gebhart/patrepeval huggingface dataset:
The Three Recombinant Domains of Human Serum Albumin (1999)

In an attempt to systematically dissect the ligand binding properties of human serum albumin (HSA), the gene segments encoding each of its three domains were defined based on their conserved homologous structural motifs and separately cloned into a secretion vector for Pichia pastoris. We were able to establish a generally applicable purification protocol based on Cibacron Blue affinity chromatography, suggesting that each of the three domains carries a binding site specific for this ligand. Proteins were characterized by SDS-polyacrylamide gel electrophoresis, isoelectric focusing, gel filtration, N-terminal sequencing, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, as well as near- and far-UV CD. In addition to the affinity chromatography ligand Cibacron Blue, binding properties toward hemin, warfarin, and diazepam, each of which represents a standard ligand for HSA, respectively, were investigated by the measurement of induced circular dichroism. Clear experimental evidence is provided here for the location of the primary hemin binding site to be on domain I of HSA, and for the primary diazepam binding site to be on domain III. Further, secondary binding sites were found for hemin to be located on domains II and III, and for diazepam on domain I. The warfarin binding site was located primarily on domain II, while on domain I, a secondary binding site and/or parts of the primary binding site were found.
Serum ferritin in acquired immune deficiency syndrome. (1986)

Ferritin has been linked to a variety of immunosuppressive effects on cell-mediated immunity. Therefore, serum ferritin was measured by radioimmunoassay in patients with acquired immune deficiency syndrome (AIDS), AIDS-related complex (ARC) and healthy heterosexual men. 13 of 15 patients with AIDS and 4 of 15 with ARC had ferritin levels greater than 300 micrograms/dl. This study suggests that the levels of serum ferritin increase with the progression of immune deficiency and might play a role in the pathogenesis of cell-mediated immune deficiency in AIDS.
Effect of Sugar Composition on the Heterogeneity of Antibod in Hybridoma Cultivation (2005)

In order to investigate the effect of the sugar composition of the medium on IgG glycosylation in mouse hybridoma cultivation, the batch culture of mouse hybridoma 3A21 (RCB 1285) was carried out under various sugar compositions. The macroheterogeneity (relative ratio of glycosylated antibody) was analyzed by an enzyme-linked lectin binding assay during cultivation. The relative ratio of glycosylated antibody decreased as cultivation progressed. However, in mannoseenriched cultivation, the relative ratio was maintained at a high level. The microheterogeneity of each oligosaccharide chain was analyzed by two-dimensional mapping techniques. The high-mannose type oligosaccharide chain content was high in mannose-enriched cultivation The content of oligosaccharide chains terminating in galactose residues, which plays an important role in the immune system, was shown to be high in galactose-enriched cultivation. Using galactose- and mannoseenriched cultivations, the number of oligosaccharide chains terminating in galactose residues could be increased.
Expression and characterization of glycogen synthase kinase-3 mutants and their effect on glycogen synthase activity in intact cells. (1996)

In these studies we expressed and characterized wild-type (WT) GSK-3 (glycogen synthase kinase-3) and its mutants, and examined their physiological effect on glycogen synthase activity. The GSK-3 mutants included mutation at serine-9 either to alanine (S9A) or glutamic acid (S9E) and an inactive mutant, K85,86MA. Expression of WT and the various mutants in a cell-free system indicated that S9A and S9E exhibit increased kinase activity as compared with WT. Subsequently, 293 cells were transiently transfected with WT GSK-3 and mutants. Cells expressing the S9A mutant exhibited higher kinase activity (2.6-fold of control cells) as compared with cells expressing WT and S9E (1.8- and 2.0-fold, respectively, of control cells). Combined, these results suggest serine-9 as a key regulatory site of GSK-3 inactivation, and indicate that glutamic acid cannot mimic the function of the phosphorylated residue. The GSK-3-expressing cell system enabled us to examine whether GSK-3 can induce changes in the endogenous glycogen synthase activity. A decrease in glycogen synthase activity (50%) was observed in cells expressing the S9A mutant. Similarly, glycogen synthase activity was suppressed in cells expressing WT and the S9E mutant (20-30%, respectively). These studies indicate that activation of GSK-3 is sufficient to inhibit glycogen synthase in intact cells, and provide evidence supporting a physiological role for GSK-3 in regulating glycogen synthase and glycogen metabolism.
Numerical characterization of hemodynamics conditions near aortic valve after implantation of left ventricular assist device (2011)

Left Ventricular Assist Devices (LVADs) are implantable mechanical pumps that temporarily aid the function of the left ventricle. The use of LVADs has been associated with thrombus formation next to the aortic valve and close to the anastomosis region, especially in patients in which the native cardiac function is negligible and the aortic valve remains closed. Stagnation points and recirculation zones have been implicated as the main fluid dynamics factors contributing to thrombus formation. The purpose of the present study was to develop and use computer simulations based on a fluid-structure interaction (FSI) solver to study flow conditions corresponding to different strategies in LVAD ascending aortic anastomosis providing a scenario with the lowest likelihood of thrombus formation. A novel FSI algorithm was developed to deal with the presence of multiple structures corresponding to different elastic properties of the native aorta and of the LVAD cannula. A sensitivity analysis of different variables was performed to assess their impact of flow conditions potentially leading to thrombus formation. It was found that the location of the anastomosis closest to the aortic valve (within 4 cm away from the valve) and at the angle of 30 minimizes the likelihood of thrombus formation. Furthermore, it was shown that the rigidity of the dacron anastomosis cannula plays almost no role in generating pathological conditions downstream from the anastomosis. Additionally, the flow analysis presented in this manuscript indicates that compliance of the cardiovascular tissue acts as a natural inhibitor of pathological flow conditions conducive to thrombus formation and should not be neglected in computer simulations.
Single-Walled Carbon Nanotube Induces Oxidative Stress and Activates Nuclear Transcription Factor-κB in Human Keratinocytes (2005)

Carbon nanotubes are now becoming an important material for use in day to day life because of their unique physical properties. The toxicological impact of these materials has not yet been studied in detail, thereby limiting their use. In the present study, the toxicity of single-walled carbon nanotubes (SWCNT) was assessed in human keratinocyte cells. The results show increased oxidative stress and inhibition of cell proliferation in response to treatment of keratinocytes with SWCNT particles. In addition, the signaling mechanism in keratinocytes upon exposure to SWCNT particles was investigated. Results from the study suggest that SWCNT particles activate NF-kappaB in a dose-dependent manner in human keratinocytes. Further, the mechanism of activation of NF-kappaB was due to the activation of stress-related kinases by SWCNT particles in keratinocytes. In conclusion, these studies show the mechanism of toxicity induced by SWCNT particles.
Adenovirus-Associated Virus Multiplication VII. Helper Requirement for Viral Deoxyribonucleic Acid and Ribonucleic Acid Synthesis (1972)

The adsorption of adenovirus-associated virus (AAV) type 2 by KB cells and the subsequent penetration of the AAV genome to the cell nucleus was measured with and without helper adenovirus type 2 (Ad2). It was found that the helper virus did not enhance either process. On the other hand, a synthesis of AAV deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) was not detected by nucleic acid hybridization after KB cells were infected with AAV type 2 alone, whereas both AAV DNA and RNA synthesis were readily detected when cells were additionally infected with Ad2 or herpes simplex virus type 1, a partial helper of AAV replication. AAV RNA synthesis was initially observed 10 to 11 hr after simultaneous infection with Ad2, but the interval between AAV infection and AAV transcription could be reduced to 4 to 5 hr when cells were first infected with Ad2 for 10 hr. It was estimated that AAV DNA synthesis accounted for 3% of the total DNA in cells after a simultaneous infection with Ad2. These findings, together with the previous observation that adenovirus provides a helper function(s) after AAV uncoating, suggest that AAV are defective only subsequent to the uncoating process, and that helper viruses may provide a factor(s) needed for initiating synthesis of AAV DNA, RNA, or both.
Determination of haplotypes from single DNA molecules: a method for single-molecule barcoding (2007)

Determining the haplotypes in a diploid individual is a major technical challenge in genetic studies of human complex traits. Here we report a method of molecular haplotyping by directly imaging multiple polymorphic sites on individual DNA molecules simultaneously. DNA fragments amplified by long-range PCR were labeled with fluorescent dyes at each polymorphic site using a modified gap-filled padlock probe ligation approach. The labeled DNA molecules were then stretched into linear form on a functionalized glass surface and imaged with multicolor total internal reflection fluorescence (TIRF) microscopy. By determining the colors and positions of the fluorescent labels with respect to the backbone at polymorphic sites, the haplotype can be inferred accurately, in a manner similar to reading a barcode, even when the DNA fragments are not fully labeled. The feasibility of this technology is demonstrated by the determination of the haplotype of a 9.3-kbp DNA fragment containing four SNPs.
Inhibition of nonsense-mediated messenger RNA decay in clinical samples facilitates detection of human MSH2 mutations with an in vivo fusion protein assay and conventional techniques. (1997)

Germ-line mutations in the human MSH2 (hMSH2) gene account for about 40% of known defects in kindreds with hereditary nonpolyposis colon cancer. We describe a simple fusion protein assay for detection of hMSH2 nonsense mutations in yeast. Detection of nonsense mutations with this assay is severely compromised in many cases by nonsense-mediated mRNA decay, a physiological process that destabilizes the mutant RNA. Triggering of nonsense-mediated decay requires mRNA scanning by the ribosome to detect the stop codon. We show that treatment of cells with the translation inhibitor puromycin suppresses nonsense-mediated decay and facilitates the detection of nonsense mutations in clinical samples by cDNA sequencing, in vitro protein truncation tests, and the yeast fusion protein assay. Given the prevalence of chain-terminating mutations in human disease genes, puromycin treatment of blood samples should improve the signal-to-noise ratio and hence the sensitivity of many RNA-based diagnostic tests. Paradoxically, the yeast hMSH2::ADE2 fusion protein assay also detects some in-frame mutations, presumably through an effect on the folding of the fusion protein.
Research, design and experiment of end effector for wafer transfer robot (2012)

Purpose Wafer transfer robots play a significant role in IC manufacturing industry and the end effector is an important component of the robots. The purpose of this paper is to improve transfer efficiency of a wafer transfer robot through study of its end effector, and at the same time to reduce wafer deformation. Design/methodology/approach Finite element method is adopted to analyze wafer deformation. For wafer transfer robot working in vacuum, for the first time, the authors apply the research of microfiber arrays inspired by gecko to the design of robot's end effector, and present equations between robot's transit acceleration and parameters of microfiber arrays. Based on these studies, a kind of micro‐array bump is designed and fixed to a structure optimized end effector. For wafer transfer robot working in atmospheric environment, the authors have analyzed the effects of different factors on wafer deformation. The pressure distributions in absorption area and calculation formula of maximal transfer acceleration are put forward. Finally, a new kind of end effector for atmospheric robot is designed according to these studies. Findings The experiments results show that transfer efficiency of wafer transfer robot has been significantly improved through application of the research in this paper. Also wafer deformation under absorption force has been controlled. Practical implications Through experiments it can be seen that the research in this paper can be used to improve robot transfer ability and decrease wafer deformation in the production environment. Also the studies of end effector lay a solid foundation for further improvement. Originality/value This is the first application of the research of gecko‐inspired microfiber arrays to vacuum wafer transfer robot. This paper also carefully analyzes effects of different factors on wafer deformation through finite element method.
Interventions for paracetamol (acetaminophen) overdose (2018)

of findings for the main comparison. Methionine and supportive treatment compared with supportive treatment for paracetamol (acetaminophen) overdose Methionine and supportive treatment compared with supportive treatment (randomised trials) for paracetamol (acetaminophen) overdose Patient or population: people with paracetamol (acetaminophen) overdose Settings: UK Intervention: methionine and supportive treatment Comparison: supportive treatment Illustrative comparative risks* (95% CI) Assumed risk Corresponding risk Outcomes Supportive treatment Methionine and supportive treatment Relative effect (95% CI) No of participants (studies) Quality of the evidence (GRADE) Comments Study population Mortality 77 per 1000 12 per 1000 (0 to 362) Peto OR 0.14 (0.00 to 6.82) 26 (1 RCT) Very low 1,2
Genome Scanning in Haemophilus influenzae for Identification of Essential Genes (1999)

We have developed a method for identifying essential genes by using an in vitro transposition system, with a small (975 bp) insertional element containing an antibiotic resistance cassette, and mapping these inserts relative to the deduced open reading frames of Haemophilus influenzae by PCR and Southern analysis. Putative essential genes are identified by two methods: mutation exclusion or zero time analysis. Mutation exclusion consists of growing an insertional library and identifying open reading frames that do not contain insertional elements: in a growing population of bacteria, insertions in essential genes are excluded. Zero time analysis consists of monitoring the fate of individual insertions after transformation in a growing culture: the loss of inserts in essential genes is observed over time. Both methods of analysis permit the identification of genes required for bacterial survival. Details of the mutant library construction and the mapping strategy, examples of mutant exclusion, and zero time analysis are presented.
Cervical necrotizing fasciitis (1994)

Nine cases of cervical necrotizing faciitis are presented. Five were odontogenic, three were pharyngeal in origin, and one developed from a soft-tissue spider bite. The bacteriology represented a polyculture of gram-positive, gram-negative, as well as anaerobic bacteria, and initial medical treatment by third-generation cephalosporin and metronidazole or clindamycin was successful and is recommended. Airway control is necessary early, as is a wide exploration of the fascial spaces of the neck, with frequent reexploration in either the operating room or at the bedside to evaluate the effects of treatment and to prevent further progression of the disease. Intensive medical support is crucial, and hyperbaric oxygen is advised for patients who are deteriorating under standard therapy.
A new oscillometric method for pulse wave analysis: comparison with a common tonometric method (2010)

In the European Society of Cardiology-European Society of Hypertension guidelines of the year 2007, the consequences of arterial stiffness and wave reflection on cardiovascular mortality have a major role. But the investigators claimed the poor availability of devices/methods providing easy and widely suitable measuring of arterial wall stiffness or their surrogates like augmentation index (AIx) or aortic systolic blood pressure (aSBP). The aim of this study was the validation of a novel method determining AIx and aSBP based on an oscillometric method using a common cuff (ARCSolver) against a validated tonometric system (SphygmoCor). aSBP and AIx measured with the SphygmoCor and ARCSolver method were compared for 302 subjects. The mean age was 56 years with an s.d. of 20 years. At least two iterations were performed in each session. This resulted in 749 measurements. For aSBP the mean difference was -0.1 mm Hg with an s.d. of 3.1 mm Hg. The mean difference for AIx was 1.2% with an s.d. of 7.9%. There was no significant difference in reproducibility of AIx for both methods. The variation estimate of inter- and intraobserver measurements was 6.3% for ARCSolver and 7.5% for SphygmoCor. The ARCSolver method is a novel method determining AIx and aSBP based on an oscillometric system with a cuff. The results agree with common accepted tonometric measurements. Its application is easy and for widespread use.
Open conductor detector system (1992)

An open phase conductor detector system consisting of one or more transmitters and a receiver which communicate through the distribution line neutral conductor is described. The design holds a promise to provide reliable protection for most down and open 5 to 35 kV distribution phase conductors in contact with high impedance surfaces. The transmitter(s) detects the open phase conductor by monitoring the phase conductor voltage using redundant inputs. When an open phase conductor is detected, the transmitter injects a signal to the distribution line neutral conductor by means of a coupling current transformer. The signal is frequency and duration coded. The receiver decodes the signal and generates a trip signal which may activate a breaker, a ground switch, or a recloser, causing isolation of the distribution line with the open (downed) phase conductor. The system is presently implemented for single distribution lines. A prototype open conductor detector system has been constructed and field tested on a Georgia Power Company distribution system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Efficacy of the β-Exotoxin of Bacillus thuringiensis to Lygus hesperus (Heteroptera: Miridae): Laboratory and Field Responses (1990)

Journal Article Efficacy of the β-Exotoxin of Bacillus thuringiensis to Lygus hesperus (Heteroptera: Miridae): Laboratory and Field Responses Get access L. K. Tanigoshi, L. K. Tanigoshi Department of Entomology, Washington State University, Pullman, Washington 99164 Search for other works by this author on: Oxford Academic PubMed Google Scholar D. F. Mayer, D. F. Mayer Department of Entomology, Washington State University, Pullman, Washington 99164 Search for other works by this author on: Oxford Academic PubMed Google Scholar J. M. Babcock, J. M. Babcock 2 Department of Entomology, Washington State University, Pullman, Washington 99164 2Current address: DowElanco, Greenfield Laboratories, 2001 West Main St., P.O. Box 708, Greenfield, Ind. 46140. Search for other works by this author on: Oxford Academic PubMed Google Scholar J. D. Lundenl J. D. Lundenl Department of Entomology, Washington State University, Pullman, Washington 99164 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 83, Issue 6, 1 December 1990, Pages 2200–2206, https://doi.org/10.1093/jee/83.6.2200 Published: 01 December 1990 Article history Received: 21 February 1989 Accepted: 06 June 1990 Published: 01 December 1990
Retinoid X Receptor Heterodimers in the Metabolic Syndrome (2005)

The principal abnormalities of the metabolic syndrome are abdominal obesity, atherogenic dyslipidemia, hypertension, insulin resistance, inflammation, and prothrombotic states. This review focuses on the retinoid X receptor (RXR) and its partners in the metabolic syndrome. RXR and its partners are nuclear receptors that function as ligand-dependent transcription factors. The ligands are lipids, and the system functions as a cellular lipid sensor. Agonists and inhibitors of these receptors are promising treatments for this widespread syndrome.
The small heat shock protein hsp27 is correlated with growth and drug resistance in human breast cancer cell lines. (1993)

An emerging body of evidence suggests that the heat shock proteins (hsp) may be involved in drug resistance. When hsp are induced by elevated temperatures, resistance to doxorubicin (Dox), but not to other commonly used chemotherapeutic agents, is induced in breast cancer cells. To evaluate the role of hsp27 in this phenomenon, we have transfected MDA-MB-231 breast cancer cells, which normally express low levels of hsp27, with a full-length hsp27 construct. These hsp27-overexpressing cells now display a 3-fold elevated resistance to Dox. Anchorage-dependent proliferation and anchorage-independent growth were also increased 2-4-fold in these transfectants. We have also derived a MCF-7 breast cancer cell line with amplified endogenous hsp27 which is highly resistant to Dox. When these cells are transfected with an antisense hsp27 construct, they are rendered sensitive to Dox (3-fold) with anchorage-dependent as well as anchorage-independent growth, similarly decreased. These results suggest that hsp27 specifically confers Dox resistance in human breast cancer cells and, furthermore, that hsp27 may be involved in the regulation of cell growth.
Improvement in retinal image quality with dynamic correction of the eye’s aberrations (2001)

We measured the improvement in retinal image quality provided by correcting the temporal variation in the eye's wave aberration with a closed-loop adaptive optics system. This system samples the eye's wave aberration at rates up to 30 Hz. Correction of the eye's aberrations can be completed in 0.25-0.5 seconds, resulting in residual rms wave-front errors as low as 0.1 microns for 6.8 mm pupils. Real-time wave-front measurements were used to determine how effectively the spatial and temporal components of the eye's wave aberration were corrected. The system provides dynamic correction of fluctuations in Zernike modes up to 5 th order with temporal frequency components up to 0.8 Hz. Temporal performance is in good agreement with predictions based on theory. Correction of the temporal variation in the eye's wave aberration increases the Strehl ratio of the point spread function nearly 3 times, and increases the contrast of images of cone photoreceptors by 33% compared with images taken with only static correction of the eye's higher order aberrations.