gebhart/patrepeval huggingface dataset:
Regulation of anaerobic citrate metabolism in Klebsiella pneumoniae (1995)

Three enzymes are specifically required for uptake and catabolism of citrate by Klebsiella pneumoniae under anaerobic conditions: a Na+ -dependent citrate carrier (CitS), citrate lyase (CitDEF), and the Na+ pump oxaloacetate decarboxylase (OadGAB). The corresponding genes are clustered on the chromosome, with the citCDEFG genes located upstream and divergent to the citS-oadGAB genes. We found that expression of citS from its native promoter in Escherichia coli requires the DNA region downstream of oadB. Nucleotide sequence analysis of this region revealed the presence of two adjacent genes, citA and citB. By sequence similarity, the predicted CitA and CitB proteins were identified as members of the two-component regulatory systems. The sensor kinase CitA contained, in the N-terminal half, two putative transmembrane helices which enclosed a presumably periplasmic domain of about 130 amino acids. The C-terminal half of the response regulator CitB harboured a helix-turn-helix motif typical of DNA-binding proteins. K. pneumoniae citB null mutants were unable to grow anaerobically with citrate as the sole carbon and energy source (Cit- phenotype). When cultivated anaerobically with citrate plus glycerol, all of the citrate-specific fermentation enzymes were synthesized in the wild type, but not in the citB mutants. This showed that citS, oadGAB and citDEF required the CitB protein for expression and therefore are part of a regulon. In the wild type, synthesis of CitS, oxaloacetate decarboxylase and citrate lyase was dependent on the presence of citrate, sodium ions and a low oxygen tension. In a citA null mutant which expressed citB constitutively at high levels, none of these signals was required for the formation of the citrate fermentation enzymes. This result suggested that citrate, Na+, and oxygen exerted their regulatory effects via the CitA/CitB system. In the presence of these signals, the citAB gene products induced their own synthesis. The positive autoregulation occurred via co-transcription of citAB with citS and oadGAB.
Selective functionalisation of saturated C–H bonds with metalloporphyrin catalysts (2011)

The recent surge of interest in metal-catalysed C-H bond functionalisation reactions reflects the importance of such reactions in biomimetic studies and organic synthesis. This critical review focuses on metalloporphyrin-catalysed saturated C-H bond functionalisation reported since the year 2000, including C-O, C-N and C-C bond formation via hydroxylation, amination and carbenoid insertion, respectively, together with a brief description of previous achievements in this area. Among the metalloporphyrin-catalysed reactions highlighted herein are the hydroxylation of steroids, cycloalkanes and benzylic hydrocarbons; intermolecular amination of steroids, cycloalkanes and benzylic or allylic hydrocarbons; intramolecular amination of sulfamate esters and organic azides; intermolecular carbenoid insertion into benzylic, allylic or alkane C-H bonds; and intramolecular carbenoid C-H insertion of tosylhydrazones. These metalloporphyrin-catalysed saturated C-H bond functionalisation reactions feature high regio-, diastereo- or enantioselectivity and/or high product turnover numbers. Mechanistic studies suggest the involvement of metal-oxo, -imido (or nitrene), and -carbene porphyrin complexes in the reactions. The reactivity of such metal-ligand multiple bonded species towards saturated C-H bonds, including mechanistic studies through both experimental and theoretical means, is also discussed (244 references).
Amplification of the response to Toll‐like receptor ligands by prolonged exposure to interleukin‐6 in mice: Implication for the pathogenesis of macrophage activation syndrome (2011)

Our findings indicate that prolonged exposure to IL-6 in vivo and in vitro leads to an exaggerated inflammatory response to TLR ligands. Hematologic and biochemical abnormalities in IL-6-transgenic mice treated with LPS show striking similarities to macrophage activation syndrome.
Ruthenium Alkoxycarbene Complexes from an Acetal Function by C−O Bond Cleavage and Alcohol Elimination (1996)

Heating solutions of acetal complexes {CpRu(CH3CN)2[η1-P-2-(Ph2P)[CH(OR)2]C6H4]}OTf (3; R = Me, Et) at 60−95 °C results in loss of one CH3CN ligand and the alcohol ROH, with concomitant formation of carbene complexes CpRu(CH3CN)[η2-C,P-2-(Ph2P)[C(OR)]C6H4]}OTf (4) in high yield. Kinetic and reactivity studies suggest that the rate-determining step of the conversion of 3 to 4 is oxidative addition of an acetal C−O bond to the ruthenium center, which occurs under neutral, mild conditions.
Inhibition of Islet Amyloid Polypeptide Fibril Formation:  A Potential Role for Heteroaromatic Interactions (2004)

The formation of amyloid fibril is associated with major human diseases, including Alzheimer's disease, prion diseases, and type 2 diabetes. Methods for efficient inhibition of amyloid fibril formation are therefore highly clinically important. A principal approach for the inhibition of amyloid formation is based on the use of modified molecular recognition elements. Here, we demonstrate efficient inhibition of amyloid formation of the type 2 diabetes-related human islet amyloid polypeptide (hIAPP) by a modified aromatic peptide fragment and a small aromatic polyphenol molecule. A molecular recognition assay using peptide array analysis suggested that molecular recognition between hIAPP and its core amyloidogenic module is mediated by aromatic rather than hydrophobic interactions. To study the possible effect of aromatic interactions on inhibition of hIAPP fibril formation, we have used peptide and small molecule inhibitors. The addition of a nonamyloidogenic peptide analogue of the core module NFGAILSS, in which phenylalanine was substituted with tyrosine (NYGAILSS), resulted in substantial inhibition of fibril formation by hIAPP. The inhibition was significantly stronger than the one achieved using a beta-sheet breaker-conjugated peptide NFGAILPP. On the basis of the molecular arrangement of the tyrosine-phenylalanine interaction, we suggest that the inhibition stems from the geometrical constrains of the heteroaromatic benzene-phenol interaction. In line with this notion, we demonstrate remarkable inhibition of hIAPP fibril formation and cytotoxicity toward pancreatic beta-cells by a small polyphenol molecule, the nontoxic phenol red compound. Taken together, our results provide further experimental support for the potential role of aromatic interactions in amyloid formation and establish a novel approach for its inhibition.
MHC class I is required for peripheral accumulation of CD8+ thymic emigrants. (1998)

MHC molecules influence the fate of T lymphocytes at two important stages of their differentiation. Recognition of self peptide/MHC complexes in the thymus determines whether immature T cells should live and mature into immunocompetent T cells or whether they should die. In the periphery, recognition of Ags presented by MHC molecules induces T cell activation, proliferation, and differentiation into effector/memory T cells. We describe in this work a third role that MHC molecules play in T cell physiology. CD8+ thymic emigrants require presence of MHC class I molecules in the periphery to seed the peripheral lymphoid organs. Numbers of CD8+ T cells are reduced severely in both the thymus and the periphery of beta2-microglobulin-deficient (beta2m[-/-]) mice. When grafted with wild-type (beta2m[+/+]) thymic epithelium, immature beta2m(-/-) T cells that populate the graft develop into functional mature CD8+ cells. However, significant numbers of peripheral CD8+ cells in grafted beta2m(-/-) mice can be observed only after injection of MHC class I-expressing cells in the periphery. Thus, naive T cells in the periphery do not passively await antigenic stimulation, but actively engage in interactions with self MHC molecules that may promote their survival.
Immune processes in the pathogenesis of Parkinson's disease - a potential role for microglia and nitric oxide. (2002)

It has been known for many years that immune system alterations occur in Parkinson's disease (PD). Changes in lymphocyte populations in cerebrospinal fluid and blood, immunoglobulin synthesis, and cytokine and acute phase protein production have been observed in patients with PD. In this regard, PD patients exhibit a lower frequency of infections and cancer, suggesting that immune system stimulation may occur. This hypothesis is further supported by the observation of T-cell activation leading to the production of interferon gamma in PD. As in other CNS degenerative diseases, in damaged regions in the brains of PD patients, there is evidence of inflammation, characterized by glial reaction (especially microglia), as well as increased expression of HLA-DR antigens, cytokines, and components of complement. These observations suggest that immune system mechanisms are involved in the pathogenesis of neuronal damage in PD. The cellular mechanisms of primary injury in PD have not been clarified, however, but it is likely that mitochondrial mutations, oxidative stress and apoptosis play a role. Furthermore, inflammation initiated by neuronal damage in the striatum and the substantia nigra in PD may aggravate the course of the disease. These observations suggest that treatment with anti-inflammatory drugs may act to slow progression of PD.
Structural Organization and Regulation of the Chicken Estrogen Receptor (1987)

We have cloned the chicken estrogen receptor (ER) from a chicken oviduct lambda gt11 library using the human ER cDNA sequence. This chicken ER sequence is virtually identical to the recently published sequence. One noteable difference is an amino acid change from glutamine to arginine located toward the central region of the sequence. The size of the ER protein predicted from the 589 amino acids is approximately 66,000 which fits well with the range of molecular weights previously published for the calf uterine and human ER (65,000-70,000). We observed the size of the chicken ER mRNA to be approximately 7.8 kilobases which is in agreement with the previously published size of 7.5 kilobases. In vivo secondary stimulation of chicken oviduct total RNA with diethylstilbestrol does not induce chicken ER mRNA. A time course following the chicken ER mRNA levels after secondary stimulation with diethylstilbestrol indicated a decrease in mRNA levels 8 h after DES administration. A similar study was performed using progesterone for the secondary stimulation. An increase in the chicken ER mRNA levels was observed 24 h after stimulation with progesterone. Two regions of very high homology were delineated by analyzing the sequence of this chicken ER cDNA and comparing it to the sequences of the human ER, human glucocorticoid, and chicken progesterone receptors and the P75-erbA fusion product of the avian erythroblastosis virus. The first concensus region is 72 amino acids in length and the second region of high homology is 62 amino acids long. Detailed comparisons of these regions for the steroid hormone receptors and v-erb A are presented. Possible functions for the individual regions of high homology are discussed.
Vehicle Intelligence and Remote Wireless OBD (2000)

&lt;div class="htmlview paragraph"&gt;This paper introduces inexpensive methods for creating intelligent vehicles using existing technology which is aimed primarily at supporting the next generation of on-board diagnostic (OBD) regulations. Whereas these regulations may require remote wireless connectivity with the vehicular ECU, the technology needed to comply with these regulations will engender additional cost which can be best justified by harnessing the same technology for other purposes.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Compliance with future OBD requirements is achieved through a proposed standard called the Automotive Telemetry Protocol (ATP), which is derived from well-known methods for remote diagnostics and management of Internet nodes. An on-board data acquisition and communications device is described which implements this protocol while simultaneously providing for alternative wireless data links between the vehicle and the Internet.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;One of the data links proposed is the IEEE 802.11 specification for wireless LAN's, using a direct sequence spread spectrum (DSSS) RF physical layer. This offers the possibility for vehicular transportation and environmental regulators to monitor high volumes of traffic, within the range of wireless LAN access points. The access points fulfill the role of Internet routers and Mobile IP mobility agents and can be strategically located relative to the highway infrastructure.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;When the on-board device is enabled for IEEE 802.11, direct inter-vehicle communications becomes feasible. The proposed ATP standard for remote OBD is adopted as the fundamental mechanism for exchange of real-time operational information between vehicles. This provides a foundation for distributed processing within an ad-hoc network of vehicles moving within range of each other on the highway, which is called &lt;i&gt;cluster intelligence&lt;/i&gt;. A basic set of services is defined that enables vehicles within a cluster to share critical operation information. This method of imbuing intelligence in the vehicles is seen as a more cost-effective approach to achieving intelligent transportation systems than one based on augmenting the electronics in the highway infrastructure beyond what is required for Internet connectivity.&lt;/div&gt;
Downlink Power Allocation for Distributed Antenna Systems in a Multi-Cell Environment (2009)

In this paper, the downlink performance of distributed antenna systems (DAS) in a multi-cell environment is investigated. The individual power constraints (IPC) for the distributed antennas and the total power constraint (TPC) for all the distributed antennas are proposed to characterize the inter-cell interference power limits and the total transmit power consumption, respectively. When the large-scale channel state information is available at the transmitter, the problem of power allocation among distributed antennas with the target of downlink ergodic capacity maximization is formulated with consideration of IPC and TPC. Based on system scale-up, an approximation of the objective function is derived, which is further proved to be concave on the transmit powers of the distributed antennas. Consequently, a simple sub-optimal power allocation scheme is proposed by substituting the approximation for the objective function. The system capacity with the suboptimal power allocation is illustrated to be quite close to the optimal one obtained by numerical optimizations.
A new method for correction of urinary stress incontinence in women (1986)

Abstract Twenty‐two patients with urinary stress incontinence confirmed by urodynamic recordings were operated on by using absorbable Dexon sutures combined with a two‐component fibrin sealant, which induced fibrosis, for the fixation of the urethrovesical junction to the retropubic periostium. The postoperative observation period ranged from 12 to 30 months, and so far no relapses or complications have been observed.
The Electrochemistry of Germanium Nitride with Lithium (2003)

was investigated for its electrochemical activity with Lithium as a possible negative electrode material for Li-ion batteries. was found to reversibly react with Li, exhibiting high capacity, 500 mAh/g, and maintaining good cycling stability. The reaction mechanism of with lithium was investigated in detail using in situ and ex situ X-ray diffraction (XRD) in reflection, in situ XRD in transmission, ex situ transmission electron microscopy, and selected-area electron diffraction (SAED). The two phases, α- and of the electrode material mostly maintained their respective crystalline microstructure during cycling. A substantial integrated intensity decrease in the XRD Bragg reflections observed during the first lithiation and the concurrent emergence of diffuse rings in SAED suggest the reaction of with lithium may be limited thereby converting only the outermost shell of the crystal. The identification of and Ge at the end of the first delithiation using SAED supports a lithium/metal nitride conversion reaction process. The formation of the matrix was found to be consistent with a 50% irreversible capacity loss in the first cycle. © 2003 The Electrochemical Society. All rights reserved.
Protecting Group Strategies in Organic Synthesis (1996)

Abstract The choice of protecting groups is one of the decisive factors in the successful realization of a complex, demanding synthetic project. The protecting groups used influence the length and efficiency of the synthesis and are often responsible for its success or failure. A wide range of blocking groups are currently available for the different functional groups; however, an overall strategy combining these different masking techniques in an advantageous and reliable manner has never been proposed or at best only for individual cases. This review attempts to make a contribution to filling this gap. First a very short overview of the most commonly used protecting groups will be given, in which they are classified according to their lability and not according to the functional group they protect. This classification clarifies coherent concepts for the development of blocking strategies. On the basis of this brief summary reliable strategies will then be illustrated and developed with selected examples from the recent literature by which protecting groups may be combined successfully and advantageously in synthetic projects of differing degrees of complexity and difficulty.
Abiotic and Biological Transformation of Tetraalkoxysilanes and Trichloroethene/cis-1,2-Dichloroethene Cometabolism Driven by Tetrabutoxysilane-Degrading Microorganisms (1999)

Attenuation of silicon-based organic compounds (tetraalkoxysilanes) by abiotic hydrolysis and biological mineralization was investigated. At Lawrence Livermore National Laboratory site 300, tetraalkoxysilanes are present along with trichloroethene (TCE) as subsurface contaminants. Under abiotic conditions, the alkoxysilanes such as tetrabutoxysilane (TBOS) and tetrakis(2-ethylbutoxy)silane (TKEBS) hydrolyze to 1-butanol and 2-ethylbutanol, respectively, and silicic acid. The rates of hydrolysis of TBOS and TKEBS were determined to evaluate the significance of the hydrolysis reaction in the attenuation process, and typical rates at pH 7, 30 °C, and 28 μmol/L initial concentration were 0.32 and 0.048 μmol/L/day, respectively. The TBOS hydrolysis reaction was observed to be acid- and base-catalyzed and independent of temperature from 15 to 30 °C. All hydrolysis experiments were conducted at concentrations above the solubility limit of TBOS and TKEBS, and the rate of hydrolysis increased with concentration of TBOS or TKEBS. An aerobic microbial culture from the local wastewater treatment plant that could grow and mineralize the alkoxysilanes was enriched. The enriched culture rapidly hydrolyzed TBOS and TKEBS and grew on the hydrolysis products. The microorganisms grown on TBOS cometabolized TCE and cis-1,2-dichloroethene (c-DCE). TCE and c-DCE degradation was inhibited by acetylene, indicating that a monooxygenase was involved in the cometabolism process. Acetylene did not inhibit the hydrolysis of TBOS or the utilization of 1-butanol, indicating that the above monooxygenase enzyme was not involved in the degradation of TBOS.
입시전형별 이공계 대학 신입생 학업성취도 비교 분석 -2012년 M 대학교 이공계 신입생을 중심으로- (2013)

In this paper, we analyzed the freshmen`s achievements on general mathematics their GPA based on ``basic mathematics diagonal test score`` among college entrance types in natural science or engineering. Also, we studied the achievements of students who were not passed the ``Basic Mathematics Diagonal Test (BMDT)`` and had to take supplementary lessons to improve their mathematics abilities four times a week during the first semester of academic year 2012 in Mokpo National University. We found some facts. First, freshmen were accepted by the university through the regular admission have a higher level of academic achievement. Second, freshmen`s academic achievement in the first semester has an effect on their academic achievement in the second semester. Finally, there are correlations between achievements of general mathematics and a curriculum of freshmen who were passed test after taking supplementary lessons.
Carbon Fibers (2001)

Abstract The earliest commercial use of carbon fibers is often attributed to Thomas Edison's carbonization of cotton and bamboo fibers for incandescent lamp filaments. This article describes the manufacture of PAN-based carbon fibers and pitch-based carbon fibers. It discusses the properties and characteristics of carbon fibers in terms of axial structure, transverse structure, and interfacial bonding. The article discusses the typical applications of carbon fibers, including aerospace and sporting goods. It concludes with a discussion on anticipated developments in carbon fibers.
LDL Receptor-Related Protein 1 Regulates the Abundance of Diverse Cell-Signaling Proteins in the Plasma Membrane Proteome (2010)

LDL receptor-related protein 1 (LRP1) is an endocytic receptor, reported to regulate the abundance of other receptors in the plasma membrane, including uPAR and tissue factor. The goal of this study was to identify novel plasma membrane proteins, involved in cell-signaling, that are regulated by LRP1. Membrane protein ectodomains were prepared from RAW 264.7 cells in which LRP1 was silenced and control cells using protease K. Peptides were identified by LC-MS/MS. By analysis of spectral counts, 31 transmembrane and secreted proteins were regulated in abundance at least 2-fold when LRP1 was silenced. Validation studies confirmed that semaphorin4D (Sema4D), plexin domain-containing protein-1 (Plxdc1), and neuropilin-1 were more abundant in the membranes of LRP1 gene-silenced cells. Regulation of Plxdc1 by LRP1 was confirmed in CHO cells, as a second model system. Plxdc1 coimmunoprecipitated with LRP1 from extracts of RAW 264.7 cells and mouse liver. Although Sema4D did not coimmunoprecipitate with LRP1, the cell-surface level of Sema4D was increased by RAP, which binds to LRP1 and inhibits binding of other ligands. These studies identify Plxdc1, Sema4D, and neuropilin-1 as novel LRP1-regulated cell-signaling proteins. Overall, LRP1 emerges as a generalized regulator of the plasma membrane proteome.
The Treatment of Infected Nonunions With Gentamicin???Polymethylmethacrylate Antibiotic Beads (1993)

Fifty-two patients enrolled in the Septopal study of infected nonunions were prospectively examined in a randomized, controlled, closed study. Patients were divided into two groups. Group 1 consisted of 24 patients treated with debridement and intravenous antibiotics for four weeks. Group 2 consisted of 28 patients treated with debridement, gentamicin-polymethylmethacrylate (Septopal) beads, and perioperative broad-spectrum parenteral antibiotics. Both groups were treated with similar methods for reconstruction of the nonunions. The demographics of the two groups were similar. The average patient age in Group 1 was 38.4 years, and in Group 2, 37.1 years. Group 1 included 21 men and three women and Group 2, 23 men and five women. The nonunions in both groups ranged from simple hypertrophic nonunions to atrophic unions to segmental defects. The end results were good in both groups. Twenty patients in Group 1 and 25 patients in Group 2 had their infections successfully arrested (83.3% and 89.3%, respectively). Nonunions were successfully healed in the two groups, with similar results (Group 1, 83.3%; Group 2, 85.7%). Infected nonunions responded equally well to either systemic treatment with long-term intravenous antibiotics or local treatment with gentamicin-polymethylmethacrylate beads.