gebhart/patrepeval huggingface dataset:
Coverage-Dependent Charge Reduction of Cationic Gold Clusters on Surfaces Prepared Using Soft Landing of Mass-Selected Ions (2012)

The ionic charge state of monodisperse multiply charged cationic gold clusters on surfaces may be controlled by selecting the coverage of mass-selected ions soft landed onto a substrate. Polydisperse diphosphine-capped gold clusters were synthesized in solution and introduced into the gas phase by electrospray ionization. Mass selection was employed to isolate a multiply charged cationic cluster species (Au11L53+, m/z = 1409, L = 1,3-bis(diphenylphosphino)propane) which was delivered to the surfaces of four different self-assembled monolayers on gold (SAMs) at controlled coverages of 1011 and 1012 clusters. Employing the spatial profiling capabilities of in situ time-of-flight secondary ion mass spectrometry (TOF-SIMS), it is shown that, in addition to the chemical functionality of the monolayer (as demonstrated previously: ACS Nano 2012, 6, 573), the coverage of cationic gold clusters on the surface may be used to control the relative abundance of different charge states of the soft landed multiply charged clusters. In the case of a 1H,1H,2H,2H-perfluorodecanethiol monolayer (FSAM) almost complete retention of charge by the deposited Au11L53+ clusters was observed at a lower coverage of 1011 clusters. In contrast, at a higher coverage of 1012 clusters, pronounced reduction of charge to Au11L52+ and Au11L5+ was observed on the FSAM. When soft landed onto 16- and 11-mercaptohexadecanoic acid surfaces on gold (16,11-COOH-SAMs), the mass-selected Au11L53+ clusters exhibited partial reduction of charge to Au11L52+ at lower coverage and additional reduction of charge to both Au11L52+ and Au11L5+ at higher coverage. On the surface of the 1-dodecanethiol (HSAM) monolayer, the most abundant charge state was found to be Au11L52+ at lower coverage and Au11L5+ at higher coverage, respectively. A coverage-dependent electron tunneling mechanism is proposed to account for the observed reduction of charge of mass-selected multiply charged gold clusters soft landed on SAMs. The results demonstrate that one of the critical parameters that influence the chemical and physical properties of supported metal clusters, ionic charge state, may be controlled by selecting the coverage of charged species soft landed onto surfaces.
Best α‐helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information (2004)

Methods that predict the topology of helical membrane proteins are standard tools when analyzing any proteome. Therefore, it is important to improve the performance of such methods. Here we introduce a novel method, PRODIV-TMHMM, which is a profile-based hidden Markov model (HMM) that also incorporates the best features of earlier HMM methods. In our tests, PRODIV-TMHMM outperforms earlier methods both when evaluated on "low-resolution" topology data and on high-resolution 3D structures. The results presented here indicate that the topology could be correctly predicted for approximately two-thirds of all membrane proteins using PRODIV-TMHMM. The importance of evolutionary information for topology prediction is emphasized by the fact that compared with using single sequences, the performance of PRODIV-TMHMM (as well as two other methods) is increased by approximately 10 percentage units by the use of homologous sequences. On a more general level, we also show that HMM-based (or similar) methods perform superiorly to methods that focus mainly on identification of the membrane regions.
Preparation and Characterization of Paclitaxel-loaded PLGA Nanoparticles Coated with Cationic SM5-1 Single-chain Antibody (2007)

The purpose of this study was to develop paclitaxel-loaded poly(lactide-co-glycolide) (PLGA) nanoparticles coated with cationic SM5-1 single-chain antibody (scFv) containing a polylysine (SMFv-polylys). SM5-1 scFv (SMFv) is derived from SM5-1 monoclonal antibody, which binds to a 230 kDa membrane protein specifically expressed on melanoma, hepatocellular carcinoma and breast cancer cells. SMFv-polylys was expressed in Escherichia coli and purified by cation-exchange chromatography. Purified SMFv-polylys was fixed to paclitaxel-loaded PLGA nanoparticles to form paclitaxel-loaded PLGA nanoparticles coated with SMFv-polylys (Ptx-NP-S). Ptx-NP-S was shown to retain the specific antigen-binding affinity of SMFv-polylys to SM5-1 binding protein-positive Ch-hep-3 cells. Finally, the cytotoxicity of Ptx-NP-S was evaluated by a non-radioactive cell proliferation assay. It was demonstrated that Ptx-NP-S had significantly enhanced in vitro cytotoxicity against Ch-hep-3 cells as compared with non-targeted paclitaxel-loaded PLGA nanoparticles. In conclusion, our results suggest that cationic SMFv-polylys has been successfully generated and may be used as targeted ligand for preparing cancer-targeted nanoparticles.
Serum amyloid A protein stimulates CCL20 production in rheumatoid synoviocytes (2009)

Objective. Although serum amyloid A (SAA) has been used as a marker of inflammation, its role in leucocyte recruitment and angiogenesis has not been well established in RA. CCL20 is a chemokine involved in the migration of CCR6-expressing Th17 cells. To study the contribution of SAA to the recruitment of Th17 cells, we investigated the effects of SAA on CCL20 production by RA synoviotytes. Methods. Synoviocytes isolated from RA patients were stimulated with recombinant SAA and cellular supernatants were analysed by CCL20-specific ELISA. CCL-20 mRNA expression was analysed by RT-PCR. Results. SAA is a most potent inducer of CCL20 secretion in RA synoviocytes compared with other inflammatory cytokines (IL-1, TNFand IL-17A). SAA stimulation induced CCL20 mRNA expression in RA synoviocytes, which was not affected by polymyxin B pre-treatment. SAA-induced CCL20 production was down-regulated by NF-B inhibition and partially by c-jun N-terminal kinase (JNK) inhibition. SAAinduced CCL20 production was also suppressed by dexamethasone or FK506. Conclusion. These findings suggest that SAA may be implicated in the recruitment of lymphocytes, including CCR6-expressing Th17 cells, in RA synovium by up-regulating CCL20 production in synoviocytes.
<I>Effect of Spinal Cord Stretching due to Head Flexion on Intramedullary Pressure</I> (1995)

The effect of the longitudinal stretching force of the spinal cord on intramedullary pressure was investigated using our method for measuring intramedullary pressure of the spinal cord with implanted balloons. The transverse compressive force against the posterior wall of the spinal column was excluded by measuring the intramedullary pressure during flexion of the head with the middle and lower cervical spine in the neutral position. The intramedullary pressure of the cervical spinal cord was measured simultaneously at the C-2, C-4, and C-6 levels in 10 mongrel dogs, in three head positions: neutral, and head extension and flexion. Head flexion caused significant increases in the intramedullary pressure at C-2, C-4, and C-6. The pressure increase in the middle to lower cervical cord must have been due to the transmission of the longitudinal stretching force of the cord itself, and may be a factor in the development of intramedullary disorders such as syringomyelia and intramedullary neoplasms.
High prevalence of hypogonadotropic hypogonadism in men referred for obesity treatment. (2008)

Reduced T levels, well into the hypogonadal range, are common in male obesity. Assessment of its clinical implications, and a search for the best mode of treatment are warranted.
Slow Transit Constipation Associated With Excess Methane Production and Its Improvement Following Rifaximin Therapy: A Case Report (2011)

Constipation, a common problem in gastroenterology practice, may result from slow colonic transit. Therapeutic options for slow transit constipations are limited. Excessive methane production by the methanogenic gut flora, which is more often found in patients with constipation, slows colonic transit. Thus, reduction in methane production with antibiotic treatment directed against methanogenic flora of the gut may accelerate colonic transit resulting in improvement in constipation. However, there is not much data to prove this hypothesis. We, therefore, report a patient with slow transit constipation associated with high methane production both in fasting state and after ingestion of glucose, whose constipation improved after treatment with non-absorbable antibiotic, rifaximin, which reduced breath methane values.
A Kinase–Anchoring Protein (Akap95) Recruits Human Chromosome-Associated Protein (Hcap-D2/Eg7) for Chromosome Condensation in Mitotic Extract (2000)

Association of the condensin multiprotein complex with chromatin is required for chromosome condensation at mitosis. What regulates condensin targeting to chromatin is largely unknown. We previously showed that the nuclear A kinase-anchoring protein, AKAP95, is implicated in chromosome condensation. We demonstrate here that AKAP95 acts as a targeting protein for human chromosome-associated protein (hCAP)-D2/Eg7, a component of the human condensin complex, to chromosomes. In HeLa cell mitotic extract, AKAP95 redistributes from the nuclear matrix to chromatin. When association of AKAP95 with chromatin is prevented, the chromatin does not condense. Condensation is rescued by a recombinant AKAP95 peptide containing the 306 COOH-terminal amino acids of AKAP95. Recombinant AKAP95 binds chromatin and elicits recruitment of Eg7 to chromosomes in a concentration-dependent manner. Amount of Eg7 recruited correlates with extent of chromosome condensation: resolution into distinct chromosomes is obtained only when near-endogenous levels of Eg7 are recruited. Eg7 and AKAP95 immunofluorescently colocalize to the central region of methanol-fixed metaphase chromosomes. GST pull-down data also suggest that AKAP95 recruits several condensin subunits. The results implicate AKAP95 as a receptor that assists condensin targeting to chromosomes.
Complex feedback regulation of bile acid synthesis in the hamster: The role of newly synthesized cholesterol (1999)

Hepatic bile acid synthesis is regulated by recirculating bile acids, possibly by modulating the availability of newly synthesized and preformed cholesterol. Because data in the hamster on this mechanism are lacking, we fitted these animals with an extracorporeal bile duct and administered tritiated water intraperitoneally to label newly formed cholesterol. After interruption of the enterohepatic circulation, physiological and double-physiological doses of conjugated cholate (25 or 50 micromol/100 g. h) or of unconjugated deoxycholate (6 or 12 micromol) were infused intraduodenally for 54 hours and compared with controls. De novo and preformed cholesterol directly secreted into bile or used for cholate and chenodeoxycholate synthesis were quantitated by high-pressure liquid chromatography (HPLC)-liquid scintillation. Directly after depletion of the bile acid pool (6-9 hours) at nearly physiological conditions, chenodeoxycholate synthesis was significantly reduced by cholate and deoxycholate by up to 45% to 51%, whereas cholate formation decreased by approximately 22% during deoxycholate. This short-term effect was mainly mediated by reduced synthesis from preformed cholesterol. After long-term bile depletion (30-54 hours), bile acid synthesis returned to control levels during 25 micromol of cholate and of both deoxycholate doses. In contrast, only 50 micromol of cholate prevented derepression of bile acid synthesis. This long-term effect was mainly attributed to a diminished formation from de novo cholesterol exceeding the reduced synthesis from preformed cholesterol. In summary, short- and long-term regulation of bile acid synthesis in hamsters differs with respect to availabilities of preformed and de novo cholesterol.
Biocatalysis in Organic Media (1992)

It is now accepted that organic media are widely applicable to biocatalytic processes. Enzyme reactions have been demonstrated in many different solvent systems containing apolar solvents with a wide range of hydrophobicities. In such systems the aqueous fraction of the solvent may vary from trace levels (the "microaqueous" reaction system) to the major constituent. The properties of enzymes in media containing both aqueous and apolar constituents are influenced by many factors including the dielectric constant, the concentration or "activity" of water, the presence of phase-interfaces, etc. All of these factors influence the structural stability of the enzyme to some degree and optimization of enzymestability in response to these factors is of critical importance in the design of any organic-solvent biocatalytic system. The presence of apolar solvents, even at low concentrations, may influence protein structure at a more subtle level, resulting in significant changes in reaction kinetics, substrate specificity and stereoselectivity. Thus "solvent engineering" can be used to exert control over reaction mechanisms, product spectrum and yield In order to take full advantage of the effects of different solvents on enzyme function in designing reaction systems, an understanding of the molecular interactions between solvent and protein is essential. For example, a detailed knowledge of the role of protein solvation shell water and the distortion of this shell by hydrophilic organic solvents may assist in the design of "solvent resistant" enzymes. Similarly, the inferred influence of low water content solvents on conformational mobility may permit us to select solvent systems which will optimise the chemical and optical purity of the reaction products.
MicroRNA-21 induces resistance to 5-fluorouracil by down-regulating human DNA MutS homolog 2 (hMSH2) (2010)

The overexpression of microRNA-21 (miR-21) is linked to a number of human tumors including colorectal cancer, where it appears to regulate the expression of tumor suppressor genes including p21, phosphatase and tensin homolog, TGFβ receptor II, and B-cell leukemia/lymphoma 2 -associated X protein. Here we demonstrate that miR-21 targets and down-regulates the core mismatch repair (MMR) recognition protein complex, human mutS homolog 2 (hMSH2) and 6 (hMSH6). Colorectal tumors that express a high level of miR-21 display reduced hMSH2 protein expression. Cells that overproduce miR-21 exhibit significantly reduced 5-fluorouracil (5-FU)-induced G2/M damage arrest and apoptosis that is characteristic of defects in the core MMR component. Moreover, xenograft studies demonstrate that miR-21 overexpression dramatically reduces the therapeutic efficacy of 5-FU. These studies suggest that the down-regulation of the MMR mutator gene associated with miR-21 overexpression may be an important clinical indicator of therapeutic efficacy in colorectal cancer.
Constructing semantic ontologies for business analytics (2010)

Business analytics (BA) involves defining organization's capabilities and requirements in order to understand how it functions to accomplish its purposes. BA is typically performed to define and validate solutions that are designed to meet organization's business needs, goals or objectives. To pursue this mission, analysts have to collect, analyse and synthesise huge amount of information. In this paper we demonstrate how constructing semantic ontologies can increase the level of automation of BA methods and techniques. This can be achieved by sophisticated semantic data analysis that can help us structure information and obtain birds-eye overview of a given domain. For the case study we take a set of abstracts from the articles presented on CompSysTech'09 conference and use OntoGen tool to semi-automatically construct ontology for the domain. The obtained results indicate that the proposed approach can be effectively used to digest textual information and present it in a more operational form of topic ontology. We argue that such approach can be useful also to generate domain knowledge in the field of BA.
Bis(imino)pyridine Iron Complexes for Aldehyde and Ketone Hydrosilylation (2008)

Bis(imino)pyridine iron dinitrogen and dialkyl complexes are well-defined precatalysts for the chemo- and regioselective reduction of aldehydes and ketones. Efficient carbonyl hydrosilylation is observed at low (0.1-1.0 mol %) catalyst loadings and with 2 equiv of either PhSiH(3) or Ph(2)SiH(2), representing one of the most active iron-catalyzed carbonyl reductions reported to date.
Synthesis of a Novel Photobase Generator Having a Base-Proliferating Group and its Application to a Negative-Type Photopolymer (2014)

筆者らはこれまで塩基触媒反応を利用したフォトポリマーの感度を向上させる目的で塩基増殖反応を組み込むことを提案しており，その有用性の実証にも成功している．しかしながら，これまでの系では光塩基発生剤と塩基増殖剤をそれぞれ添加しなければならず，樹脂に対する添加量も多くなってしまう欠点があった．そこで本研究では塩基増殖基を有する光塩基発生剤(1)を合成しエポキシポリマーと組合せて感光特性を評価したところ，膜の深部まで十分に光が到達しないような厚い膜において，光塩基発生能しかない光塩基発生剤を用いた系と比べて飛躍的な高感度化が観測された．これは露光後の加熱により1の塩基増殖反応が進行し塩基濃度が増大したためと考えられる．
Internet agents: spiders, wanderers, brokers, and bots (1996)

This reference guide to one of the latest technologies on the Internet not only describes the benefits of using Agents and Bots and applying them to everyday scenarios, but also addresses the impact of Bots on a network's resources. -- Teaches users how to effectively manage network server resources -- Demonstrates time- and cost-saving features of spiders, wanderers, brokers, and bots-helping users become more productive -- Contains a current listing of all Agents, Bots, and Spiders available on the Internet today
Cholinergic Changes in the APP23 Transgenic Mouse Model of Cerebral Amyloidosis (2002)

Alzheimer's Disease (AD) is a neurodegenerative disorder that is characterized by extracellular deposits of amyloid-beta peptide (Abeta) and a severe depletion of the cholinergic system, although the relationship between these two events is poorly understood. In the neocortex, there is a loss of cholinergic fibers and receptors and a decrease of both choline acetyltransferase (ChAT) and acetylcholinesterase enzyme activities. The nucleus basalis of Meynert (NBM), which provides the major cholinergic input to the neocortex, undergoes profound neuron loss in AD. In the present study, we have examined the cholinergic alterations in amyloid precursor protein transgenic mice (APP23), a mouse model of cerebral beta-amyloidosis. In aged APP23 mice, our results reveal modest decreases in cortical cholinergic enzyme activity compared with age-matched wild-type mice. Total cholinergic fiber length was more severely affected, with 29 and 35% decreases in the neocortex of aged APP23 mice compared with age-matched wild-type mice and young transgenic mice, respectively. However, there was no loss of cholinergic basal forebrain neurons in these aged APP23 mice, suggesting that the cortical cholinergic deficit in APP23 mice is locally induced by the deposition of amyloid and is not caused by a loss of cholinergic basal forebrain neurons. To study the impact of cholinergic basal forebrain degeneration on cortical amyloid deposition, we performed unilateral NBM lesions in adult APP23 mice. Three to 8 months after lesioning, a 38% reduction in ChAT activity and significant cholinergic fiber loss were observed in the ipsilateral frontal cortex. There was a 19% decrease in Abeta levels of the ipsilateral compared with contralateral frontal cortex with no change in the ratio of Abeta40 to Abeta42. We conclude that the severe cholinergic deficit in AD is caused by both the loss of cholinergic basal forebrain neurons and locally by cerebral amyloidosis in the neocortex. Moreover, our results suggest that disruption of the basal cholinergic forebrain system does not promote cerebral amyloidosis in APP23 transgenic mice.
Cutaneous Responses to Cholera Skin Toxin in Man. I. Responses in Unimmunized American Males (1972)

Journal Article Cutaneous Responses to Cholera Skin Toxin in Man. I. Responses in Unimmunized American Males Get access John P. Craig, John P. Craig Search for other works by this author on: Oxford Academic PubMed Google Scholar Edward R. Eichner, Edward R. Eichner Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard B. Hornick Richard B. Hornick Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 125, Issue 3, March 1972, Pages 203–215, https://doi.org/10.1093/infdis/125.3.203 Published: 01 March 1972 Article history Received: 08 September 1970 Revision received: 17 September 1971 Published: 01 March 1972
Function and Characteristics of PINK1 in Mitochondria (2013)

Mutations in phosphatase and tensin homologue-induced kinase 1 (PINK1) cause recessively inherited Parkinson's disease, a neurodegenerative disorder linked to mitochondrial dysfunction. Studies support the notion of neuroprotective roles for the PINK1, as it protects cells from damage-mediated mitochondrial dysfunction, oxidative stress, and cell apoptosis. PARL is a mitochondrial resident rhomboid serine protease, and it has been reported to mediate the cleavage of the PINK1. Interestingly, impaired mitophagy, an important autophagic quality control mechanism that clears the cells of damaged mitochondria, may also be an underlying mechanism of disease pathogenesis in patients for Parkinson's disease with the PARL mutations. Functional studies have revealed that PINK1 recruits Parkin to mitochondria to initiate the mitophagy. PINK1 is posttranslationally processed, whose level is definitely regulated in healthy steady state of mitochondria. As a consequence, PINK1 plays a pivotal role in mitochondrial healthy homeostasis.
Increasing dietary fiber intake in terms of kiwifruit improves constipation in Chinese patients (2007)

Increasing dietary fiber intake is effective in relieving chronic constipation in Chinese population.
Biosensors for continuous in vivo glucose monitoring (1988)

The authors have developed a ferrocene-mediated amperometric glucose oxidase enzyme electrode for continuous in vivo measurement of subcutaneous tissue glucose in man. This sensor can be used to detect hypoglycemia. In vitro studies have shown that the response time of the sensor is less than one minute and probably does not contribute significantly to the observed phase lag between the nadir for the blood and subcutaneous glucose. In the subjects studied to date, the mean delay was about 3 min, but the range was 0-15 minutes.< <ETX>&gt;</ETX>
Covalent crosslinking of von Willebrand factor to fibrin (1986)

Abstract Factor XIIIa crosslinks a limited number of substrates via epsilon(gamma-glutamyl)-lysyl bond formation. It crosslinks fibrin to itself, alpha 2-plasmin inhibitor and fibronectin to fibrin, and fibronectin to collagen. Results presented here show that plasma von Willebrand factor (vWF) is a substrate for factor XIIIa and can be crosslinked to fibrin during gel formation. vWF-fibrin crosslinking was studied in purified systems and in plasma with 125I-vWF and 131I- fibrinogen. vWF incorporation into fibrin increased with time or increasing factor XIIIa. After electrophoresis of dissolved clots, distribution of 125I and 131I was measured and showed that vWF was crosslinked to the alpha chain of fibrin and entered the high-mol-wt alpha polymer. vWF-fibrin crosslinking decreased the initial rate of alpha polymer formation. Crosslinking of vWF polymer to itself could not be demonstrated under physiologic conditions but occurred if vWF was reduced first. Factor XIIIa catalyzed incorporation of putrescine into both monomeric and polymeric vWF. Altogether, these studies indicate that factor XIIIa can readily form covalent bonds between glutamine in vWF and lysine in fibrin alpha chains. This reaction occurs readily in vitro when plasma clotting is slow and may occur in vivo under similar conditions.