gebhart/patrepeval huggingface dataset:
Control of D-lactic acid content in P(LA-3HB) copolymer in the yeast Saccharomyces cerevisiae using a synthetic gene expression system (2022)

The fully biobased polyhydroxyalkanoate (PHA) polymers provide interesting alternatives for petrochemical derived plastic materials. The mechanical properties of some PHAs, including the common poly(3-hydroxybutyrate) (PHB), are limited, but tunable by addition of other monomers into the polymer chain. In this study we present a precise synthetic biology method to adjust lactate monomer fraction of a polymer by controlling the monomer formation <i>in vivo</i> at gene expression level, independent of cultivation conditions. We used the modified doxycycline-based Tet-On approach to adjust the expression of the stereospecific D-lactate dehydrogenase gene (<i>ldhA</i>) from <i>Leuconostoc mesenteroides</i> to control D-lactic acid formation in yeast <i>Saccharomyces cerevisiae</i>. The synthetic Tet-On transcription factor with a VP16 activation domain was continuously expressed and its binding to a synthetic promoter with eight transcription factor specific binding sites upstream of the <i>ldhA</i> gene was controlled with the doxycycline concentration in the media. The increase in doxycycline concentration correlated positively with <i>ldhA</i> expression, D-lactic acid production, poly(D-lactic acid) (PDLA) accumulation <i>in vivo</i>, and D-lactic acid content in the poly(D-lactate-<i>co</i>-3-hydroxybutyrate) P(LA-3HB) copolymer. We demonstrated that the D-lactic acid content of the P(LA-3HB) copolymer can be adjusted linearly from 6 mol% to 93 mol% <i>in vivo</i> in <i>S. cerevisiae</i>. These results highlight the power of controlling gene expression and monomer formation in the tuning of the polymer composition. In addition, we obtained 5.6% PDLA and 19% P(LA-3HB) of the cell dry weight (CDW), which are over two- and five-fold higher accumulation levels, respectively, than reported in the previous studies with yeast. We also compared two engineered PHA synthases and discovered that in <i>S. cerevisiae</i> the PHA synthase PhaC1437<sub>Ps6-19</sub> produced P(LA-3HB) copolymers with lower D-lactic acid content, but with higher molecular weight, in comparison to the PHA synthase PhaC1Pre.
Effects of Iron Supplementation and Depletion on Hypoxic Pulmonary Hypertension (2009)

clinicaltrials.gov Identifier: NCT00952302.
Low Energy Diet-induced and Bariatric Surgery-induced Weight Loss Decreases Branched-chain and Aromatic Amino Acids in Plasma and Tissue (P21-078-19) (2019)

Plasma levels of branched-chain amino acids (BCAA) and aromatic amino acids (AAA) phenylalanine (phe) and tyrosine (tyr) have been associated with obesity, insulin resistance and risk of type 2 diabetes. This study aimed to investigate the response of circulating plasma and tissue levels of BCAA and AAA to weight loss, and to correlate the level of these metabolites in plasma and tissue in obese women. 28 obese (mean BMI 46.2 kg/m2) women underwent low energy diet (LED)-induced weight loss (−9.2 ± 4.2 kg) followed by bariatric surgery-induced weight loss (−23.6 ± 2.5 kg). Plasma at baseline (t0), post-LED/pre-surgery (t1) and 6-month post-surgery (t2) as well as biopsies of subcutaneous abdomen adipose tissue (SAfat), superficial thigh adipose tissue (Tfat) and vastus lateralis thigh muscle (Tmuscle) at both t1 and t2 were collected, and profiled using mass spectrometry-based metabolomics approach. Paired t-tests were applied to assess between-timepoint differences, and Pearson correlation used to calculate correlation coefficient of metabolite levels between plasma and tissue. Plasma BCAA and AAA were all significantly reduced post-LED at t1 (fold-change of 0.76–0.85 for val, leu, ile, tyr and phe, P < 0.05) and 6-month post-surgery at t2 (fold-change of 0.74–0.85 for val, leu, ile, tyr and phe, P < 0.05) as compared to baseline t0; but not significant between t1 and t2, although trends of decrease were observed. Among the 3 tissue biopsies, only SAfat showed significantly decreased levels of tyr, leu and ile at t2 compared to t1 (fold-change for tyr 0.63, leu 0.66, ile 0.68, P < 0.05). In addition, plasma levels of val and ile were correlated with Tfat levels at both t1 and t2 (r2 = 0.47–0.57), and that of val, ile and leu were correlated with Tmuscle at t1 only (r2 = 0.64–0.67). Circulating levels of BCAA and AAA were decreased by weight loss interventions. The decrease following an LED program was sustained after bariatric surgery without further significant decrease. Bariatric surgery also decreased BCAA levels in SAfat; moreover, our data suggested that plasma BCAA levels correlated well with peripheral tissue Tfat and Tmuscle. The New Zealand National Science Challenge High-Value Nutrition program.
“Real-time” disintegration analysis and D-optimal experimental design for the optimization of diclofenac sodium fast-dissolving films (2012)

The objective of this work was to study the dissolution and mechanical properties of fast-dissolving films prepared from a tertiary mixture of pullulan, polyvinylpyrrolidone and hypromellose. Disintegration studies were performed in real-time by probe spectroscopy to detect the onset of film disintegration. Tensile strength and elastic modulus of the films were measured by texture analysis. Disintegration time of the films ranged from 21 to 105 seconds whereas their mechanical properties ranged from approximately 2 to 49 MPa for tensile strength and 1 to 21 MPa% for young's modulus. After generating polynomial models correlating the variables using a D-Optimal mixture design, an optimal formulation with desired responses was proposed by the statistical package. For validation, a new film formulation loaded with diclofenac sodium based on the optimized composition was prepared and tested for dissolution and tensile strength. Dissolution of the optimized film was found to commence almost immediately with 50% of the drug released within one minute. Tensile strength and young's modulus of the film were 11.21 MPa and 6, 78 MPa%, respectively. Real-time spectroscopy in conjunction with statistical design were shown to be very efficient for the optimization and development of non-conventional intraoral delivery system such as fast dissolving films.
The Load as an Energy Asset in a Distributed DC SmartGrid Architecture (2011)

DC power systems can be made more reliable by considering the load as an important energy asset. Currently the ability to manage the total system is available only through a centralized controller, which limits flexibility, reconfigurability, and reliability. These limitations can be avoided while still providing system level coordination through the use of distributed controls based on local information. All elements of the power system including source, loads, and the network itself have influence, interaction, and coupling to all other elements. Therefore, it is necessary to model and control a microgrid as a system of systems that share some common aspects, such as voltage levels, but can operate independently. Using local information in the form of the bus voltage, these techniques do not rely on a centralized controller, which improves system reliability. However, it is important to design the microgrid in such a manner as to take advantage of the energy not just from the generation sources, but also the energy stored in the individual points-of-load as well.
Classifying Security Threats in Cloud Networking (2015)

A central component of managing risks in cloud computing is to understand the nature of security threats. The relevance of security concerns are evidenced by the efforts from both the academic community and technological organizations such as NIST, ENISA and CSA, to investigate security threats and vulnerabilities related to cloud systems. Provisioning secure virtual networks (SVNs) in a multi-tenant environment is a fundamental aspect to ensure trust in public cloud systems and to encourage their adoption. However, comparing existing SVN-oriented solutions is a difficult task due to the lack of studies summarizing the main concerns of network virtualization and providing a comprehensive list of threats those solutions should cover. To address this issue, this paper presents a threat classification for cloud networking, describing threat categories and attack scenarios that should be taken into account when designing, comparing, or categorizing solutions. The classification is based o n the CSA threat report, building upon studies and surveys from the specialized literature to extend the CSA list of threats and to allow a more detailed analysis of cloud network virtualization issues.
Inter-digitation approach to encapsulation of C60: [C60 ⊂ (p-phenylcalix[5]arene)2]Dedicated to Professor Jerry L. Atwood on the occasion of his 60th birthday. (2002)

p-Phenylcalix[5]arene shows a strong and selective binding of C60 in toluene resulting in crystallisation of a hemispherically inter-digitated 2:1 complex; the receptor itself crystallizes from toluene with self assembly through phenyl group inclusion.
Bridging the Gap between Physical Location and Online Social Networks (2010)

This paper examines the location traces of 489 users of a location sharing social network for relationships between the users ’ mobility patterns and structural properties of their underlying social network. We introduce a novel set of location-based features for analyzing the social context of a geographic region, including location entropy, which measures the diversity of unique visitors of a location. Using these features, we provide a model for predicting friendship between two users by analyzing their location trails. Our model achieves significant gains over simpler models based only on direct properties of the co-location histories, such as the number of co-locations. We also show a positive relationship between the entropy of the locations the user visits and the number of social ties that user has in the network. We discuss how the offline mobility of users can have implications for both researchers and designers of online social networks.
A pair of homoeolog ClpP5 genes underlies a virescent yellow‐like mutant and its modifier in maize (2014)

Gene-background interaction is a commonly observed phenomenon in many species, but the molecular mechanisms of such an interaction is less well understood. Here we report the cloning of a maize mutant gene and its modifier. A recessive mutant with a virescent yellow-like (vyl) phenotype was identified in an ethyl methanesulfonate-mutagenized population derived from the maize inbred line B73. Homozygous mutant maize plants exhibited a yellow leaf phenotype after emergence but gradually recovered and became indistinguishable from wild-type plants after approximately 2 weeks. Taking the positional cloning approach, the Chr.9_ClpP5 gene, one of the proteolytic subunits of the chloroplast Clp protease complex, was identified and validated as the candidate gene for vyl. When introgressed by backcross into the maize inbred line PH09B, the mutant phenotype of vyl lasted much longer in the greenhouse and was lethal in the field, implying the presence of a modifier(s) for vyl. A major modifier locus was identified on chromosome 1, and a paralogous ClpP5 gene was isolated and confirmed as the candidate for the vyl-modifier. Expression of Chr.1_ClpP5 is induced significantly in B73 by the vyl mutation, while the expression of Chr.1_ClpP5 in PH09B is not responsive to the vyl mutation. Moreover, expression and sequence analysis suggests that the PH09B Chr.1_ClpP5 allele is functionally weaker than the B73 allele. We propose that functional redundancy between duplicated paralogous genes is the molecular mechanism for the interaction between vyl and its modifier.
On-Chip Single Particle Spectroscopy (2009)

We demonstrate on-chip optical trapping of micron-sized dielectric spheres using supercontinuum light and silicon nitride waveguides. The broadband source enables scattering spectroscopy to be performed on single particles trapped by a high-confinement waveguide.
Fat Embolism and the Adult Respiratory Distress Syndrome (1974)

In a group of 15 adults with the fat embolism syndrome, the main clinical and laboratory findings were fever, dyspnea, and tachypnea; restlessness and confusion; petechiae in the skin; bilateral diffuse alveolar infiltrates on chest roentgenograms; hypoxemia and hypocalcemia; and lipuria. Treatment included the administration of oxygen, mechanical ventilation, blood transfusion, and high doses of steroids. Despite advances in therapy (particularly administration of oxygen and steroids), the fat embolism syndrome often may be irreversible.
Sequence of a pseudogene in the legumin gene family of pea (Pisum sativumL.) (1985)

A second legumin gene, denoted psi Leg D, has been located on the pea genomic clone lambda Leg 1, approx. 1.3 Kbases 3' of Leg A, in the same orientation. The complete sequence of psi Leg D shows that it is a pseudogene, having two stop codons near the 5' end of its predicted coding sequence, as well as deletions and frame shift errors when compared to Leg A. No transcripts from this gene could be detected in developing pea seeds. Leg A and psi Leg D are homologous over their coding sequences, and partially homologous in the intron sequences and the immediate 5' flanking sequences. Other flanking sequences of the two genes show no significant homology, apart from the presence of polyadenylation signals 3' to both coding sequences. The introns in the two genes occur in corresponding positions in the sequences, but a deletion in psi Leg D affects the 3' boundary of IVS-2. Hybridisation of psi Leg D to pea genomic DNA suggests that it does not represent a hitherto undetected sub-family of legumin genes.
FGF Regulates TGF-β Signaling and Endothelial-to-Mesenchymal Transition via Control of let-7 miRNA Expression (2012)

Maintenance of normal endothelial function is critical to various aspects of blood vessel function, but its regulation is poorly understood. In this study, we show that disruption of baseline fibroblast growth factor (FGF) signaling to the endothelium leads to a dramatic reduction in let-7 miRNA levels that, in turn, increases expression of transforming growth factor (TGF)-β ligands and receptors and activation of TGF-β signaling, leading to endothelial-to-mesenchymal transition (Endo-MT). We also find that Endo-MT is an important driver of neointima formation in a murine transplant arteriopathy model and in rejection of human transplant lesions. The decline in endothelial FGF signaling input is due to the appearance of an FGF resistance state that is characterized by inflammation-dependent reduction in expression and activation of key components of the FGF signaling cascade. These results establish FGF signaling as a critical factor in maintenance of endothelial homeostasis and point to an unexpected role of Endo-MT in vascular pathology.
Differential Regulation of T-cell mediated anti-tumor memory and cross-protection against the same tumor in lungs versus skin (2018)

A major advantage of immunotherapy of cancer is that effector cells induced at one site should be able to kill metastatic cancer cells in other sites or tissues. However, different tissues have unique immune components, and very little is known about whether effector T cells induced against tumors in one tissue can work against the same tumors in other tissues. Here, we used CT26 murine tumor models to investigate anti-tumor immune responses in the skin and lungs and characterized cross-protection between the two tissues. Blockade of the function of Treg cells with anti-CD25 allowed for T cell-dependent rejection of s.c. tumors. When these mice were simultaneously inoculated i.v. with CT26, they also rejected tumors in the lung. Interestingly, in the absence of s.c. tumors, anti-CD25 treatment alone had no effect on lung tumor growth. These observations suggested that T cell-mediated anti-tumor protective immunity induced against s.c. tumors can also protect against lung metastases of the same tumors. In contrast, NKT cell-deficiency in CD1d<sup>-/-</sup> mice conferred significant protection against lung tumors but had no effect on the growth of tumors in the skin, and tumor rejection induced against the CT26 in the lung did not confer protection for the same tumor cells in the skin. Thus, effector cells against the same tumor do not work in all tissues, and the induction site of the effector T cells is critical to control metastasis. Further, the regulation of tumor immunity may be different for the same tumor in different anatomical locations.
Can the current behavior of faulty and fault-free ICs and the impact on diagnosis (2002)

The purpose of this paper is to analyze the current behavior of faulty and fault free integrated circuits (ICs) and its impact on diagnosis. More specifically, we first show that normal sub-threshold current can be modeled by a Gaussian distribution. Then, we investigate faulty IC current variations caused to the load connected to nodes involved in bridging faults. Finally, we propose some modifications to a diagnosis method based on maximum likelihood estimation to deal with these behaviors.
Protection of fast and sensitive preamplifiers (1991)

An extremely simple and inexpensive scheme for the protection of preamplifiers is reported. A protection scheme consisting of seven pairs of back-to-back diodes was used to measure low voltage level (&amp;lt;0.1 V), high frequency (400 MHz) signals with a relatively high gain of ∼35. The protection scheme could limit the voltage surge caused by a 100 kV breakdown in a compressed gas test gap to less than ∼3 V at the input of the preamplifier thereby providing adequate protection.
Effect Of The pH On The Topography And Nanomechanics Of Whey Protein Microgel Particles Investigated By Atomic Force Microscopy (2018)

International audience
Testing and application of diffusion samplers to identify temporal trends in volatile-organic compounds (2001)

TCE), and cw-l,2-dichloroethene (cw-l
Digesting the Elephant -- Experiences with Interactive Production Quality Path Tracing of the Moana Island Scene (2020)

New algorithmic and hardware developments over the past two decades have enabled interactive ray tracing of small to modest sized scenes, and are finding growing popularity in scientific visualization and games. However, interactive ray tracing has not been as widely explored in the context of production film rendering, where challenges due to the complexity of the models and, from a practical standpoint, their unavailability to the wider research community, have posed significant challenges. The recent release of the Disney Moana Island Scene has made one such model available to the community for experimentation. In this paper, we detail the challenges posed by this scene to an interactive ray tracer, and the solutions we have employed and developed to enable interactive path tracing of the scene with full geometric and shading detail, with the goal of providing insight and guidance to other researchers.
Evidence for a recruitment and sequestration mechanism in Huntington'sdisease (1999)

Polyglutamine (polyQ) extension in the coding sequence of mutant huntingtin causes neuronal degeneration associated with the formation of insoluble polyQ aggregates in Huntington's disease. We constructed an array of CAG/CAA triplet repeats, coding for a range of 25-300 glutamine residues, which was used to generate expression constructs with minimal flanking sequence. Normal-length (25 glutamine residues) polyQ did not aggregate when transfected alone. Remarkably, when co-transfected with extended (100-300 glutamine residues) polyQ tracts, normal-length polyQ-containing peptides were trapped in insoluble detergent-resistant aggregates. Aggregates formed in the cytoplasm but were visible in the nucleus only when a strong nuclear localization signal was present. Intermolecular interactions between polyQ tracts mediated the localization of heterogeneous aggregates into the nucleolus by nucleolin protein. Our results suggest that extended polyQ can interact with cellular polyQ-containing proteins, transport them to ectopic cellular locations, and form heterogeneous polyQ aggregates. We provide evidence for a recruitment mechanism for pathogenesis in the polyQ neurodegenerative disorders. In susceptible cells, extended polyQ tracts in huntingtin might interact with and sequester or deplete certain endogenous polyQ-containing cellular proteins.
Cyclotron resonance: From E.O. Lawrence to microchips (1990)

Summary form only given. First used by E.O. Lawrence for the cyclotron particle accelerator, cyclotron resonance motion has had a major impact on many aspects of plasma science, ranging from microwave power generation such as in the magnetron tube, precise mass measurement, isotope separation and plasma heating and processing for microelectronics and other materials applications. Cyclotron motion can also be produced by time-varying electric fields as well as swept frequency excitation. In the plasma processing area. cyclotron resonance is being studied for applications in the production of new materials with unusual and superior properties, for developing new chemical compounds and processes, and for altering and refining materials and surfaces. It has direct applications to semiconductor fabrication, materials synthesis, polymers, anticorrosion coatings, machine tools, metallurgy, electrical and electronics devices, hazardous waste removal, and high-performance ceramics
Global haemostasis and point of care testing (2012)

The evaluation of the coagulation profile has used so far either clotting-based or chromogenic assays with different endpoints. Clotting-based techniques are the most used worldwide, and they certainly are useful for diagnosis of clotting factor deficiencies. However, the information provided is relatively limited, and therefore the individual profile of coagulation is poorly assessed. This is reflected by the weak correlation between the results of these assays and the clinical phenotype. Among the assays that benefited from technological advances, thrombin generation and thromboelastography are probably the most actively investigated, but they require specific instruments and are not fully automated. Their standardisation level is rapidly progressing, and they are progressively entering the clinical scene, with the attempt to provide additional information on the coagulation process and a meaningful clinical correlation. These inherited bleeding disorders frequently require replacement therapy using clotting factor concentrates that increase the plasma level of the missing clotting factor. The classical adjustment of the therapy is mainly based on the measurement of the plasma clotting activity of the protein administered. If one considers that a certain level of thrombin generated would predict clinical efficacy, monitoring of thrombin formation might offer new possibilities to individually predict the bleeding phenotype, select the most adapted therapeutic product and tailor the dose. The same holds true for thromboelastography/thromboelastometry which evaluate fibrin formation as well as clot resistance to fibrinolytic challenge, one step further down in the coagulation process. In this regard, these 2 assays could be seen as complementary in terms of information provided on the coagulation profile at the individual level.