gebhart/patrepeval huggingface dataset:
Inheritance and Interaction of Low Palmitic and Low Linolenic Soybean (2002)

Decreasing the palmitic and linolenic acid content of soybean [Glycine max (L.) Merrill] oil would help improve its nutritional quality and oxidative stability. The altered fatty acid profile in soybean germplasm lines with decreased levels of palmitic and linolenic acid have been developed at the University of Guelph, Canada, by combining different mutant alleles through hybridization. The objectives of this study were to determine the inheritance and interaction of palmitic and linolenic acid levels in RG3 and RG1, and the effects of these altered fatty acid levels on other fatty acids. RG3 and RG1 (low palmitic ≈45 g kg−1 and linolenic ≈40 g kg−1) were crossed reciprocally to several soybean lines with altered or normal fatty acid profiles. Analysis of the reciprocal F2 generations indicated no maternal or cytoplasmic effects for palmitic or linolenic acid content. Chi-square analyses of the F2 generation demonstrated that RG3 and RG1 contained two alleles, fap1 and fapx, that controlled palmitic acid content. In addition, RG1 had a third allele, fan, which reduced its linolenic acid content. Calculation of gene substitution values indicated additive gene action at the fap1 and fan loci, whereas the fapx locus involved partial dominance. Correlation coefficients indicated no association between palmitic and linolenic acid. Decreases in palmitic and linolenic acid content were associated primarily with increases in linoleic acid content. Since fap1, fapx, and fan were inherited independently of each other and appeared to behave in an additive manner, RG3 and RG1 can be used in breeding programs as additional valuable sources of germplasm with altered fatty acid profiles.
Texture Tiling on 3D Models Using Automatic Polycube-maps and Wang Tiles (2010)

In mapping textures onto 3D models, it is essential to eliminate all seams and avoid excessive distortions. To achieve these goals, texture tiling provides an alternative approach for texturing surfaces. In this paper, a texture tiling approach that combines poly-cube-maps and Wang tiles for 3D models is proposed. The poly-cube of a 3D model is first constructed automatically and a tiling mechanism is then used to fill the tiles on the polycube. Finally, rectangular cells which are transformed from the polycube are generated and textures are mapped onto the 3D model. The results show that the proposed approach leads to seamless texture mapping on 3D models.
Papillomavirus-Like Particles Induce Acute Activation of Dendritic Cells (2001)

The role of viral structural proteins in the initiation of adaptive immune responses is poorly understood. To address this issue, we focused on the effect of noninfectious papillomavirus-like particles (VLPs) on dendritic cell (DC) activation. We found that murine bone marrow-derived dendritic cells (BMDCs) effectively bound and rapidly internalized bovine papillomavirus VLPS: Exposure to fully assembled VLPs of bovine papillomavirus, human papillomavirus (HPV)16 or HPV18, but not to predominately disordered HPV16 capsomers, induced acute phenotypic maturation of BMDCS: Structurally similar polyomavirus VLPs bound to the DC surface and were internalized, but failed to induce maturation. DCs that had incorporated HPV16 VLPs produced proinflammatory cytokines IL-6 and TNF-alpha; however, the release of these cytokines was delayed relative to LPS activation. Production of IL-12p70 by VLP-exposed DCs required the addition of syngeneic T cells or rIFN-gamma. Finally, BMDCs pulsed with HPV16 VLPs induced Th1-dominated primary T cell responses in vitro. Our data provide evidence that DCs respond to intact papillomavirus capsids and that they play a central role in VLP-induced immunity. These results offer a mechanistic explanation for the striking ability of papillomavirus VLP-based vaccines to induce potent T and B cell responses even in the absence of adjuvant.
Structural Kinematics of In-Parallel-Actuated Robot-Arms (1983)

An alternative is here put forward to counterbalance the present-day preoccupation with series-actuated robot-arms. A systematic study of robots and manipulators, now concentrating on “in-parallel” actuator-arrangements, reveals many geometries applicable either to entire robot-arms or to parts of otherwise series-actuated arms. No survey of this kind is possible without drawing heavily on the theory of screw systems. Having established a means of enumerating possible geometries, screw theory is again invoked to highlight, in broad terms, the patterns considered to be most promising. Criteria for avoiding undesirable robot-arm-configurations are touched upon, and certain aspects of the performance of in-parallel-actuated robot-arms are compared and contrasted with those of series-actuated arms. Within the bounds here set (thought to be realistic) the survey on its own is intended to be exhaustive, but many details remain to be investigated. This paper aims to do no more than edge open the door a little further towards in-parallel actuation in robot-arms; others may then consider that further study could be productive.
ACAT-2, A Second Mammalian Acyl-CoA:Cholesterol Acyltransferase (1998)

The synthesis of cholesterol esters by acyl-CoA:cholesterol acyltransferase (ACAT, EC 2.3.1.26) is an important component of cellular cholesterol homeostasis. Cholesterol ester formation also is hypothesized to be important in several physiologic processes, including intestinal cholesterol absorption, hepatic lipoprotein production, and macrophage foam cell formation in atherosclerotic lesions. Mouse tissue expression studies and the disruption of the mouse ACAT gene (Acact) have indicated that more than one ACAT exists in mammals and specifically that another enzyme is important in mouse liver and intestine. We now describe a second mammalian ACAT enzyme, designated ACAT-2, that is 44% identical to the first cloned mouse ACAT (henceforth designated ACAT-1). Infection of H5 insect cells with an ACAT-2 recombinant baculovirus resulted in expression of a approximately 46-kDa protein in cell membranes that was associated with high levels of cholesterol esterification activity. Both ACAT-1 and ACAT-2 also catalyzed the esterification of the 3beta-hydroxyl group of a variety of oxysterols. Cholesterol esterification activities for ACAT-1 and ACAT-2 exhibited different IC50 values when assayed in the presence of several ACAT-specific inhibitors, demonstrating that ACAT inhibitors can selectively target specific forms of ACAT. ACAT-2 was expressed primarily in mouse liver and small intestine, supporting the hypothesis that ACAT-2 contributes to cholesterol esterification in these tissues. The mouse ACAT-2 gene (Acact2) maps to chromosome 15 in a region containing a quantitative trait locus influencing plasma cholesterol levels. The identification and cloning of ACAT-2 will facilitate molecular approaches to understanding the role of ACAT enzymes in mammalian biology.
Determination of the sequence coding for the β subunit of the human high‐affinity IgE receptor (1992)

The cDNA encoding the beta subunit of the human high-affinity IgE receptor was cloned by a combination of various polymerase chain reactions (PCR). A major portion of the beta cDNA was amplified using primers homologous within the sequences of rat and mouse. The 3' unknown sequence was preferentially amplified using the RNA template-specific PCR and the improved two-step PCR. The 5' unknown sequence was specifically amplified by our newly developed PCR walking. Random heptanucleotides tagged with a unique sequence at the 5' end were used as the walking primer. Finally, the entire coding region was amplified and sequenced. The two extracellular loops of the human beta subunit were the least homologous to those of rat and mouse.
Transversion‐enriched sequence saturation mutagenesis (SeSaM‐Tv+): A random mutagenesis method with consecutive nucleotide exchanges that complements the bias of error‐prone PCR (2007)

The sequence saturation mutagenesis (SeSaM) method has been advanced to a random mutagenesis method with adjustable mutational biases. SeSaM offers, for example, a bias that is complementary to error-prone (ep) PCR and is enriched in transversions (SeSaM-Tv(+)). dNTP alpha S and three degenerate bases (P, K and I) are used to control mutational bias flexibly. After quantifying incorporation rates of dPTP, dKTP and dITP by terminal transferase using a luciferase-based assay and investigating the read and/or write activities of eight DNA polymerases, a transversion-enriched protocol has been developed. In a mutant library generated using dGTP alpha S and dPTP, transversion frequencies of 16.22-22.58% (G-->T) and 6.38-9.69% (G-->C) were achieved. These mutational spectra are complementary and occur twice as frequently in comparison to standard epPCR methods employing Taq DNA polymerase. For generating more complex mutant libraries, the occurrence of consecutive nucleotide exchanges was increased by 10(5)-10(6)-fold compared to epPCR. Finally, 16.7% of all sequenced mutants contained consecutive nucleotide exchanges composed mainly of a transversion followed by a transition.
Making sense of itraconazole pharmacokinetics (2005)

The triazole, itraconazole, has a wide spectrum of antifungal activity in vitro. Confirming this activity in vivo has been a long and difficult task because of problems with formulation, delivery and uncertainty about effective bioavailability. The physicochemical properties of the drug make it insoluble in water but strongly protein bound. The absorption and blood levels of the original capsular formulation were predictable with non-linear, saturation kinetics in normal volunteers. Tissue penetration was high and sustained. In neutropenic patients with haematological malignancies, levels were very variable and the doses required to achieve effective antifungal levels were higher than predicted from normal subjects' results. The solubility of the drug and predictability of blood levels were improved by the formulation of an oral solution with cyclodextrin. Wash-out times were prolonged in patients with this new formulation implying that tissue penetration was maintained. A high volume of distribution suggests that loading may be necessary. An intravenous cyclodextrin solution is also now available allowing rapid loading and avoidance of the well-known gut side effects of the oral solution. Clinical studies have suggested minimum bioavailable dosage and minimum trough blood levels for effective prophylaxis against systemic fungal infection. Interactions are also now well documented and manageable. The drug can be measured reliably, quickly and comparatively cheaply by HPLC in serum and plasma. The frequency of such testing in clinical practice depends on the need to ensure adequate levels and to avoid unwanted toxicity.
Structural Basis for the Differential Toxicity of Cholera Toxin and Escherichia coli Heat-labile Enterotoxin (1999)

Cholera toxin (Ctx) and E. coli heat-labile enterotoxin (Etx) are structurally and functionally similar AB5 toxins with over 80% sequence identity. When their action in polarized human epithelial (T84) cells was monitored by measuring toxin-induced Cl- ion secretion, Ctx was found to be the more potent of the two toxins. Here, we examine the structural basis for this difference in toxicity by engineering a set of mutant and hybrid toxins and testing their activity in T84 cells. This revealed that the differential toxicity of Ctx and Etx was (i) not due to differences in the A-subunit's C-terminal KDEL targeting motif (which is RDEL in Etx), as a KDEL to RDEL substitution had no effect on cholera toxin activity; (ii) not attributable to the enzymatically active A1-fragment, as hybrid toxins in which the A1-fragment in Ctx was substituted for that of Etx (and vice versa) did not alter relative toxicity; and (iii) not due to the B-subunit, as the replacement of the B-subunit in Ctx for that of Etx caused no alteration in toxicity, thus excluding the possibility that the broader receptor specificity of EtxB is responsible for reduced activity. Remarkably, the difference in toxicity could be mapped to a 10-amino acid segment of the A2-fragment that penetrates the central pore of the B-subunit pentamer. A comparison of the in vitro stability of two hybrid toxins, differing only in this 10-amino acid segment, revealed that the Ctx A2-segment conferred a greater stability to the interaction between the A- and B-subunits than the corresponding segment from Etx A2. This suggests that the reason for the relative potency of Ctx compared with Etx stems from the increased ability of the A2-fragment of Ctx to maintain holotoxin stability during uptake and transport into intestinal epithelia.
Dual targeting of CCR2 and CX3CR1 in an arterial injury model of vascular inflammation (2010)

In this study we have shown that blocking CCR2 with a low molecular weight antagonist ameliorates the inflammatory response to vascular injury. The protective effect of CCR2 blockade is increased in the presence of CX3CR1 deficiency suggesting that CX3CR1 and CCR2 have non-redundant functions in the progression of vascular inflammation.
Differentiation of human NK cells into NK1 and NK2 subsets. (1998)

Human NK cells cultured in the presence of IL-12 or IL-4 differentiate into cell populations with distinct patterns of cytokine secretion similar to Th1 and Th2 cells. NK cells grown in IL-12 (NK1) produce IL-10 and IFN-gamma, whereas NK cells grown in IL-4 (NK2) produce IL-5 and IL-13. Although these NK cell subsets do not differ in cytotoxic activity, NK1 cells express higher levels of cell surface CD95 (Fas) Ag than NK2 cells and are more sensitive to Ab or chemically induced apoptosis. Like Th1 cells, NK1 cells accumulate much higher levels of the IL-12Rbeta2-chain mRNA and are significantly more responsive to IL-12 than NK2 cells at the level of activation of STAT4 transcription factor. The identification of NK cell subsets that are analogous to T cell subsets suggests a new role for NK cells in innate inflammatory responses and in their effect on adaptive immunity.
Glycogen Synthase Kinase-3β Is a Negative Regulator of Cardiomyocyte Hypertrophy (2000)

Hypertrophy is a basic cellular response to a variety of stressors and growth factors, and has been best characterized in myocytes. Pathologic hypertrophy of cardiac myocytes leads to heart failure, a major cause of death and disability in the developed world. Several cytosolic signaling pathways have been identified that transduce prohypertrophic signals, but to date, little work has focused on signaling pathways that might negatively regulate hypertrophy. Herein, we report that glycogen synthase kinase-3beta (GSK-3beta), a protein kinase previously implicated in processes as diverse as development and tumorigenesis, is inactivated by hypertrophic stimuli via a phosphoinositide 3-kinase-dependent protein kinase that phosphorylates GSK-3beta on ser 9. Using adenovirus-mediated gene transfer of GSK-3beta containing a ser 9 to alanine mutation, which prevents inactivation by hypertrophic stimuli, we demonstrate that inactivation of GSK-3beta is required for cardiomyocytes to undergo hypertrophy. Furthermore, our data suggest that GSK-3beta regulates the hypertrophic response, at least in part, by modulating the nuclear/cytoplasmic partitioning of a member of the nuclear factor of activated T cells family of transcription factors. The identification of GSK-3beta as a transducer of antihypertrophic signals suggests that novel therapeutic strategies to treat hypertrophic diseases of the heart could be designed that target components of the GSK-3 pathway.
UbcH10 is the cancer-related E2 ubiquitin-conjugating enzyme. (2003)

Ubiquitin-dependent proteolysis by the 26S proteasome plays a pivotal role in cell cycle progression as well as in tumorigenesis. In this pathway, ubiquitin-conjugating enzyme (E2), together with ubiquitin ligase (E3), transfers ubiquitin to the specific substrate protein(s); however, little is known about the potential contribution of E2 to tumorigenesis. In this study, we examined the expression levels of 17 E2 genes in 25 different human normal tissues and 24 human cancerous cell lines by using a quantitative real-time reverse transcription-PCR. Among the E2 gene family, the expression level of UbcH10 was extremely low in many of the normal tissues but prominent in the majority of cancerous cell lines. Intriguingly, UbcH10 was expressed at high levels in primary tumors derived from the lung, stomach, uterus, and bladder as compared with their corresponding normal tissues, suggesting that UbcH10 is involved in tumorigenesis or progression of the tumor. To further investigate a possible contribution of UbcH10 to malignant transformation and tumor cell proliferation, NIH3T3 cells were transfected with the expression plasmid encoding UbcH10, and stable transfectants were subsequently established. UbcH10-overexpressing cells exhibited an increased incorporation of bromodeoxyuridine, an enhanced growth rate, an increase in saturation density, and a promotion of colony formation in soft agar medium as compared with parental NIH3T3 cells and the control transfectants. Collectively, our present results provide the first evidence that UbcH10 is highly expressed in various human primary tumors and that UbcH10 has an ability to promote cell growth and malignant transformation.
Antibody response to OspC-I synthetic peptide derived from outer surface protein C of Borrelia burgdorferi in sera from Japanese forestry workers (1999)

The prevalence of antibodies against Lyme disease spirochaetes in serum samples from 80 forestry workers at high occupational risk of Lyme disease was surveyed by enzyme-linked immunosorbent assay (ELISA) with the OspC-I synthetic peptide. The peptide is part of the outer surface protein C (OspC) amino acid sequence located in the region conserved among Borrelia burgdorferi sensu stricto or sensu lato. Positivity for antibodies against OspC-I was observed in 25 (313%) of the forestry workers. Of these positive cases, 12 (15.0%) and 19 (23.8%) were positive for immunoglobulin M (IgM) and IgG antibody, respectively. Among 62 workers who were negative for IgG antibody against B. garinii or B. japonica in our previous study, 9 (14.5%) and 4 (6.5%) were positive for IgM and IgG antibody, respectively, in OspC-I ELISA. These results demonstrate for the first time that Lyme disease in forestry workers can be revealed using OspC-I ELISA. We conclude that forestry workers who show positive results for antibodies against OspC-I have very likely been exposed to Lyme disease spirochaetes, and that those who show positivity for IgM antibody against OspC-I may be in the early stage of Lyme disease.
Exploitation of nanoparticle-protein interactions for early disease detection (2019)

The main diagnostic tools for primary and metastatic central nervous system (CNS) tumors are the anamnestic neurological examination and the imaging tests, which are expensive and lack specificity. In recent years, the shell of macromolecules which forms on nanoparticles (NPs) when they are exposed to human blood, also known as hard corona (HC), became a powerful tool in diagnostics. Indeed, HC can act as a “nano-concentrator” of serum proteins and can detect minor changes in the protein concentration at the very early stages of disease development. In this paper, we characterized lipid NP HC formed in blood samples from patients affected by meningeal tumors. We found that the HCs of meningeal tumor patients could be discriminated from those of healthy subjects. Our results show that emerging HC-based technologies will pave the way for early diagnosis of CNS cancer.
The structure of isopannarin (1983)

The structure proposed by Yosioka for the product obtained by the treatment of the depsidone pannarin (2-chloro-3-hydroxy-8-methoxy-1,6,9-trimethyl-11-oxo-11H-dibenzo[b,e][1,4]dioxepin-4-carbaldehyde) (2) with concentrated sulfuric acid is revised to 5-chloro-6-hydroxy-4'-methoxy-2',4,5'-trimethyl-3,6'-dioxo- 2,3 -dihydrospiro[benzofuran-2,1'- cyclohexa - 2',4'- dienel-7-carbaldehyde (5).
Discrimination of Bacteria Using Surface-Enhanced Raman Spectroscopy (2003)

Raman spectroscopy has recently been shown to be a potentially powerful whole-organism fingerprinting technique and is attracting interest within microbial systematics for the rapid identification of bacteria and fungi. However, while the Raman effect is so weak that only approximately 1 in 10(8) incident photons are Raman scattered (so that collection times are in the order of minutes), it can be greatly enhanced (by some 10(3)-10(6)-fold) if the molecules are attached to, or microscopically close to, a suitably roughened surface, a technique known as surface-enhanced Raman scattering (SERS). In this study, SERS, employing an aggregated silver colloid substrate, was used to analyze a collection of clinical bacterial isolates associated with urinary tract infections. While each spectrum took 10 s to collect, to acquire reproducible data, 50 spectra were collected making the spectral acquisition times per bacterium approximately 8 min. The multivariate statistical techniques of discriminant function analysis (DFA) and hierarchical cluster analysis (HCA) were applied in order to group these organisms based on their spectral fingerprints. The resultant ordination plots and dendrograms showed correct groupings for these organisms, including discrimination to strain level for a sample group of Escherichia coli, which was validated by projection of test spectra into DFA and HCA space. We believe this to be the first report showing bacterial discrimination using SERS.
Chemical and Instrumental Approaches to Treat Hyperpigmentation (2003)

Many modalities of treatment for acquired skin hyperpigmentation are available including chemical agents or physical therapies, but none are completely satisfactory. Depigmenting compounds should act selectively on hyperactivated melanocytes, without short- or long-term side-effects, and induce a permanent removal of undesired pigment. Since 1961 hydroquinone, a tyrosinase inhibitor, has been introduced and its therapeutic efficacy demonstrated, and other whitening agents specifically acting on tyrosinase by different mechanisms have been proposed. Compounds with depigmenting activity are now numerous and the classification of molecules, based on their mechanism of action, has become difficult. Systematic studies to assess both the efficacy and the safety of such molecules are necessary. Moreover, the evidence that bleaching compounds are fairly ineffective on dermal accumulation of melanin has prompted investigations on the effectiveness of physical therapies, such as lasers. This review which describes the different approaches to obtain depigmentation, suggests a classification of whitening molecules on the basis of the mechanism by which they interfere with melanogenesis, and confirms the necessity to apply standardized protocols to evaluate depigmenting treatments.
Excitonic gain and stimulated ultraviolet emission in nanocrystalline zinc-oxide powder (2000)

We have studied ultraviolet photoluminescence from high-purity zinc-oxide powder over a wide temperature range (2–293 K). At low temperatures, the spontaneous emission is due to radiative recombination of excitons bound to donors and acceptors. At high temperature (&amp;gt;90 K), it mainly consists of recombination of free excitons, with exciton–exciton collision-induced recombination dominating the spectrum at higher pumping intensities. Emission from the exciton–exciton collision process shows clear stimulated-emission behavior. At sufficiently high pumping intensity, the stimulated emission band shifts abruptly to a longer wavelength due to the formation of an electron–hole plasma. Sharp emission peaks are observed in the stimulated emission bands. The possible origins of these sharp peaks are discussed.