gebhart/patrepeval huggingface dataset:
Molecular Characterization of True and Ectopic Gene Targeting Events at the Acetolactate Synthase Gene in Arabidopsis (2006)

Precise modification of plant genomes via gene targeting (GT) is important for the study of gene function in vivo. A reliable GT system using the protoporphyrinogen oxidase (PPO) gene in Arabidopsis was reported 4 years ago; however, there are no subsequent successful reports of GT in Arabidopsis. A previous study showed ectopic gene targeting (EGT) of the endogenous gene in two-thirds of GT plants, which was an obstacle to efficient true gene targeting (TGT). The endogenous acetolactate synthase (ALS) gene is involved in the biosynthesis of branched chain amino acids in plants and is the site of action of several herbicides. To confirm the generality of the GT system in Arabidopsis, and to characterize the EGT event in plants in detail, we converted ALS from a herbicide (imazapyr)-susceptible to a -resistant form by GT. We obtained two imazapyr-resistant plants following GT. One of the targeting events was TGT while the other was EGT. After detailed Southern blotting, PCR and nucleotide sequence analysis of the EGT plant, we determined the genomic position and structure of the ectopically targeted site. Based on our findings, we discuss the possible mechanisms of EGT in plants.
Oxidative metabolism in muscle (1997)

Oxidative metabolism is the dominant source of energy for skeletal muscle. Near-infrared spectroscopy allows the non-invasive measurement of local oxygenation, blood flow and oxygen consumption. Although several muscle studies have been made using various near-infrared optical techniques, it is still difficult to interpret the local muscle metabolism properly. The main findings of near-infrared spectroscopy muscle studies in human physiology and clinical medicine are summarized. The advantages and problems of near-infrared spectroscopy measurements, in resting and exercising skeletal muscles studies, are discussed through some representative examples.
Xylitol production is increased by expression of codon-optimized Neurospora crassa xylose reductase gene in Candida tropicalis (2011)

Xylose reductase (XR) is the first enzyme in D: -xylose metabolism, catalyzing the reduction of D: -xylose to xylitol. Formation of XR in the yeast Candida tropicalis is significantly repressed in cells grown on medium that contains glucose as carbon and energy source, because of the repressive effect of glucose. This is one reason why glucose is not a suitable co-substrate for cell growth in industrial xylitol production. XR from the ascomycete Neurospora crassa (NcXR) has high catalytic efficiency; however, NcXR is not expressed in C. tropicalis because of difference in codon usage between the two species. In this study, NcXR codons were changed to those preferred in C. tropicalis. This codon-optimized NcXR gene (termed NXRG) was placed under control of a constitutive glyceraldehyde-3-phosphate dehydrogenase (GAPDH) promoter derived from C. tropicalis, and integrated into the genome of xylitol dehydrogenase gene (XYL2)-disrupted C. tropicalis. High expression level of NXRG was confirmed by determining XR activity in cells grown on glucose medium. The resulting recombinant strain, LNG2, showed high XR activity (2.86 U (mg of protein)(-1)), whereas parent strain BSXDH-3 showed no activity. In xylitol fermentation using glucose as a co-substrate with xylose, LNG2 showed xylitol production rate 1.44 g L(-1) h(-1) and xylitol yield of 96% at 44 h, which were 73 and 62%, respectively, higher than corresponding values for BSXDH-3 (rate 0.83 g L(-1) h(-1); yield 59%).
An accurate method for determination of receptor-ligand and enzyme-inhibitor dissociation constants from displacement curves. (1987)

Receptor-ligand dissociation constants are usually calculated from the displacement curve of a radioactively labeled ligand bound to the receptor. The formula used is restricted to cases in which the concentration of receptor is negligible compared to the concentration of both the displacing ligand and the radioactive ligand used. In this study, we rigorously derive a simple equation that can be used for calculating receptor-ligand dissociation constants for any set of experimental conditions. A linearized form of this equation provides a convenient plot from which the dissociation constant of the displacing ligand can be directly obtained. The plot is also a test for the competitive mode of binding. This exact equation now allows us to estimate the error incurred by the conventionally used equations. Similarly, we show that for competitive inhibition in enzymology, one can derive the analogous formula. Our new formula is free of the usual restrictions--namely, that the enzyme concentration is very small compared to the concentration of both the substrate and the inhibitor. It may therefore be applied to any set of experimental conditions.
Solid dispersions: a review. (2009)

Solid dispersions have attracted considerable interest as an efficient means of improving the dissolution rate and hence the bioavailability of a range of hydrophobic drugs. This article reviews the various preparation techniques for solid dispersion and compiles some of the recent technology transfers. The different types of solid dispersions based on the molecular arrangement have been highlighted. Some of the practical aspects to be considered for the preparation of solid dispersions, such as selection of carrier and methods of physicochemical characterization, along with an insight into the molecular arrangement of drugs in solid dispersions are also discussed. Finally, an in-depth rationale for limited commercialization of solid dispersions and recent revival has been considered.
Lung tissue remodeling in the acute respiratory distress syndrome (2003)

Acute respiratory distress syndrome (ARDS) is characterized by diffuse alveolar damage, and evolves progressively with three phases: exsudative, fibroproliferative, and fibrotic. In the exudative phase, there are interstitial and alveolar edemas with hyaline membrane. The fibroproliferative phase is characterized by exudate organization and fibroelastogenesis. There is proliferation of type II pneumocytes to cover the damaged epithelial surface, followed by differentiation into type I pneumocytes. The fibroproliferative phase starts early, and its severity is related to the patient’s prognosis. The alterations observed in the phenotype of the pulmonary parenchyma cells steer the tissue remodeling towards either progressive fibrosis or the restoration of normal alveolar architecture. The fibrotic phase is characterized by abnormal and excessive deposition of extracellular matrix proteins, mainly collagen. The dynamic control of collagen deposition and degradation is regulated by metalloproteinases and their tissular regulators. The deposition of proteoglycans in the extracellular matrix of ARDS patients needs better study. The regulation of extracellular matrix remodeling, in normal conditions or in several pulmonary diseases, such as ARDS, results from a complex mechanism that integrate the transcription of elements that destroy the matrix protein and produce activation/inhibition of several cellular types of lung tissue. This review article will analyze the ECM organization in ARDS, the different pulmonary parenchyma remodeling mechanisms, and the role of cytokines in the regulation of the different matrix components during the remodeling process.
Vitamin D and Vitamin D Analogs as Cancer Chemopreventive Agents (2003)

Epidemiologic studies have associated vitamin D, attained through nutrition and sun exposure, with reduced cancer risk. Although dose-limiting hypercalcemia has limited the use of natural vitamin D in cancer prevention, several promising new synthetic vitamin D analogs (deltanoids) are under development. Examples are KH-1060, EB-1089, 1alpha-hydroxyvitamin D5, vitamin D2, and QW-1624F2-2. Clinical targets for deltanoids include colon, prostate, and breast. Studies to elucidate the molecular mechanisms underlying the observed efficacy of deltanoids are ongoing. The vitamin D receptor, a steroid/thyroid receptor superfamily member, appears to control most deltanoid effects on proliferation, apoptosis, differentiation, and angiogenesis.
Identification of a General O-linked Protein Glycosylation System in Acinetobacter baumannii and Its Role in Virulence and Biofilm Formation (2012)

Acinetobacter baumannii is an emerging cause of nosocomial infections. The isolation of strains resistant to multiple antibiotics is increasing at alarming rates. Although A. baumannii is considered as one of the more threatening "superbugs" for our healthcare system, little is known about the factors contributing to its pathogenesis. In this work we show that A. baumannii ATCC 17978 possesses an O-glycosylation system responsible for the glycosylation of multiple proteins. 2D-DIGE and mass spectrometry methods identified seven A. baumannii glycoproteins, of yet unknown function. The glycan structure was determined using a combination of MS and NMR techniques and consists of a branched pentasaccharide containing N-acetylgalactosamine, glucose, galactose, N-acetylglucosamine, and a derivative of glucuronic acid. A glycosylation deficient strain was generated by homologous recombination. This strain did not show any growth defects, but exhibited a severely diminished capacity to generate biofilms. Disruption of the glycosylation machinery also resulted in reduced virulence in two infection models, the amoebae Dictyostelium discoideum and the larvae of the insect Galleria mellonella, and reduced in vivo fitness in a mouse model of peritoneal sepsis. Despite A. baumannii genome plasticity, the O-glycosylation machinery appears to be present in all clinical isolates tested as well as in all of the genomes sequenced. This suggests the existence of a strong evolutionary pressure to retain this system. These results together indicate that O-glycosylation in A. baumannii is required for full virulence and therefore represents a novel target for the development of new antibiotics.
Functional Consequences of Interactions between Pax9 and Msx1 Genes in Normal and Abnormal Tooth Development (2006)

Pax9 and Msx1 encode transcription factors that are known to be essential for the switch in odontogenic potential from the epithelium to the mesenchyme. Multiple lines of evidence suggest that these molecules play an important role in the maintenance of mesenchymal Bmp4 expression, which ultimately drives morphogenesis of the dental organ. Here we demonstrate that Pax9 is able to directly regulate Msx1 expression and interact with Msx1 at the protein level to enhance its ability to transactivate Msx1 and Bmp4 expression during tooth development. In addition, we tested how a missense mutation (T62C) in the paired domain of PAX9 that is responsible for human tooth agenesis (1) affects its functions. Our data indicate that although the mutant Pax9 protein (L21P) can bind to the Msx1 protein, it fails to transactivate the Msx1 and Bmp4 promoter, presumably because of its inability to bind cognate paired domain recognition sequences. In addition, synergistic transcriptional activation of the Bmp4 promoter was lost with coexpression of mutant Pax9 and wild-type Msx1. This suggests that Pax9 is critical for the regulation of Bmp4 expression through its paired domain rather than Msx1. Our findings demonstrate the partnership of Pax9 and Msx1 in a signaling pathway that involves Bmp4. Furthermore, the regulation of Bmp4 expression by the interaction of Pax9 with Msx1 at the level of transcription and through formation of a protein complex determines the fate of the transition from bud to cap stage during tooth development.
Vitamin E Reduces Cisplatin Ototoxicity (2004)

Vitamin E appears to have a protective effect against cisplatin ototoxicity.
Meningococcal infections. 2. Field trial of group C meningococcal polysaccharide vaccine in 1969-70. (1971)

A second large-scale field trial of group C meningococcal polysaccharide vaccine in US Army recruits confirmed the efficacy and safety of the vaccine. When the results of all studies over a 2-year period were combined, the reduction in group-specific disease rates was 89.5%.
Soluble activin receptor type IIB treatment does not cause fat loss in mice with diet‐induced obesity (2011)

The growth factor myostatin (MSTN) negatively regulates skeletal muscle mass. Mstn gene deletion in mice causes increased muscle mass, reduced adiposity and resistance to genetic or diet-induced obesity (DIO). Pharmacologic MSTN inhibition in mice also causes increased muscle mass and resistance to DIO. To test whether MSTN inhibition causes weight loss in mice that are already obese, we inhibited MSTN in mice fed a high-fat diet (HFD). Mice were fed a diet containing 60% kcal from fat for 12 weeks followed by treatment with a soluble MSTN receptor derived from the activin receptor type IIB extracellular domain. During the next 12 weeks of soluble receptor treatment and HFD feeding, lean mass increased without a loss of adipose mass. Glucose metabolism was also similar between groups. Our results suggest that MSTN inhibition may be ineffective at inducing weight loss in obese patients.
The Prevalence and Role of Hemoglobin Variants in Biometric Screening of a Multiethnic Population (2017)

This study represents one of the largest epidemiologic investigations into the prevalence of Hb variants in a North American metropolitan, multiethnic workforce and their dependents and reinforces the importance of method selection in populations with Hb variants.
Bacterial fitness and plasmid loss: the importance of culture conditions and plasmid size (1998)

Several pBluescript-derived plasmids of various sizes were constructed to study the effects of multicopy plasmid size on bacterial fitness and plasmid loss. Transformed and untransformed bacterial clones were grown in media with or without ampicillin. Bacterial fitness (measured by growth rate), plasmid presence or absence, and plasmid copy number were assessed during successive subculturings. In selective media (minimal medium or Luria Broth plus ampicillin), the clone transformed with the largest plasmid (pBluescript with a 9000-bp insert) had a significantly longer lag phase than all other clones. In nonselective media the rate of plasmid loss during successive subculturings was greatest in the clone with the largest insert. The clone with the largest insert displayed a lower plasmid copy number than clones with a small insert or no insert at all. Plasmid loss in the form of segregational instability and plasmid copy number reduction in nonselective environments are important to the understanding of the evolution of the bacteria-plasmid associations and the appreciation of the potential for altering the genetic properties of a clone maintained or subcultured on a standard medium.
Co-expression of cytokine and suicide genes to enhance the activity and safety of tumor-specific cytotoxic T lymphocytes (2007)

The antitumor effect of adoptively transferred tumor-specific cytotoxic T lymphocytes (CTLs) is impaired by the limited capacity of these cells to expand within the tumor microenvironment. Administration of interleukin 2 (IL-2) has been used to overcome this limitation, but the systemic toxicity and the expansion of unwanted cells, including regulatory T cells, limit the clinical value of this strategy. To discover whether transgenic expression of lymphokines by the CTLs themselves might overcome these limitations, we evaluated the effects of transgenic expression of IL-2 and IL-15 in our model of Epstein Barr Virus-specific CTLs (EBV-CTLs). We found that transgenic expression of IL-2 or IL-15 increased the expansion of EBV-CTLs both in vitro and in vivo in a severe combined immunodeficiency disease (SCID) mouse model and enhanced antitumor activity. Although the proliferation of these cytokine genes transduced CTLs remained strictly antigen dependent, clinical application of this approach likely requires the inclusion of a suicide gene to deal with the potential development of T-cell mutants with autonomous growth. We found that the incorporation of an inducible caspase-9 suicide gene allowed efficient elimination of transgenic CTLs after exposure to a chemical inducer of dimerization, thereby increasing the safety and feasibility of the approach.
Functional dyspepsia (2011)

There is gradual progress in our understanding of the symptom pattern, impact and pathophysiology of functional dyspepsia. The areas of recent advances including the recognition of low-grade duodenal inflammation, central nervous system processing and the exploration of novel pharmacotherapeutic approaches are summarized in this review.
Proteins encoded by Agrobacterium tumefaciens Ti plasmid DNA (T-DNA) in crown gall tumors (1980)

In order to detect proteins that may be produced in crown gall tumors as a result of expression of incorporated Agrobacterium tumefaciens Ti plasmid DNA (T-DNA), we have isolated mRNA complementary to T-DNA and translated this in a protein-synthesizing system derived from wheat germ. mRNA prepared from cultured E1 tumor from Nicotiana tabacum hybridized with HindIII fragment 1 sequences of T-DNA immobilized on cellulose nitrate filters. Two proteins of 30,000 and 16,500 M(r) were produced when this selected RNA was released and translated. Other tumor lines from N. tabacum were investigated, and a protein of slightly less than 30,000 M(r) was encoded by HindIII fragment 1 sequences of 15955/01 tumor. No products were observed for 15955/1 tumor line, which differs from E1/B6-806 and 15955/01 in that it does not produce octopine. mRNA species of each of the tumor lines hybridized to Bst I fragment 8 sequences of T-DNA and produced a common protein of 15,000 M(r). Because this protein is derived from the region of the T-DNA that is conserved in octopine- and nopaline-type crown gall tumors, it may play a role in oncogenicity.
Traffic sign recognition in noisy outdoor scenes (2002)

This paper presents a noise-tolerant traffic sign recognition method by using both color and shape attributes. First a discriminant analysis is carried out to obtain the color coordinate system giving the best separation between traffic signs and other objects in the scene. Then a recognition algorithm is devised by cascading three modules: an ART2 neural network module to perform color segmentation, a log-polar-exponential grid and Fourier transformation module to extract invariant traffic sign signatures, a backpropagation neural network module to classify such signatures. The performance of this method is evaluated by examining the effect of various noise sources, which may occur in actual outdoor scenes, on the recognition rate. The results obtained indicate the noise-tolerance of the developed methodology.
Hydrocarbon oxidation with iodosylbenzene catalysed by the sterically hindered iron(III) 5-(pentafluorophenyl)-10,15,20-tris(2,6-dichlorophenyl)porphyrin in homogeneous solution and covalently bound to silica (1998)

Iron(III) 5-(pentafluorophenyl)-10,15,20-tris(2,6-dichlorophenyl)porphyrin has been synthesised and used to catalyse hydrocarbon oxidation by iodosylbenzene. In homogeneous solution it is shown to be a stable and effective catalyst for alkene epoxidation and alkane hydroxylation with a selectivity and reactivity closer to iron(III) tetrakis(pentafluorophenyl)porphyrin than to iron(III) tetrakis(2,6-dichlorophenyl)porphyrin. The new sterically hindered iron porphyrin has also been covalently bound, by nucleophilic aromatic substitution to aminopropylated silica. The resulting heterogenised catalyst is also stable towards oxidation but is less reactive than its homogeneous analogue.
Radar Sensing Using Ultra Wideband – Design and Implementation (2012)

Ultra-wideband (UWB) has received significant attention for applications in target positioning and wireless communications recently. The extremely short pulses in turn generate a very wide bandwidth and offer several advantages, such as large throughput, covertness, robustness to jamming, lower power, and coexistence with current radio services. UWB not only can transmit a huge amount of data over a short distance at very low power, but also has the capability to pass through physical objects that tend to reflect signals with narrow bandwidth.
Controlled Synthesis of Cell-Laden Microgels by Radical-Free Gelation in Droplet Microfluidics (2012)

Micrometer-sized hydrogel particles that contain living cells can be fabricated with exquisite control through the use of droplet-based microfluidics and bioinert polymers such as polyethyleneglycol (PEG) and hyperbranched polyglycerol (hPG). However, in existing techniques, the microgel gelation is often achieved through harmful reactions with free radicals. This is detrimental for the viability of the encapsulated cells. To overcome this limitation, we present a technique that combines droplet microfluidic templating with bio-orthogonal thiol-ene click reactions to fabricate monodisperse, cell-laden microgel particles. The gelation of these microgels is achieved via the nucleophilic Michael addition of dithiolated PEG macro-cross-linkers to acrylated hPG building blocks and does not require any initiator. We systematically vary the microgel properties through the use of PEG linkers with different molecular weights along with different concentrations of macromonomers to investigate the influence of these parameters on the viability and proliferation of encapsulated yeast cells. We also demonstrate the encapsulation of mammalian cells including fibroblasts and lymphoblasts.
Nested antiresonant nodeless hollow core fiber (2014)

We propose a novel hollow core fiber design based on nested and non-touching antiresonant tube elements arranged around a central core. We demonstrate through numerical simulations that such a design can achieve considerably lower loss than other state-of-the-art hollow fibers. By adding additional pairs of coherently reflecting surfaces without introducing nodes, the Hollow Core Nested Antiresonant Nodeless Fiber (HC-NANF) can achieve values of confinement loss similar or lower than that of its already low surface scattering loss, while maintaining multiple and octave-wide antiresonant windows of operation. As a result, the HC-NANF can in principle reach a total value of loss - including leakage, surface scattering and bend contributions - that is lower than that of conventional solid fibers. Besides, through resonant out-coupling of high order modes they can be made to behave as effectively single mode fibers.
Syndecans, cell surface heparan sulfate proteoglycans, are induced by a proline-rich antimicrobial peptide from wounds. (1994)

Cell surface heparan sulfate proteoglycans, such as the syndecans, are required for cellular responses to heparin-binding growth factors and extracellular matrix components. Expression of syndecan-1 and -4 is induced in mesenchymal cells during wound repair in the mouse, consistent with a role for syndecans in regulating cell proliferation and migration in response to these effectors. Here we show that wound fluid contains inductive activity that mimics the in vivo induction in time of appearance, specificity for mesenchymal cells, and selectivity for syndecan-1 and -4. We have purified and synthesized a 4.8-kDa proline-rich protein from wound fluid that reproduces this induction of syndecan-1 and -4 in cultured cells. This peptide, identical to the antibacterial peptide PR-39, is released into the wound by the cellular infiltrate and induces syndecan expression at the same peptide concentrations that lyse bacteria. These results indicate that wounds contain a multifunctional protein that induces mammalian cells to express cell surface heparan sulfate proteoglycans as part of the wound repair process and that kills bacteria as part of a nonimmune defense mechanism.