gebhart/patrepeval huggingface dataset:
Using Synthetic Biological Parts and Microbioreactors to Explore the Protein Expression Characteristics of Escherichia coli (2013)

Synthetic biology has developed numerous parts for the precise control of protein expression. However, relatively little is known about the burden these place on a host, or their reliability under varying environmental conditions. To address this, we made use of synthetic transcriptional and translational elements to create a combinatorial library of constructs that modulated expression strength of a green fluorescent protein. Combining this library with a microbioreactor platform, we were able to perform a detailed large-scale assessment of transient expression and growth characteristics of two Escherichia coli strains across several temperatures. This revealed significant differences in the robustness of both strains to differing types of protein expression, and a complex response of transcriptional and translational elements to differing temperatures. This study supports the development of reliable synthetic biological systems capable of working across different hosts and environmental contexts. Plasmids developed during this work have been made publicly available to act as a reference set for future research.
Effect of amikacin, cephalothin, clindamycin and vancomycin on in vitro fibroblast growth (2004)

The effect of four antibiotics (amikacin, clindamycin, cephalothin and vancomycin) was investigated considering that bacterial infection in fibroblasts cultures is a very frequent event. The investigation included the effect of the antibiotics on fibroblast growth and on the activity of the enzyme glucocerebrosidase. The antibiotics were added to the fibroblast cultures and cell growth was evaluated by counting the number of cells and their viability. After cell harvesting, the enzyme activity and content of protein were measured. The results allowed us to conclude that none of the antibiotics affected the cellular number nor the cellular viability. The content of protein decreased when cephalothin and clindamycin were added to the cultures, and glucocerebrosidase was affected in the presence of amikacin. Vancomycin did not interfere with any of the parameters analyzed, so it was chosen to be used in cell cultures to prevent the contamination by gram positive bacteria.
Molecular modelling of D2-like dopamine receptors (1992)

Three-dimensional computer models of the rat D2, D3 and D4 dopamine receptor subtypes have been constructed based on the diffraction co-ordinates for bacteriorhodopsin, another membrane-bound protein containing seven transmembrane domains presumed to be arranged in a similar spatial orientation. Models were assembled by aligning the putative transmembrane domains of the dopamine receptors with those of bacteriorhodopsin using sequence similarities, and then superimposing these modelled alpha-helices on to the bacteriorhodopsin-derived co-ordinates. These models explore the potential hydrogen bonding, electrostatic and stacking interactions within the receptor which may be important for maintaining the conformation of these receptors, and thereby provide target sites for agonist binding. Proposed interactions between the catecholamine ligands and these receptors appear to account for the affinity, although not the specificity, of these agonist ligands for the different dopamine receptor subtypes. Such models will be useful for establishing structure-function relationships between ligands and the dopamine receptors, and may ultimately provide a template for the design of receptor-specific drugs.
Three-dimensional scene reconstruction using multiview images and depth camera (2005)

This paper presents a novel multi-depth map fusion approach for the 3D scene reconstruction. Traditional stereo matching techniques that estimate disparities between two images often produce inaccurate depth map because of occlusion and homogeneous area. On the other hand, Depth map obtained from the depth camera is globally accurate but noisy and provides a limited depth range. In order to compensate pros and cons of these two methods, we propose a depth map fusion method that fuses the multi-depth maps from stereo matching and the depth camera. Using a 3-view camera system that includes a depth camera for the center-view, we first obtain 3-view images and a depth map from the center-view depth camera. Then we calculate camera parameters by camera calibration. Using the camera parameters, we rectify left and right-view images with respect to the center-view image for satisfying the well-known epipolar constraint. Using the center-view image as a reference, we obtain two depth maps by stereo matching between the center-left image pair and the center-right image pair. After preprocessing each depth map, we pick an appropriate depth value for each pixel from the processed depth maps based on the depth reliability. Simulation results obtained by our proposed method showed improvements in some background regions.
The future of fungal susceptibility testing (2014)

The antifungal treatment failures and the emergence of resistant fungal strains have stimulated the need for reproducible and clinically relevant antifungal susceptibility testing (AFST). While the standard reference methods are not intended for routine use, commercial methods are widely used for performing AFST. However, to accelerate AFST and to improve the detection of antifungal resistance, which is the most challenging goal of AFST, novel assays have been developed. Following brief drug exposures of fungal cells, the new antifungal susceptibility end points seem to provide a reliable means of identifying fungal isolates, which harbor mutations that have been associated with antifungal resistance. This article summarizes the recent progress in AFST that is destined to enhance its clinical utility in the near future.
Monolithically integrated semiconductor optical amplifier and electroabsorption modulator with dual-waveguide spot-size converter input (2000)

We have demonstrated a semiconductor optical amplifier and electroabsorption modulator monolithically integrated with a novel dual-waveguide spot-size converter at the input for low-loss coupling to planar lightguide circuit silica waveguides or cleaved single-mode optical fiber. These devices exhibit greater than 10 dB fiber-to-fiber gain, output power of +4 dBm, 3-dB modulation bandwidth of 6 GHz, and modulator extinction ratios of 20 dB dc and 14.4 dB RF for a 2.4-V/sub pp/ drive.
N- and 6-O-Sulfated Heparan Sulfates Mediate Internalization of Coxsackievirus B3 Variant PD into CHO-K1 Cells (2006)

Recently, it was demonstrated that the coxsackievirus B3 variant PD (CVB3 PD) is able to infect coxsackievirus-adenovirus receptor (CAR)-lacking cells by using heparan sulfates (HS) as additional receptors (A. E. Zautner, U. Korner, A. Henke, C. Badorff, and M. Schmidtke, J. Virol. 77:10071-10077, 2003). For this study, competition experiments with growth factors binding to known HS sequences as well as with specifically desulfated heparins were performed with Chinese hamster ovary cells (CHO-K1) to determine the structural requirements of HS for interaction with CVB3. Hepatocyte growth factor interacting with HS sequences containing [IdUA-GlcNSO(3)(6OSO(3))](n), but not basic fibroblast growth factor binding to [HexUA-GlcNSO(3)-HexUA-GlcNSO(3)-IdUA(2OSO(3))](n), was shown to compete effectively with CVB3 PD for cell surface HS. Whereas unmodified heparin and 2-O-desulfated heparin strongly inhibited the CVB3 PD-induced cytopathic effect, the antiviral activity was markedly reduced after N-, O- and 6-O-desulfation of heparin. Taken together, these results indicate that 6-O- and N-sulfation of GlcNAc of HS is crucial for HS interaction with CVB3 PD and that the disaccharide [IdUA-GlcNSO(3)(6OSO(3))](n) is involved in viral binding. Results from experiments with various inhibitors of endocytic pathways suggest that HS-mediated virus internalization is pH dependent. Despite the fact that CVB3 PD initiates infection about four times slower by making use of HS as a receptor than by using CAR, the time required for a complete viral life cycle in Chinese hamster ovary cells was independent of the utilized receptor.
Nicotine induces cell proliferation by -arrestin-mediated activation of Src and Rb-Raf-1 pathways (2006)

Recent studies have shown that nicotine, a component of cigarette smoke, can stimulate the proliferation of non-neuronal cells. While nicotine is not carcinogenic by itself, it has been shown to induce cell proliferation and angiogenesis. Here we find that mitogenic effects of nicotine in non-small cell lung cancers (NSCLCs) are analogous to those of growth factors and involve activation of Src, induction of Rb-Raf-1 interaction, and phosphorylation of Rb. Analysis of human NSCLC tumors show enhanced levels of Rb-Raf-1 complexes compared with adjacent normal tissue. The mitogenic effects of nicotine were mediated via the alpha7-nAChR subunit and resulted in enhanced recruitment of E2F1 and Raf-1 on proliferative promoters in NSCLC cell lines and human lung tumors. Nicotine stimulation of NSCLC cells caused dissociation of Rb from these promoters. Proliferative signaling via nicotinic acetylcholine receptors (nAChRs) required the scaffolding protein beta-arrestin; ablation of beta-arrestin or disruption of the Rb-Raf-1 interaction blocked nicotine-induced proliferation of NSCLCs. Additionally, suppression of beta-arrestin also blocked activation of Src, suppressed levels of phosphorylated ERK, and abrogated Rb-Raf-1 binding in response to nicotine. It appears that nicotine induces cell proliferation by beta-arrestin-mediated activation of the Src and Rb-Raf-1 pathways.
La autonomía y la resolución de conflictos étnicos: los acuerdos de San Andrés Larráinzar (2003)

La autora estudia la respuesta gubernamental a partir de los Acuerdos de San Andres Larrainzar, Chiapas Q996). El articulo se inicia con la ubicacion del conflicto y la negociacion entre rebeldes y gobierno federal. En segundo lugar, analiza los principios y compromisos vertidos en los Acuerdos de San Andres y discute el valor de estos compromisos para tres expresiones historicas y de actualidad teorica sobre la nacion: el fin de la gran narrativa del mestizoismo, la modernidad y el multiculturalismo. En tercer lugar estudia la intensidad que experimento el pais entero y, particularmente, la ciudad de Mexico en marzo de 2001 con la marcha zapatista; y el fracaso de la estrategia de Vicente Fox respecto a la Ley Cocopa para capitalizar politicamente la paz en Chiapas. En la cuarta parte, haciendo referencia al articulo cuarto constitucional, la autora se centra en el debate teorico sobre la autonomia, la autodeterminacion y la libre determinacion. El articulo termina haciendo referencia al tipo de autonomia reglamentado en las leyes de los estados de Oaxaca y Quintana Roo; ademas, apunta algunas reflexiones respecto a la situacion de incertidumbre existente entre la legislatura federal, el EZLN y el gobierno
Support Vector Machine for Behavior-Based Driver Identification System (2010)

We present an intelligent driver identification system to handle vehicle theft based on modeling dynamic human behaviors. We propose to recognize illegitimate drivers through their driving behaviors. Since human driving behaviors belong to a dynamic biometrical feature which is complex and difficult to imitate compared with static features such as passwords and fingerprints, we find that this novel idea of utilizing human dynamic features for enhanced security application is more effective. In this paper, we first describe our experimental platform for collecting and modeling human driving behaviors. Then we compare fast Fourier transform (FFT), principal component analysis (PCA), and independent component analysis (ICA) for data preprocessing. Using machine learning method of support vector machine (SVM), we derive the individual driving behavior model and we then demonstrate the procedure for recognizing different drivers by analyzing the corresponding models. The experimental results of learning algorithms and evaluation are described.
Transglutaminase-mediated processing of fibronectin by endothelial cell monolayers (1994)

We studied the interaction of [125I]fibronectin with human umbilical vein endothelial cells. Endothelial cell monolayers cross-linked [125I]fibronectin which had been preadsorbed to gelatin-coated dishes. The cross-linking of the substrate-immobilized [125I]fibronectin was mediated by cell-associated tissue transglutaminase and occurred more rapidly during the first 30 min after endothelial cell seeding but also continued for several hours after the cells were fully spread. The processing of the [125I]fibronectin was associated with the basolateral surface of the endothelial cell, as demonstrated by the finding that cross-linking did not occur when [125I]fibronectin was presented to the apical surface of confluent monolayers. Transglutaminase activity was not necessary for attachment and spreading of HUVEC on a fibronectin/gelatin matrix. The presence of a nonpeptidyl transglutaminase inactivator rendered the cells more susceptible to detachment by trypsin and destabilized the association of fibronectin with the subendothelial extracellular matrix. Thus, endothelial cells process fibronectin into cross-linked multimers due to the expression of tissue transglutaminase at the basal surface of the cell. This process may serve to stabilize the extracellular matrix and to firmly anchor the cells to the basement membrane.
Sodium butyrate alters erythropoietin glycosylation via multiple mechanisms (2007)

Recombinant human erythropoietin (rHuEPO) produced in a human kidney fibrosarcoma cell line, HT1080, was used as a model to study the effects of sodium butyrate (SB) on protein glycosylation. Treatment with 2 mM SB resulted in complex changes with respect to sugar nucleotide pools including an increase in UDP-Gal and a decrease in UDP-GlcNac. In addition, polylactosamine structures present on rHuEPO increased after SB treatment. To determine if these phenotypic changes correlated with changes in mRNA abundance, we profiled mRNA levels over a 24-h period in the presence or absence of SB using oligonucleotide microarrays. By filtering our data through a functional glycomics gene list associated with the processes of glycan degradation, glycan synthesis, and sugar nucleotide synthesis and transport we identified 26 genes with significantly altered mRNA levels. We were able to correlate the changes in message in six of these genes with measurable phenotypic changes within our system including: neu1, b3gnt6, siat4b, b3gnt1, slc17a5, and galt. Interestingly, for the two genes: cmas and gale, our measurable phenotypic changes did not correlate with changes in mRNA expression. These data demonstrate both the utility and pit falls of coupling biochemical analysis with high throughput oligonucleotide microarrays to predict how changes in cell culture environments will impact glycoprotein oligosaccharide content.
Video Object Detection with an Aligned Spatial-Temporal Memory (2017)

We introduce Spatial-Temporal Memory Networks for video object detection. At its core, a novel Spatial-Temporal Memory module (STMM) serves as the recurrent computation unit to model long-term temporal appearance and motion dynamics. The STMM's design enables full integration of pretrained backbone CNN weights, which we find to be critical for accurate detection. Furthermore, in order to tackle object motion in videos, we propose a novel MatchTrans module to align the spatial-temporal memory from frame to frame. Our method produces state-of-the-art results on the benchmark ImageNet VID dataset, and our ablative studies clearly demonstrate the contribution of our different design choices. We release our code and models at http://fanyix.cs.ucdavis.edu/project/stmn/project.html.
Progress in Understanding The Mechanisms of Action of 5-Aminosalicylic Acid (2000)

Head, Division of Gastroenterology, The Albert M Yunich MD Professor of Medicine, Albany Medical College, Albany, New York, USA Reprint requests and correspondence: Head, Division of Gastroenterology, Albany Medical College MC 48, 47 New Scotland Avenue, Albany, NY, 12208 Received August. 23, 2000; accepted August. 30, 2000
Long-term safety of ustekinumab in patients with moderate-to-severe psoriasis: final results from 5 years of follow-up (2013)

No dose-related or cumulative toxicity was observed with increasing duration of ustekinumab exposure for up to 5 years. Rates of AEs reported in ustekinumab psoriasis trials are generally comparable with those reported for other biologics approved for the treatment of moderate-to-severe psoriasis.
Factors Predictive of Response to Hormone Therapy in Breast Cancer (2008)

Available clinical data are inconclusive to support preferential use of aromatase inhibitors over tamoxifen in progesterone-receptor-negative and HER-2-positive tumors, but it was also clear that lower estrogen receptors, lower progesterone receptors, and positive HER-2 are associated with lower responsiveness to any type of endocrine therapy. Tumors overexpressing HER-2 are endocrine resistant and they require the blockage of the HER-2 pathway in addition to estrogen deprivation. Recent molecular studies have shown that endocrine responsiveness is to a large extent influenced by estrogen-receptor-related pathways. In the future, the key to the correct tailoring of hormone therapy will probably be the ability to subtype estrogen-receptor-positive breast cancer.
Fetal Haemoglobin Production and the Sickle Gene in the Oases of Eastern Saudi Arabia (1978)

Fetal haemoglobin (HbF) levels have been measured in 137 normal (AA) subjects, 109 with the sickle-cell trait (AS) and 237 with sickle-cell anaemia (SS) from the oasis population of Eastern Saudi Arabia. In addition the proportion of F-cells has been estimated in 71 AA, 51 AS and 34 SS subjects. The mean HbF% (and the range of F-cells %) were: AA 0.77 (0.3--18), AS 1.38 (2.3--43) and SS 25.56 (33--98). The distribution of Hb F was always heterocellular. The influence of pregnancy accounts for most of the excess female subjects with sickle-cell trait showing raised Hb F and F-cells. Whilst the normal Arabs and those with sickle-cell trait did not differ from comparable groups of American blacks, both the % Hb F and % F-cells in Saudi Arabian patients with sickle-cell anaemia were much higher than in Blacks. The high Hb F levels in individuals with sickle-cell anaemia are not due to coexistent glucose-6-phosphate dehydrogenase deficiency or alpha-thalassaemia trait, and the Hb F level showed an inverse correlation with the degree of haemolysis. These findings indicate that the unusually elevated levels of Hb F are not due to an associated high frequency of a gene for hetero-cellular hereditary persistence of fetal haemoglobin in the oasis population, but rather from a genetically determined absolute increase in Hb F production related in some way to the SS genotype.
Oleaginous Yeasts: Biochemical Events Related with Lipid Synthesis and Potential Biotechnological Applications (2012)

The last years there has been a significant rise in the number of publications in the international literature that deal with the production of oils and fats deriving from microbial sources (the so called “single cell oils – SCOs”) that could be used as precursors for the synthesis of bio-diesel or as “tailor-made” lipids amenable for the replacement of expensive fatty materials found in the plant or animal kingdom [1,2]. These lipids are produced by the so-called “oleaginous” microorganisms (microorganisms principally belonging to yeasts, fungi and algae and to lesser extent bacteria, capable of storing quantities of lipids higher than 20%, wt/wt, in their dry weight) [1,3-5]. Remarkable differences in biochemical and kinetic level exist between the process of lipid accumulation when glucose or similarly metabolized compounds are used as substrates (“de novo” lipid synthesis) compared with that performed when hydrophobic materials are used as substrates (“ex novo” lipid synthesis). De novo lipid biosynthesis in the oleaginous microorganisms is non-growth associated process, conducted due to change of intra-cellular concentration of various metabolites after nitrogen depletion into the culture medium. Nitrogen exhaustion leads to a rapid decrease of the concentration of cellular AMP, which is further cleaved in order for nitrogen to be offered to the microorganism. Cellular AMP concentration decrease alters the Krebs cycle function; NAD + - (and in various cases NADP + isocitrate) dehydrogenase, allosterically activated by intracellular AMP, loses its activity and the carbon flow, hence, is directed towards the accumulation of intra-mitochondrial citric acid. When the concentration of citric acid inside the mitochondria becomes higher than a critical value, it is secreted inside the cytoplasm. Then, citric acid is cleaved by ATP-citrate lyase, enzyme-key showing the oleaginous character of the microorganisms, into acetyl-CoA and oxaloacetate and acetyl-CoA, by virtue of the action of fatty acid synthetase generates cellular fatty acids and subsequently triacylglycerols (TAGs), that are the most common form of lipophilic compounds found in the oleaginous microorganisms [1,3-5]. In the non-lipid producing microorganisms, nitrogen exhaustions provokes secretion of the previously hyper-synthesized citric acid into the growth medium (case of the fungus Aspergillus niger and many of the strains of the yeast Yarrowia lipolytica) or results in a block in the level of 6-phosphofructokinase (with mechanisms similar to the ones related with the decrease of activity of NAD
Serological response of melanoma patients to vaccines prepared from VSV lysates of autologous and allogeneic cultured melanoma cells (1985)

Melanoma patients were vaccinated with cell-free lysates prepared from vesicular stomatitis virus (VSV)-infected cultured autologous and allogeneic melanoma cells. Eleven patients received vaccines produced from the melanoma cell line SK-MEL-13. This cell line, derived from the melanoma of Patient AH, expresses a differentiation antigen (initially defined by autologous antibody) that is restricted to melanomas and other cells of neural crest origin (an example of a Class 2 melanoma antigen). Thirteen patients received vaccines prepared from autologous melanoma cells, the only known source of autologous unique (Class 1) melanoma antigens. VSV lysates were used for vaccination because VSV infection of tumor cells has been shown to augment the immunogenicity of tumor antigens. All patients but one vaccinated with VSV lysates of autologous melanoma cells developed antibodies against VSV, and all patients vaccinated with VSV lysates of SK-MEL-13 developed antibodies against HLA-related antigens. Antibodies against a Class 1 (unique) melanoma antigen were detected in only one case, and antibodies against Class 2 (shared) melanoma antigens were not found in any of the patients. The authors conclude that VSV lysates of melanoma cells are not effective in increasing the serologic response of melanoma patients to Class 1 or 2 melanoma antigens.