gebhart/patrepeval huggingface dataset:
Genomics reveals traces of fungal phenylpropanoid-flavonoid metabolic pathway in the f ilamentous fungus Aspergillus oryzae. (2005)

Fungal secondary metabolites constitute a wide variety of compounds which either play a vital role in agricultural, pharmaceutical and industrial contexts, or have devastating effects on agriculture, animal and human affairs by virtue of their toxigenicity. Owing to their beneficial and deleterious characteristics, these complex compounds and the genes responsible for their synthesis have been the subjects of extensive investigation by microbiologists and pharmacologists. A majority of the fungal secondary metabolic genes are classified as type I polyketide synthases (PKS) which are often clustered with other secondary metabolism related genes. In this review we discuss on the significance of our recent discovery of chalcone synthase (CHS) genes belonging to the type III PKS superfamily in an industrially important fungus, Aspergillus oryzae. CHS genes are known to play a vital role in the biosynthesis of flavonoids in plants. A comparative genome analyses revealed the unique character of A. oryzae with four CHS-like genes (csyA, csyB, csyC and csyD) amongst other Aspergilli (Aspergillus nidulans and Aspergillus fumigatus) which contained none of the CHS-like genes. Some other fungi such as Neurospora crassa, Fusarium graminearum, Magnaporthe grisea, Podospora anserina and Phanerochaete chrysosporium also contained putative type III PKSs, with a phylogenic distinction from bacteria and plants. The enzymatically active nature of these newly discovered homologues is expected owing to the conservation in the catalytic residues across the different species of plants and fungi, and also by the fact that a majority of these genes (csyA, csyB and csyD) were expressed in A. oryzae. While this finding brings filamentous fungi closer to plants and bacteria which until recently were the only ones considered to possess the type III PKSs, the presence of putative genes encoding other principal enzymes involved in the phenylpropanoid and flavonoid biosynthesis (viz., phenylalanine ammonia-lyase, cinnamic acid hydroxylase and p-coumarate CoA ligase) in the A. oryzae genome undoubtedly prove the extent of its metabolic diversity. Since many of these genes have not been identified earlier, knowledge on their corresponding products or activities remain undeciphered. In future, it is anticipated that these enzymes may be reasonable targets for metabolic engineering in fungi to produce agriculturally and nutritionally important metabolites.
Nomadic radio (1999)

Mobile workers need seamless access to communication and information services on portable devices. However current solutions overwhelm users with intrusive and ambiguous notifications. In this paper, we describe scaleable auditory techniques and a contextual notification model for providing timely information, while minimizing interruptions. Users actions influence local adaptation in the model. These techniques are demonstrated in Nomadic Radio, an audio-only wearable computing platform.
Cooperative Ideas about Cooperative Strategies (2004)

There is little precedence for rational design of pharmacological strategies that utilize multiple sites of action. However, such pharmaceutical and nutraceutical multitasking may be just the ticket to combat the multifactorial nature of neurodegeneration. This paper summarizes the discussion on several cooperative ideas, particularly on intellectual property issue, current research funding status, and limitations of public and private funding.
Solubility, chemical and photochemical stability of curcumin in surfactant solutions. Studies of curcumin and curcuminoids, XXVIII. (2002)

The natural compound curcumin was incorporated into various micellar systems in order to improve the water solubility and the hydrolytic and photochemical stability. The presence of micellar structures resulted in an increase in water solubility at pH 5 by a factor of at least 10(5). The hydrolytic stability of curcumin under alkaline conditions was strongly improved by incorporation into micelles while the photodecomposition rate was increased compared to curcumin in hydrogen bonding organic solvents or aqueous solutions. The ability of curcumin to act as a photosensitizer was dependent on the type of micelles and pH of the medium.
Multiple affinity domains for the detection, purification and immobilization of recombinant proteins (1996)

Affinity systems based on specific molecular recognition are valuable tools for detection, purification and immobilization of recombinant proteins. Here, novel multipartite affinity fusion vectors were assembled and investigated to allow flexible binding and elution conditions. The rationale for the assembly of different combinations of affinity domains was to take advantage of the wide variety of molecular interactions of these domains for purification, solubilization, detection and immobilization. In total, seven different affinity tags representing five different types of tag-ligand interactions were studied: (i) monoclonal antibodies-peptides (T7-tag and FLAG peptide); (ii) streptavidin-peptide (Strep-tag); (iii) hexahistidyl-metal ions (His6-tag; (iv) bacterial receptors-serum proteins (staphyloccal protein A-Fc and streptococcal protein G-serum albumin); (v) streptavidin-biotin (in vivo biotinylated peptide). Selected tags were evaluated for the production and purification of Escherichia coli DNA polymerase I (Klenow fragment). On the basis of the results, a vector (pAff2c) was assembled using a novel combination of affinity domains: (i) an in vivo biotinylated peptide; (ii) a His6 sequence, and (iii) a highly soluble serum albumin binding region. Using these three affinities, a wide variety of conditions can be employed for both the binding and the elution steps.
Whispering-gallery-mode resonators as frequency references I Fundamental limitations (2007)

We discuss thermodynamic as well as quantum limitations of the stability of resonance frequencies of solid-state whispering-gallery-mode resonators. We show that the relative frequency stability of a millimeter scale resonator can reach one part per 10−12 per 1 s integration time.
Antibiotics, obesity and the link to microbes - what are we doing to our children? (2016)

Exposure to antibiotics exerts a devastating impact on the intestinal microbial community. Epidemiological studies have provided evidence indicating that early or repeated childhood exposure to antibiotics is associated with increased risk of overweight later in childhood but the causal role of this exposure in obesity development is not clear. However, data from studies conducted using experimental animal models indicate that antibiotic-induced changes in the gut microbiota influence host metabolism and lead to fat accumulation. The intestinal microbiota perturbation caused by antibiotic exposure in the perinatal period appears to program the host to an obesity-prone metabolic phenotype, which persists after the antibiotics have been discontinued and the gut microbiota has recovered. These observations may have serious implications in the clinical setting, since a substantial number of human infants are subjected to antibiotic treatment through the mother during delivery or directly in the immediate neonatal period. The clinical significance of these exposures remains unknown. Prudent use of antibiotics is paramount not only to reduce the propagation of antibiotic-resistant organisms but also to minimize the potentially detrimental long-term metabolic consequences of early antibiotic exposure. Improved means of reliably detecting neonates with bacterial infection would reduce the need for empirical antibiotic exposure initiated based on nonspecific symptoms and signs or risk factors. Finally, means to support healthy microbial contact in neonates and infants requiring antibiotic treatment are needed.
Curb detection and tracking using 3D-LIDAR scanner (2012)

This paper presents a novel road curb detection method using 3D-LIDAR scanner. To detect the curbs, the ground points are separated from the pointcloud first. Then the candidate curb points are selected using three spatial cues: the elevation difference, gradient value and normal orientation. Afterwards the false curb points caused by obstacles are removed using the short-term memory technique. Next the curbs are fitted using the parabola model. Finally, the particle filter is used to smooth the curb detection result. The proposed approach was evaluated on a dataset collected by an autonomous ground vehicle driving around the Ford Research campus and downtown Dearborn. Our curb detection results are accurate and robust despite variations introduced by moving vehicles and pedestrians, static obstacles, road curvature changes, etc.
Saccharomyces boulardiidecreases inflammation and intestinal colonization byCandida albicansin a mouse model of chemically-induced colitis (2007)

The present study was designed to investigate the effects of Saccharomyces boulardii on inflammation and intestinal colonization by Candida albicans in a BALB/c mouse model of colitis that had been induced by dextran-sulfate-sodium (DSS). Colonization with C. albicans was established by oral gavage with a 200 microL suspension of 10(7) yeast cells. A 1.5% solution of DSS was administered in drinking water 1 h after C. albicans oral challenge, while 10(7) cells of S. boulardii was inoculated daily by oral gavage for 1 week. Faeces were collected daily for 2 weeks. Seven groups of mice consisting of those that were administered either C. albicans or S. boulardii or both were sacrificed after 14 days and samples of the colon were taken for histological scoring and real-time PCR (RT-PCR) analysis of inflammatory cytokines and toll-like receptors (TLRs). Compared to control animals that did not receive DSS, the number of C. albicans colonies recovered from faeces was significantly greater in mice receiving DSS. In contrast, the colony forming units (CFUs) of C. albicans were greatly reduced in mice receiving S. boulardii. The administration of this yeast decreased the severity of DSS-induced clinical scores and histological inflammation. At the mRNA expression level, an increase in TLR2 and TLR4 resulting from the presence of S. boulardii was associated with a reduction in the inflammatory cytokines TNFalpha and INFgamma. In mice receiving DSS and C. albicans, TLR4 was over-expressed by stimulation with both yeasts, but TLR2 and TNFalpha, which were increased by the administration of C. albicans alone, were decreased in the presence of S. boulardii. These results indicate that S. boulardii decreased inflammation and C. albicans colonization in this BALB/c mouse model of colitis.
A Mathematical Model for a Rolling Mill Thickness Control System and Its Digital Simulation (1996)

A mathematical model for a rolling mill thickness control system is given in block diagram. The system includes a hydraulic servo-control sub-system and a mechanical sub-system as a connection of multiple mass-spring-friction systems. As it is difficult and complex to achieve a transfer function for the whole system, a block diagram oriented digital simulation program is coded. The mathematical model is described in a diagram composed of 23 connected typical blocks. The mathematical model in block diagram is transferred into an equation of state for the closed-loop control system, which is solved by the fourth-order Runge-Kutta method. An actually rolled thickness-varying strip compares closely with computer simulation results. From the simulation, the basic characteristics of the mill thickness control system and the causes of thickness-varying strip errors are analysed, then suggestions to improve the thickness accuracy are provided.
Activation of the tumor necrosis factor-alpha system in the liver in chronic hepatitis B virus infection. (1996)

To determine the status of the tumor necrosis factor-alpha (TNFalpha) system in the liver in chronic hepatitis B virus (HBV) infection, hepatic expression of TNFalpha, its two receptors (TNFR-A, TNFR-B), HLA class I antigens (HLA-I), and HBV core antigen (HBcAg) were studied by immunohistochemistry in 24 patients with chronic HBV infection. TNFalpha was detected exclusively in the infiltrating mononuclear cells (MNC) in 19 of 24 patients. The expression of TNFalpha in infiltrating MNC correlated with serum markers of HBV replication and liver histology. TNFR were detected in hepatocytes, sinusoidal cells, and infiltrating MNC. The expression of TNFR correlated with liver histology (p < 0.01) but had no bearing on viral replication. There was a parallel expression of TNFalpha and TNFR (p < 0.01). Hepatocytic expression of HLA-I was increased, and this was related to liver histology but not with TNF alpha nor TNFR. These data indicate that the TNFalpha system is activated in the liver in chronic HBV infection.
Regulation of Ca2+/calmodulin-dependent protein kinase II by Ca2+/calmodulin-independent autophosphorylation. (1988)

The autophosphorylation of Ca2+/calmodulin-dependent protein kinase II (CaM-KII) results in the generation of kinase activity that is largely Ca2+/CaM-independent. We report that continued Ca2+/CaM-independent autophosphorylation of CaM-KII results in the generation of distinct phosphopeptides as identified by high performance liquid chromatography and enzymatic properties that are different than those observed for Ca2+/CaM-dependent autophosphorylation. These Ca2+/CaM-independent properties include (a) increased catalytic activity, (b) higher substrate affinity for the phosphorylation of synapsin I, and (c) decreased CaM-binding to both CaM-KII subunits as analyzed by gel overlays. Our results indicate that the autophosphorylation of only one subunit per holoenzyme is required to generate the Ca2+/CaM-independent CaM-KII. We suggest a two-step process by which autophosphorylation regulates CaM-KII. Step I requires Ca2+/CaM and underlies initial kinase activation. Step II involves continued autophosphorylation of the Ca2+/CaM-independent kinase and results in increased affinity for its substrate synapsin I and decreased affinity for calmodulin. These results indicate a complex mechanism through which autophosphorylation of CaM-KII may regulate its activity in response to transient fluctuations in intracellular calcium.
Molecular cloning of brevican, a novel brain proteoglycan of the aggrecan/versican family (1994)

To clone novel brain proteoglycans, we employed a strategy based on polyclonal antisera that recognize multiple proteoglycan core proteins. By using an antiserum raised against a fraction enriched for proteoglycans, we isolated three groups of cDNAs from a bovine brain lambda gt11 library. One of the cDNA groups has been fully sequenced and shown to encode a novel proteoglycan core protein of the aggrecan/versican family. This proteoglycan, named brevican, carries chondroitin sulfate chains, and, like other members of the family, contains a hyaluronic acid-binding domain in its N-terminal region, an epidermal growth factor-like repeat, a lectin-like and a complement regulatory protein-like domains in its C-terminal region. In contrast, the central region of brevican is much shorter than that of aggrecan, versican, or neurocan, and shows little homology with these proteoglycans. Brevican core protein exists as a 145 kDa full-length form and a 80 kDa N terminally truncated form. A significant amount of brevican devoid of any glycosaminoglycan chains is present in the brain, indicating that brevican is a "part-time" proteoglycan. Northern blot analysis reveals that a single 3.3-kilobase brevican transcript is present predominantly in the brain, and that it is expressed in primary cerebellar astrocytes but not in neurons.
Interaction between dual NADPH-dependent reactions of paraquat in mouse brain microsomes. (1991)

Paraquat stimulated NADPH-dependent lipid peroxidation in mouse brain microsomes, while it suppressed lipid peroxidation induced by NADPH plus ascorbate. The stimulation of lipid peroxidation by paraquat was inhibited by N-ethylmaleimide (NEM). However, NEM attenuated the inhibitory effect of paraquat on lipid peroxidation elicited by NADPH in combination with ascorbate. These results suggest that an NADPH-dependent reaction which is susceptible to NEM might share an electron from NADPH with the alternative reaction, lipid peroxidation, in the presence of paraquat in mouse brain microsomes.
2×2 silicon integrated optical phased array for beam steering applications (2015)

A 2×2 silicon integrated optical phased array based on edge couplers for beam steering applications is proposed and investigated. Results show that a steering range of over 30° can be realized in both lateral and vertical directions.
Functional interaction between human histocompatibility leukocyte antigen (HLA) class II and mouse CD4 molecule in antigen recognition by T cells in HLA-DR and DQ transgenic mice. (1994)

Studies in vitro have suggested that a species barrier exists in functional interaction between human histocompatibility leukocyte antigen (HLA) class II and mouse CD4 molecules. However, whether mouse CD4+ T cells restricted by HLA class II molecules are generated in HLA class II transgenic mice and respond to peptide antigens across this barrier has remained unclear. In an analysis of T cell responses to synthetic peptides in mice transgenic for HLA-DR51 and -DQ6, we found that DR51 and DQ6 transgenic mice acquired significant T cell response to influenza hemagglutinin-derived peptide 307-319 (HA 307) and Streptococcus pyogenes M12 protein-derived peptide 347-397 (M6C2), respectively. Inhibition studies with several monoclonal antibodies showed that transgenic HLA class II molecules presented these peptides to mouse CD4+ T cells. Furthermore, T cell lines specific for HA 307 or M6C2 obtained from the transgenic mice could respond to the peptide in the context of relevant HLA class II molecules expressed on mouse L cell transfectants that lack the expression of mouse MHC class II. These findings indicate that interaction between HLA class II and mouse CD4 molecules is sufficient for provoking peptide-specific HLA class II-restricted T cell responses in HLA class II transgenic mice.
Spatiotemporal integration of light by the cat X-cell center under photopic and scotopic conditions (2005)

Visual responses to stimulation at high temporal frequency are generally considered to result from signals that avoid light adaptive gain adjustment, simply reflecting linear summation of luminance. Under conditions of high photopic illuminance, the center of the receptive field of the cat X-cell has been shown to expand in size when stimulated at high temporal frequency, raising the possibility that there is spatiotemporal interaction in luminance summation. Here we show that this expansion maintains constant the product of the center's luminance summing area and the temporal period of luminance modulation, implying that spatial and temporal integration of luminance can be traded for one another by the X-cell center. As such the X-cell has a spatiotemporal window for luminance integration that fuses the classical concepts of a spatial window of luminance integration (Ricco's Law) with a temporal window of luminance integration (Bloch's Law). We were interested to determine whether this tradeoff between spatial and temporal summation of luminance occurs also at lower light levels, where the temporal-frequency bandwidth of the X-cell is narrower. We found that it does not. Center radius does not expand with temporal frequency under either low photopic or scotopic conditions. These results are discussed within the context of the known retinal circuitry that underlies the X-cell center for photopic and scotopic conditions.
Amino Acid Deprivation Promotes Tumor Angiogenesis through the GCN2/ATF4 Pathway (2013)

As tumors continue to grow and exceed their blood supply, nutrients become limited leading to deficiencies in amino acids (AAD), glucose (GD), and oxygen (hypoxia). These alterations result in significant changes in gene expression. While tumors have been shown to overcome the stress associated with GD or hypoxia by stimulating vascular endothelial growth factor (VEGF)-mediated angiogenesis, the role of AAD in tumor angiogenesis remains to be elucidated. We found that in human tumors, the expression of the general control non-derepressible 2 (GCN2, an AAD sensor) kinase is elevated at both protein and mRNA levels. In vitro studies revealed that VEGF expression is universally induced by AAD treatment in all five cell lines tested (five of five). This is in contrast to two other angiogenesis mediators interleukin-6 (two of five) and fibroblast growth factor 2 (two of five) that have a more restricted expression. Suppressing GCN2 expression significantly decreased AAD-induced VEGF expression. Silencing activating transcription factor 4 (ATF4), a downstream transcription factor of the GCN2 signaling pathway, is also associated with strong inhibition of AAD-induced VEGF expression. PKR-like kinase, the key player in GD-induced unfolded protein response is not involved in this process. In vivo xenograft tumor studies in nonobese diabetic/severe combined immunodeficient mice confirmed that knockdown of GCN2 in tumor cells retards tumor growth and decreases tumor blood vessel density. Our results reveal that the GCN2/ATF4 pathway promotes tumor growth and angiogenesis through AAD-mediated VEGF expression and, thus, is a potential target in cancer therapy.
Membrane Permeabilization by Oligomeric α-Synuclein: In Search of the Mechanism (2010)

The dye efflux from negatively charged vesicles upon addition of α-synuclein has been hypothesized to occur through the formation of oligomeric membrane pores. However, our results show that the dye efflux characteristics are consistent with bilayer defects caused by membrane instability. These data shed new insights into potential mechanisms of toxicity of oligomeric α-synuclein species.
Differential expression of volume‐regulated anion channels during cell cycle progression of human cervical cancer cells (2000)

This study investigated the volume-regulated anion channel (VRAC) of human cervical cancer SiHa cells under various culture conditions, testing the hypothesis that the progression of the cell cycle is accompanied by differential expression of VRAC activity. Exponentially growing SiHa cells expressed VRACs, as indicated by the presence of large outwardly rectifying currents activated by hypotonic stress with the anion permeability sequence I- > Br- > Cl-. VRACs were potently inhibited by tamoxifen with an IC50 of 4.6 [mu]M. Fluorescence-activated cell sorting (FACS) experiments showed that 59 +/- 0.5, 5 +/- 0.5 and 36 +/- 1.1% of unsynchronized, exponentially growing cervical cancer SiHa cells were in G0/G1, S and G2/M stage, respectively. Treatment with aphidicolin (5 [mu]M) arrested 88 +/- 1.4% of cells at the G0/G1 stage. Arrest of cell growth in the G0/G1 phase was accompanied by a significant decrease of VRAC activity. The normalized hypotonicity-induced current decreased from 48 +/- 5.2 pA pF-1 at +100 mV in unsynchronized cells to 15 +/- 2.6 pA pF-1 at +100 mV in aphidicolin-treated cells. After removal of aphidicolin, culturing in medium containing 10% fetal calf serum triggered a rapid re-entry into the cell cycle and a concomitant recovery of VRAC density. Pharmacological blockade of VRACs by tamoxifen or NPPB caused proliferating cervical cancer cells to arrest in the G0/G1 stage, suggesting that activity of this channel is critical for G1/S checkpoint progression. This study provides new information on the functional significance of VRACs in the cell cycle clock of human cervical cancer cells.