gebhart/patrepeval huggingface dataset:
In vitro reconstitution and steady-state analysis of the fatty acid synthase from <i>Escherichia coli</i> (2011)

Microbial fatty acid derivatives are emerging as promising alternatives to fossil fuel derived transportation fuels. Among bacterial fatty acid synthases (FAS), the Escherichia coli FAS is perhaps the most well studied, but little is known about its steady-state kinetic behavior. Here we describe the reconstitution of E. coli FAS using purified protein components and report detailed kinetic analysis of this reconstituted system. When all ketosynthases are present at 1 μM, the maximum rate of free fatty acid synthesis of the FAS exceeded 100 μM/ min. The steady-state turnover frequency was not significantly inhibited at high concentrations of any substrate or cofactor. FAS activity was saturated with respect to most individual protein components when their concentrations exceeded 1 μM. The exceptions were FabI and FabZ, which increased FAS activity up to concentrations of 10 μM; FabH and FabF, which decreased FAS activity at concentrations higher than 1 μM; and holo-ACP and TesA, which gave maximum FAS activity at 30 μM concentrations. Analysis of the S36T mutant of the ACP revealed that the unusual dependence of FAS activity on holo-ACP concentration was due, at least in part, to the acyl-phosphopantetheine moiety. MALDI-TOF mass spectrometry analysis of the reaction mixture further revealed medium and long chain fatty acyl-ACP intermediates as predominant ACP species. We speculate that one or more of such intermediates are key allosteric regulators of FAS turnover. Our findings provide a new basis for assessing the scope and limitations of using E. coli as a biocatalyst for the production of diesel-like fuels.
<i>Yersinia</i> Inhibits Host Signaling by Acetylating MAPK Kinases (2006)

Pathogenic Yersinia spp. secrete the effector YopJ (YopP) into host cells to counteract cytokine production and to induce programmed cell death (apoptosis). YopJ achieves these aims by inactivating mitogen-activated protein kinase (MAPK) and nuclear factor kappaB signaling pathways. YopJ was shown to bind to members of the MAPK kinase (MKK) family and was predicted to have protease activity toward ubiquitin (Ub)-like proteins. In a recent report, YopJ was demonstrated to inactivate MKKs via acetylation of critical serine or threonine residues. The ramifications of these exciting results are discussed in the context of other studies implicating YopJ as a Ub-like protease.
Expedient Synthesis of 3-Benzoylflavones by PCC Oxidation of 3-Benzylideneflavanones (2008)

E-mail: kimjn@chonnam.ac.krReceived July 29, 2008Key Words : Baylis-Hillman adducts, Flavanones, PCC, FlavonesThe synthesis and chemical transformation of 3-arylidene-flavanones (3-arylidenechroman-4-ones) and related com-pounds received much attention due to the abundance of thismoiety in many natural products and biologically activesubstances.
Clinical Evaluation of an Automatic Sensitivity Adjustment Feature in a Dual Chamber Pacemaker (1990)

The clinical evaluation of a new automatic sensitivity adjustment feature in the Cosmos II, Model #284-05 is described. This feature, designed to maintain a 2:1 safety margin for sensing intrinsic signals, was activated by way of special programmer software in ten patients at two centers. While the feature worked satisfactorily in some cases, it did not perform as expected, and undersensing in both chambers was observed. This may have been due to biasing the adjustment toward maximum rather than minimum electrograms. This study suggested that electrograms may vary by more than 100% which underscores the importance of this feature, and reinforces the need for continued development.
특집 : 일차진료에서 흔히 접하는 수분 전해질 문제 ; 이뇨제 사용의 원칙과 실제 (2011)

Diuretic drugs are the most commonly used agents to control edema or volume overload. However, the clinical use of diuretics is not confined to edema control. Recently, diuretics have been revisited for the management of various diseases, including hypertension and congestive heart failure. Diuretics are classified mainly by their sites of action in the renal tubules, and have unique characteristics and adverse effects according to their mechanisms of action. To use diuretics adequately, it is very important to understand their characteristics. (Korean J Med 2011;80:8-14)
Genetic Modification of Crop Responses to Imidazolinone Herbicides (1990)

Resistance to imidazolinone herbicides is being introduced into commercial corn varieties. The program to create these hybrids has proceeded through the initiation, implementation and mutant characterization phases, and is currently in the final commercial development phase. Resistant corn was produced by in vitro selection and regeneration of resistant plants. Genetic analyses established that resistance is conferred by a single, semidominant mutant allele. Biochemical analyses demonstrated that resistance is due to altered forms of the enzyme acetohydroxyacid synthase. Commercial sales of imidazolinone-resistant hybrid corn are expected to begin in 1992. This paper tracks the imidazolinone-resistant corn project from its inception through development of the commercial product.
Enzyme‐assisted synthesis of the glucuronide conjugate of psilocin, an hallucinogenic component of magic mushrooms (2011)

An enzyme-assisted synthesis of psilocin glucuronide (PCG), a metabolite excreted in the urine of magic mushroom (MM) users, is described. In the presence of Aroclor 1254 pretreated rat liver microsomes, psilocin and the cofactor UDPGA were incubated for 20 h. Purification by HPLC gave PCG in 19% yield (3.6 mg). The compound structure was characterized by MS and NMR. The milligram amounts of PCG produced by this method will allow the direct identification and quantification of PCG in the urine of MM users.
The Zeamine Antibiotics Affect the Integrity of Bacterial Membranes (2014)

The zeamines (zeamine, zeamine I, and zeamine II) constitute an unusual class of cationic polyamine-polyketide-nonribosomal peptide antibiotics produced by Serratia plymuthica RVH1. They exhibit potent bactericidal activity, killing a broad range of Gram-negative and Gram-positive bacteria, including multidrug-resistant pathogens. Examination of their specific mode of action and molecular target revealed that the zeamines affect the integrity of cell membranes. The zeamines provoke rapid release of carboxyfluorescein from unilamellar vesicles with different phospholipid compositions, demonstrating that they can interact directly with the lipid bilayer in the absence of a specific target. DNA, RNA, fatty acid, and protein biosynthetic processes ceased simultaneously at subinhibitory levels of the antibiotics, presumably as a direct consequence of membrane disruption. The zeamine antibiotics also facilitated the uptake of small molecules, such as 1-N-phenylnaphtylamine, indicating their ability to permeabilize the Gram-negative outer membrane (OM). The valine-linked polyketide moiety present in zeamine and zeamine I was found to increase the efficiency of this process. In contrast, translocation of the large hydrophilic fluorescent peptidoglycan binding protein PBDKZ-GFP was not facilitated, suggesting that the zeamines cause subtle perturbation of the OM rather than drastic alterations or defined pore formation. At zeamine concentrations above those required for growth inhibition, membrane lysis occurred as indicated by time-lapse microscopy. Together, these findings show that the bactericidal activity of the zeamines derives from generalized membrane permeabilization, which likely is initiated by electrostatic interactions with negatively charged membrane components.
Mode-hopping noise reduction by rf modulation of the pump current of an injection semiconductor laser with an external cavity (1994)

An experimental investigation was made of the influence of rf modulation of the pump current on the mode-hopping noise of a semiconductor injection laser coupled to an external nonselective mirror. The modulation frequencies were of the order of the intermode interval of the system. When two or more modes were generated, the imposition of rf modulation on the laser pump current reduced the intensity of the mode-hopping noise in a separate spectral mode. The maximum reduction (by an order of magnitude) occurred at a modulation frequency equal to the frequency interval between the modes of the laser with the external cavity or to harmonics of this frequency. When one mode was generated, the imposition of rf modulation at the same frequency as the intermode interval increased the mode-hopping noise.
Oxidative stress inhibits the proliferation, induces premature senescence and promotes a catabolic phenotype in human nucleus pulposus intervertebral disc cells (2015)

Aged and degenerated intervertebral discs are characterised by a significant increase in the number of senescent cells, which may be associated with the deterioration of this tissue due to their catabolic phenotype. On the other hand, carboxymethyl-lysine has been found to be accumulated with ageing in the proteins of the disc, evidencing the existence of oxidative stress in this tissue. Accordingly, here we investigated the effect of oxidative stress on the physiology of human nucleus pulposus cells. Hydrogen peroxide (H2O2) at subcytotoxic concentrations transiently increased the intracellular levels of reactive oxygen species, activated the p38 MAPK, ERKs, JNKs and Akt signalling pathways and induced the nuclear translocation of NF-κΒ and Nrf2. It also provoked DNA damage and triggered a DNA repair response by activating the ATM-Chk2-p53-p21(WAF1)-pRb pathway, ultimately resulting in a G1 cell cycle delay and the decrease of cells' proliferation. Prolonged exposure to H2O2 led to premature cellular senescence, as characterised by the inhibition of proliferation, the enhanced senescence-associated β galactosidase staining and the over-expression of known molecular markers, without though a significant decrease in the chromosome telomere length. H2O2-senescent cells were found to possess a catabolic phenotype, mainly characterised by the up-regulation of extracellular matrix-degrading enzymes (MMP-1, -2, -9 and ADAMTS-5) and the down-regulation of their inhibitors (TIMPs), as well as of several proteoglycans, including aggrecan, the major component of the nucleus pulposus. The senescent phenotype could be reversed by N-acetyl-L-cysteine, supporting the use of antioxidants for the improvement of disc physiology and the deceleration of disc degeneration.
Steroid receptor interactions in human breast carcinoma (1980)

Sucrose gradient centrifugation of estrogen and progestin receptors in cytosol preparations revealed that the majority of human breast tumors contained two molecular forms sedimenting at either 8S or 4S. Few tumors exhibited profiles containing predominately the 8S form or the 4S form alone. Molecular heterogeneity of the estrogen receptors in cytosol was demonstrated with regard to surface charge using ion-exchange chromatography and isoelectric focusing. The molecular properties of estrogen receptors in breast tumor biopsy specimens appear to be related to clinical responsiveness of patients given hormonal manipulations. These data and other findings related to the clinical utility of steroid receptor quantification impose a requirement for rigid quality control of analyses by the laboratory. The composition, evaluation, and distribution of tissue reference powders for establishing uniformity and quality control of steroid receptor analyses used in cooperative clinical trials of breast cancer treatment are described. This approach ensures meaningful correlations between laboratory results and clinical response.
Graph-theoretic connectivity control of mobile robot networks (2011)

We provide a theoretical framework for controlling graph connectivity in mobile robot networks. We discuss proximity-based communication models composed of disk-based or uniformly-fading-signal-strength communication links. A graph-theoretic definition of connectivity is provided, as well as an equivalent definition based on algebraic graph theory, which employs the adjacency and Laplacian matrices of the graph and their spectral properties. Based on these results, we discuss centralized and distributed algorithms to maintain, increase, and control connectivity in mobile robot networks. The various approaches discussed in this paper range from convex optimization and subgradient-descent algorithms, for the maximization of the algebraic connectivity of the network, to potential fields and hybrid systems that maintain communication links or control the network topology in a least restrictive manner. Common to these approaches is the use of mobility to control the topology of the underlying communication network. We discuss applications of connectivity control to multirobot rendezvous, flocking and formation control, where so far, network connectivity has been considered an assumption.
Extensive genetic polymorphism in the human tumor necrosis factor region and relation to extended HLA haplotypes. (1991)

We have identified three polymorphic microsatellites (which we call TNFa, TNFb, and TNFc) within a 12-kilobase region of the human major histocompatibility complex (MHC) that includes the tumor necrosis factor (TNF) locus. TNFc is located within the first intron of the TNF-beta gene and has only 2 alleles. TNFa and TNFb are 3.5 kilobases upstream (telomeric) of the TNF-beta gene and have at least 13 and 7 alleles, respectively. TNFa, -b, and -c alleles are in linkage disequilibrium with alleles at other loci within the MHC, including class I, class II, and class III. TNFa, -b, and -c alleles are also associated with extended HLA haplotypes. These TNF polymorphisms will allow a thorough genetic analysis of the involvement of TNF in MHC-linked pathologies.
A Unified Interpretation of High-Temperature Pore Size Expansion Processes in MCM-41 Mesoporous Silicas (1999)

A unified interpretation is presented for high-temperature (ca. 423 K) unit-cell enlargement of MCM-41 synthesized in the presence of cetyltrimethylammonium (CTMA+) surfactants without auxiliary organics. Such processes during postsynthesis hydrothermal treatments and direct syntheses were reported by several research groups to afford large-unit-cell (d spacing up to 7 nm) and large-pore (up to 7 nm) MCM-41 materials, but their structures were claimed to be different and the proposed mechanisms of the processes were not consistent with each other. The current study demonstrates significant structural similarities of large-pore MCM-41 materials prepared using direct syntheses and postsynthesis treatments, reveals the common mechanism of their formation, and discusses its implications for preparation of large-pore materials, including new synthesis procedures. The proposed comprehensive description of the mechanism of the unit-cell-enlargement processes involves the in situ generation of N,N-dimethylhexadecylamine (DMHA) and its swelling action as a driving force of the pore size enlargement. The swelling properties of DMHA were confirmed by a successful synthesis of large-pore MCM-41 in mild conditions in the presence of DMHA and preparation of silicas with pore sizes up to 11 nm and extremely large-pore volumes up to 2.4 cm3/g via restructuring of 3.5 nm MCM-41 in aqueous emulsions of long-chain amines (dimethyldecylamine or DMHA). The neutral amine is formed during the high-temperature processes as a result of decomposition of CTMA+ cations, which is likely to be accompanied by migration of tetramethylammonium cations (TMA+) to the silica−surfactant interface or is possibly related with replacement of CTMA+ by TMA+ at the interface. The reasons for the pore volume increase and surface area decrease during the pore size enlargement are discussed. Moreover, it is suggested that the unit-cell expansion in the direction perpendicular to the pore channels is accompanied by shrinkage of the structure in the direction parallel to the channels.
Basic Biomechanics of the Musculoskeletal System (1989)

Unique in its direct and comprehensive approach, this Third Edition presents a working knowledge of biomechanical principles for use in the evaluation and treatment of musculoskeletal dysfunction. Three sections address the biomechanics of musculoskeletal tissues and structures, the biomechanics of joints, and applied biomechanics. This edition's new introductory chapter explains the importance of biomechanics study and includes the International System of Units appendix. A new section on Applied Biomechanics includes chapters on fracture fixation; arthroplasty; standing, sitting, and lying; and gait. Boxes with biomechanical computations promote comprehension of biomechanical principles. Practical examples and clinical case studies apply biomechanical knowledge to practice. Additional illustrations, including radiological images, enhance comprehension. A Brandon-Hill recommended title.
Human Embryonic Stem Cells Form Functional Thyroid Follicles (2015)

The induced expression of PAX8 and NKX2-1 in hES cells was followed by differentiation into thyroid epithelial cells and their commitment to form functional three-dimensional neo-follicular structures. The data provide proof of principal that hES cells can be committed to thyroid cell speciation under appropriate conditions.
Macroscopic Postmortem Findings in 235 Surgical Intensive Care Patients with Sepsis (2009)

Relevant postmortem findings explaining death in surgical ICU patients who died because of sepsis/septic shock were a continuous septic focus in approximately 80% and cardiac pathologies in 50%. The most frequently affected organs were the lungs, abdomen, and urogenital tract. More diagnostic, therapeutic and scientific efforts should be launched to identify and control the infectious focus in patients with sepsis and septic shock.
Comparative Study of Seeding and Culture Methods to Vascular Smooth Muscle Cells on Biodegradable Scaffold (2004)

How to improve the cell culture method on scaffolds is important in the tissue engineering fileld. In this study, we optimized seeding and culture methods to vascular smooth muscle cells (VSMCs) on biodegradable polymer scaffold. The primary culture of VSMCs obtained from canine external jugular vein was accomplished by applying the explant-derived method. The primary cultured VSMCs were seeded into scaffolds and then cultured by using various different methods; static or dynamic seeding, static or dynamic culture. The difference in proliferative response of VSMCs was analyzed with an alamar blue assay. Cell- polymer construct was examined by histochemical method and scanning electron microscopy. Mesh type scaffold (10x10x0.4mm) was made of polyglycolic acid (PGA) suture thread. The PGA mesh type scaffold was 45% in porosity, and 0.03g in weight. The primary cultured VSMCs were confirmed with immunohistochemical staining using monoclonal anti-alpha-smooth muscle actin. The density and distribution of proliferated VSMCs within the scaffold and cellular adherence on the surface of the scaffold showed better results in the static seeding condition than in the dynamic condition. Under the same condition of seeding method as the static condition, the dynamic culture condition showed enhanced proliferation rates of the VSMCs when compared to the static culture condition. In conclusion, to improve the VSMCs proliferation in vitro, static seeding is better than the dynamic condition. In the culture condition, however, culture under the dynamic status is better than the static condition. This was a pilot study to manufacture artificial vascular vessel by tissue engineering.
American Experience With Low-Dose Thalidomide Therapy for Severe Cutaneous Lupus Erythematosus (1999)

A low starting dose of thalidomide as a monotherapy with continued sun avoidance is a safe and effective treatment for the various cutaneous manifestations of lupus erythematosus after traditional therapeutic options have failed to control disease. Our experience with low-dose, long-term thalidomide therapy suggests that peripheral neuropathy is not as common as suggested by other studies (up to 50% of patients treated with thalidomide in some series).
Matrix vesicles contain metalloproteinases that degrade proteoglycans (1992)

This study explored whether extracellular matrix processing enzymes are present in matrix vesicles produced by rat costochondral resting zone and growth zone chondrocytes in culture. It was found that there was a differential distribution of enzyme activities related to the cartilage zone from which the cells were isolated. There was a 3-fold enrichment of total and active acid metalloproteinase in growth zone chondrocyte (GC) matrix vesicles whereas no enrichment in enzyme activity was observed in resting zone chondrocyte (RC) matrix vesicles. Total and active neutral metalloproteinase were similarly enriched 2-fold in GC matrix vesicles. TIMP, plasminogen activator and beta-glucuronidase activities were highest in the plasma membranes of both cell types. No collagenase, lysozyme, or hyaluronidase activity was found. The data indicate that matrix vesicles are selectively enriched in enzymes that degrade proteoglycans. The highest concentrations of these enzymes are found in matrix vesicles produced by growth zone chondrocytes, suggesting that this may be a mechanism by which the more differentiated cell modulates the matrix for calcification.
Up-regulated macrophage migration inhibitory factor protects apoptosis of dermal fibroblasts in patients with systemic sclerosis (2008)

Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine that has been demonstrated to regulate the apoptosis of several cell types. Dysregulated apoptosis of fibroblasts has been implicated in a variety of fibrotic diseases, including systemic sclerosis (SSc). In this study, we investigated the role of MIF in the apoptosis of dermal fibroblasts. The concentrations of MIF were measured in sera and in culture supernatants of peripheral blood mononuclear cells (PBMCs) and dermal fibroblasts by enzyme-linked immunosorbent assay. The degree of apoptosis was determined by colorimetric assay, and signalling pathways were examined by Western blot. The results showed that serum levels of MIF were significantly higher in patients with SSc (n = 47) than in healthy controls (n = 56). Stimulation of PBMCs by anti-CD3 and anti-CD28 increased the production of MIF by fourfold over the constitutive levels. SSc dermal fibroblasts produced higher amounts of MIF than normal dermal fibroblasts. When treated with sodium nitroprusside (SNP), SSc dermal fibroblasts showed a lower degree of apoptosis compared with normal dermal fibroblasts. Exogenous MIF (1-100 ng/ml) inhibited SNP-induced apoptosis of dermal fibroblasts dose-dependently. Both extracellular regulated kinase (ERK) inhibitor (PD98059) and protein kinase B (Akt) inhibitor (LY294002) almost completely blocked the inhibitory effect of MIF on apoptosis. Furthermore, MIF increased the expression of Bcl-2, phospho-ERK and phospho-Akt activity in dermal fibroblasts. Taken together, our data suggest that MIF released by activated T cells and dermal fibroblasts decreases the apoptosis of dermal fibroblasts through activation of ERK, Akt and Bcl-2 signalling pathways, which might be associated with excessive fibrosis in SSc.
Preparation of frozen reference sera and examples of applications (1984)

We describe procedures for preparation of human serum from ACD bank blood and bovine serum from slaughter house blood. Preparation techniques including filtration and dialysis are described in detail as well as how to obtain desired concentrations. Special attention has been drawn to procedures yielding low lactate dehydrogenase activity. Long-term storage should take place at -75 degrees C. Different frozen reference sera have been used for calibration purposes, internal quality control and external quality assessment.