sub-nm resolution in 3D. For undistorted rendering and accurate measurement of object dimensions the data must be acquired over the entire ±90° tilt range and the accuracy of the alignment of the projected images must be better than the desired resolution of the reconstructed volume [1]. Here we discuss high resolution ET investigation of semiconductor devices using nano-dot fiducial markers on samples without a missing wedge.
Polymer design for 157-nm chemically amplified resists (2001)

Based on UV measurements at 157nm of in-house fluoropolymers we have selected (alpha) -trifluoromethylacrylate and norbornene bearing a pendant hexafluoroisopropanol group as our building blocks for 157nm resist polymers. Polymers consisting of these repeat units have an optical density/micrometers of 3 or below at 157nm. We have found that the (alpha) -trifluoromethylacrylate derivatives conveniently undergo radical copolymerization with norornenes, which has provided a breakthrough in preparation of our 157nm resist polymers. This approach offers flexibility and versatility because an acidic moiety or acid-labile group can be placed in either acrylate or norbornene repeat unit. Other platforms of interest include all acrylic, all-norbornene, and acrylic-styrenic polymers.
Capacity and coverage enhancement in heterogeneous networks (2011)

Disruptive innovations in mobile broadband system design are required to help network providers meet the exponential growth in mobile traffic demand with relatively flat revenues per bit. Heterogeneous network architecture is one of the most promising low-cost approaches to provide significant areal capacity gain and indoor coverage improvement. In this introductory article, we provide a brief overview of heterogeneous network architectures comprising hierarchical multitier multiple radio access technologies (RAT) deployments based on newer infrastructure elements. We begin with presenting possible deployment scenarios of heterogeneous networks to better illustrate the concepts of multitier and multi-RAT. We then focus on multitier deployments with single RAT and investigate the challenges associated with enabling single frequency reuse across tiers. Based on the spectrum usage, heterogeneous networks can be categorized into single carrier usage, where all devices within the network share the same spectrum, and distinct carrier usage, where different types of devices are allocated separate spectra. For single carrier usage, we show that interference management schemes are critical for reducing the resulting cross-tier interference, and present several techniques that provide significant capacity and coverage improvements. The article also describes industry trends, standardization efforts, and future research directions in this rich area of investigation.
Steroidal Saponins from the Rhizome ofParis polyphyllaand Their Cytotoxic Activities (2008)

Two new furostanol saponins and one new spirostanol saponin were isolated from the rhizome of Paris polyphylla Smith var. yunnanensis, together with 18 known steroidal saponins. The structures of the new steroidal saponins were elucidated as 26-O-beta-D-glucopyranosyl-(25R)-5-ene-furost-3 beta, 17 alpha, 22 alpha, 26-tetrol-3-O-alpha-L-arabinofuranosyl-(1-->4)-[alpha-L-rhamnopyranosyl-(1-->2)]-beta-D-glucopyranoside (2, parisyunnanoside A), 26-O-beta-D-glucopyranosyl-(25R)-5, 20 (22)-diene-furost-3 beta, 26-diol-3-O-alpha-L-arabinofuranosyl-(1-->4)-[alpha-L-rhamnopyranosyl-(1-->2)]-beta-D-glucopyranoside (7, parisyunnanoside B), and (25R)-spirost-5-ene-3 beta, 12 alpha-diol-3-O-alpha-L-rhamnopyranosyl-(1-->4)-alpha-L-rhamnopyranosyl-(1-->4)-[alpha-L-rhamnopyranosyl-(1-->2)]-beta-D-glucopyranoside (13, parisyunnanoside C) by MS and 1 D and 2 D NMR analysis. The isolated compounds were evaluated for their cytotoxicity against HL-60 human promyelocytic leukemia cells. Our results showed that the spirostanol framework of the aglycone and the terminal alpha-L-rhamnopyranosyl with 1-->2 linkage to the sugar chain of saponins at C-3 are essential for their high cytotoxicity, whereas the hydroxy group substitution at C-12 or C-17 of the aglycone causes a reduction in their activity.
Community-based supplementary feeding for promoting the growth of children under five years of age in low and middle income countries (2012)

The scarcity of available studies and their heterogeneity makes it difficult to reach any firm conclusions. The review findings suggest supplementary feeding has a negligible impact on child growth; however, the pooled results should be interpreted with great caution because the studies included in the review are clinically diverse. Future studies should address issues of research design, including sample size calculation, to detect meaningful clinical effects and adequate intervention allocation concealment. In the meantime, families and children in need should be provided appropriate feeding, health care and sanitation without waiting for new RCTs to establish a research basis for feeding children.
An α-1,6-and α-1,3-linked glucan produced by Leuconostoc citreum ABK-1 alternansucrase with nanoparticle and film-forming properties (2018)

Alternansucrase catalyses the sequential transfer of glucose residues from sucrose onto another sucrose molecule to form a long chain polymer, known as "alternan". The alternansucrase-encoding gene from Leuconostoc citreum ABK-1 (Lcalt) was successfully cloned and expressed in Escherichia coli. Lcalt encoded LcALT of 2,057 amino acid residues; the enzyme possessed an optimum temperature and pH of 40 °C and 5.0, respectively, and its' activity was stimulated up to 2.4-fold by the presence of Mn<sup>2+</sup>. Kinetic studies of LcALT showed a high transglycosylation activity, with K<sub>m</sub> 32.2 ± 3.2 mM and kcat 290 ± 12 s<sup>-1</sup>. Alternan generated by LcALT (Lc-alternan) harbours partially alternating α-1,6 and α- 1,3 glycosidic linkages confirmed by NMR spectroscopy, methylation analysis, and partial hydrolysis of Lc-alternan products. In contrast to previously reported alternans, Lc-alternan can undergo self-assembly, forming nanoparticles with an average size of 90 nm in solution. At concentrations above 15% (w/v), Lc-alternan nanoparticles disassemble and form a high viscosity solution, while this polymer forms a transparent film once dried.
Chemogenomics with Peptide Secondary Structure Mimetics (2003)

There is increasing evidence that redox regulation of transcription, particularly activator protein-1 (AP-1) and nuclear factor kappa B (NF-kappaB), is important in inflammatory diseases. Human thioredoxin (TRX), a member of the oxidoreductase superfamily, was initially identified, as a factor which augments the production of interleukin-2 receptor alpha (IL-2R alpha) in human T-cell lymphotropic virus type 1 (HTLV-1) infected patient T-cells. Substrates for the redox activity of TRX bind the active site cleft in extended strand structure. The rapid generation of high numbers of peptide secondary structure mimetics through solid-phase synthesis is a key technology for the identification of pharmaceutical leads based on such protein-peptide interactions. In this manuscript, we describe a chemogenomic approach utilizing an extended strand templated library to develop small molecule inhibitors to validate oxidoreductase molecular targets in a murine asthma model.
Cerebral hypoxemia-ischemia and reoxygenation with 21% or 100% oxygen in newborn piglets: Effects on extracellular levels of excitatory amino acids and microcirculation (2001)

Significantly higher levels of excitatory amino acids in striatum, significantly lower mean arterial pressure, and a significantly greater degree of hypoperfusion in cerebral cortex were found after reoxygenation with 21% oxygen compared with 100% oxygen in normocapnic, hypoxemic-ischemic newborn piglets. This suggests a less favorable outcome in the group receiving room air.
Modelling Considerations for Coupled Lines in CMOS Back-End-Of-Line at mm-Wave Frequencies (2022)

&lt;p&gt;We investigate the effect of passivation contouring, surface roughness, and sidewall etch tapering on the FEM modelling accuracy of mm-wave couplers in CMOS BEOL. It is found that accurate passivation contouring leads to a marginal improvement of 0.15 dB in peak coupling prediction accuracy, but introducing a sidewall taper of 104ᵒ can improve the prediction of peak coupling by up to 0.37 dB. Including surface roughness of 5 % and 10 % of metal thickness did not have a notable improvement on prediction of peak coupling.&lt;/p&gt;
Identification of Lethal microRNAs Specific for Head and Neck Cancer (2013)

These six microRNAs might be developed as novel anti-cancer agents and highlight ATM as an interesting novel therapeutic target for head and neck cancer.
Tumor cell progression and differentiation in metastasis. (1991)

The development and evolution of tumors is regulated by both genetic and epigenetic events. It is thought that these processes tend to drive neoplastic development in opposing directions so that tumor progression, predominantly as a consequence of mutational events, leads to increasing tumor aggression. Conversely the induction of differentiation, largely through epigenetic mechanisms, tends to cause tumors to evolve to a more benign phenotype. However, these generalizations are a simplistic view of a complex dynamic event where both processes can be overlaid within a single neoplasm. Using malignant melanoma as a model system the alterations in gene expression and their effects upon metastatic dissemination, that accompany some of these changes, both natural and induced, are described.
Narrowing of the Hailey–Hailey Disease Gene Region on Chromosome 3q and Identification of One Kindred with a Deletion in This Region (1995)

Hailey-Hailey disease is a cutaneous abnormality transmitted as an autosomal dominant trait in which impaired interkeratinocyte adhesion produces recurrent blisters in characteristic skin sites. We report here a confirmation of the initial mapping of the mutant gene to chromosome 3q in an additional seven kindreds, narrowing of the candidate region to the sequences flanked by D3S1589 and D3S1541, and the finding in one family of a genomic DNA deletion whose centromeric end is located between these two flanking markers.
Hepatocyte Transplantation Using the Domino Concept in a Child with Tetrabiopterin Nonresponsive Phenylketonuria (2012)

Phenylketonuria is a metabolic disease caused by phenylalanine hydroxylase deficiency. Treatment is based on a strict natural protein-restricted diet that is associated with the risk of malnutrition and severe psychosocial burden. Oral administration of tetrahydrobiopterin can increase residual enzyme activity, but most patients with severe clinical phenotypes are nonresponders. We performed liver cell transplantation in a 6-year-old boy with severe tetrahydrobiopterin nonresponsive phenylketonuria who failed to comply with diet prescriptions. The transplanted hepatocytes were obtained in part from an explanted glycogen storage type 1b liver. Following two infusions, blood phenylalanine levels returned within the therapeutic target while the phenylalanine half-life assessed by loading tests decreased from 43 to 19 h. However, 3 months later, blood phenylalanine concentrations increased and the phenylalanine intake had to be reduced. Cell-based therapy is a promising therapeutic option in phenylketonuria, and the domino concept may solve the issue of cell sources for hepatocyte transplantation.
Induction of systemic resistance in Arabidopsis thaliana in response to a culture filtrate from a plant growth‐promoting fungus, Phoma sp. GS8‐3 (2008)

The plant growth-promoting fungus (PGPF), Phoma sp. GS8-3, isolated from a zoysia grass rhizosphere, is capable of protecting cucumber plants against virulent pathogens. This fungus was investigated in terms of the underlying mechanisms and ability to elicit systemic resistance in Arabidopsis thaliana. Root treatment of Arabidopsis plants with a culture filtrate (CF) from Phoma sp. GS8-3 elicited systemic resistance against the bacterial speck pathogen Pseudomonas syringae pv. tomato DC3000 (Pst), with restricted disease development and inhibited pathogen proliferation. Pathway-specific mutant plants, such as jar1 (jasmonic acid insensitive) and ein2 (ethylene insensitive), and transgenic NahG plants (impaired in salicylate signalling) were protected after application of the CF, demonstrating that these pathways are dispensable (at least individually) in CF-mediated resistance. Similarly, NPR1 interference in npr1 mutants had no effect on CF-induced resistance. Gene expression studies revealed that CF treatment stimulated the systemic expression of both the SA-inducible PR-1 and JA/ET-inducible PDF1.2 genes. However, pathogenic challenge to CF-treated plants was associated with potentiated expression of the PR-1 gene and down-regulated expression of the PDF1.2 gene. The observed down-regulation of the PDF1.2 gene in CF-treated plants indicates that there may be cross-talk between SA- and JA/ET-dependent signalling pathways during the pathogenic infection process. In conclusion, our data suggest that CF of Phoma sp. GS8-3 induces resistance in Arabidopsis in a manner where SA and JA/ET may play a role in defence signalling.
Méthodes d’évaluation du potentiel antioxydant dans les aliments (2004)

Maitriser l’oxydation est indispensable pour gerer l’evolution des systemes biologiques dans leur complexite, en particulier dans le cas des aliments dont la degradation peut avoir des consequences en securite alimentaire. Les differentes methodes d’evaluation de l’activite antioxydante d’un additif alimentaire sont presentees apres examen du contexte et des mecanismes d’oxydation. L’activite anti-oxydante est evaluee soit par le dosage des produits formes (en particulier des hydroperoxydes) par des techniques photometriques plus ou moins directes, soit par la mesure de l’efficacite du compose a pieger des radicaux libres. Les methodes comparant le piegeage d’un additif avec celui d’un anti-oxydant de reference, le Trolox®, sont applicables a des produits varies quelle que soit l’hydrophilie ou l’hydrophobie du milieu.
Effects of ambient velocity shear on nonlinear internal wave associated mixing at the Columbia River plume front (2009)

Large‐amplitude nonlinear internal waves (NLIWs) are frequently observed propagating away from Columbia River tidal plume fronts. They are generated because of the deceleration of the frontal bulge. During the River Influences on Shelf Ecosystems project cruises, the velocity, density structure and acoustic backscatter of the plume fronts and frontal NLIWs were observed using a towed vehicle, vessel‐mounted instrumentation, and a vessel X band radar. These observations indicate that in the presence of strong ambient velocity shear, the NLIWs with maximum amplitudes occur well below the density interface and at a depth deeper than in the absence of shear. This deepening of the NLIW shear is associated with intensified vertical mixing below the interface. This is consistent with a dynamic analysis of NLIWs under the influence of sheared ambient flow, obtained from a high‐order KdV model. There are two mechanisms responsible for the vertical turbulent mixing intensification. The nonlinear interaction between ambient shear and the NLIWs increases total velocity shear and causes the gradient Richardson number Ri g to decrease below a critical value in certain depth ranges. Also, because of the presence of the ambient shear, the maximum NLIW velocity shear occurs at a depth below the density interface where there is less stratification.