gebhart/patrepeval huggingface dataset:
Studies on the conformational changes in the bacterial cell wall biosynthetic enzyme UDP‐N‐acetylglucosamine enolpyruvyltransferase (MurA) (1998)

The enzyme UDP-N-acetylglucosamine (UDP-GlcNAc) enolpyruvyltransferase (MurA), the target of the antibiotic fosfomycin, was investigated by small-angle X-ray scattering (SAXS) and fluorescence spectroscopy to detect conformational changes that had been proposed on the basis of the crystal structure of unliganded and liganded MurA. The SAXS data indicate that binding of UDP-GlcNAc to free enzyme results in substantial conformational changes, which can be interpreted as the transition from an open to a closed form. Fosfomycin did not affect the structure of free enzyme or sugar-nucleotide-bound MurA. Phosphoenolpyruvate (pyruvate-P) appeared to induce a structural change upon addition to free enzyme, which differed from that observed upon binding of UDP-GlcNAc. Fluorescence experiments were performed using the hydrophobic fluorescence probe 8-anilino-1-naphthalene sulfonate (ANS). The fluorescence quenching of MurA/ANS solutions upon addition of UDP-GlcNAc or pyruvate-P was concentration dependent in a saturating manner, yielding apparent dissociation constants of K(d(UDP-GlCNAc)) = 59 microM and K(d(pyruvate-P)) = 240 microM. The results suggest that binding of substrates does not exclusively follow an ordered mechanism with UDP-GlcNAc binding first, although binding of UDP-GlcNAc to free enzyme is preferred and possibly influenced by pyruvate-P. The reaction thus appears to follow an induced-fit mechanism, in which the binding site for fosfomycin, and presumably also for pyruvate-P, is created by the interaction of free enzyme with the sugar nucleotide. The methods described here provide a tool for the characterization of site-directed mutants of MurA and the interaction of this enzyme with potential inhibitors.
12/15-Lipoxygenase Inhibition or Knockout Reduces Warfarin-Associated Hemorrhagic Transformation After Experimental Stroke (2017)

In addition to its benefits in infarct size reduction, 12/15-LOX inhibition also may independently reduce HT in warfarin-treated mice. ML351 should be further evaluated as stroke treatment in anticoagulated patients suffering a stroke, either alone or in conjunction with tissue-type plasminogen activator.
Biophysical analysis of the Mycobacteria tuberculosis peptide binding protein DppA reveals a stringent peptide binding pocket (2021)

The peptide binding protein DppA is an ABC transporter found in prokaryotes that has the potential to be used as drug delivery tool for hybrid antibiotic compounds. Understanding the motifs and structures that bind to DppA is critical to the development of these bivalent compounds. This study focused on the biophysical analysis of the MtDppA from M. tuberculosis. Analysis of the crystal structure revealed a SVA tripeptide was co-crystallized with the protein. Further peptide analysis demonstrated MtDppA shows very little affinity for dipeptides but rather preferentially binds to peptides that are 3-4 amino acids in length. The structure-activity relationships (SAR) between MtDppA and tripeptides with varied amino acid substitutions were evaluated using thermal shift, SPR, and molecular dynamics simulations. Efforts to identify novel ligands for use as alternative scaffolds through the thermal shift screening of 35,000 compounds against MtDppA were unsuccessful, indicating that the MtDppA binding pocket is highly specialized for uptake of peptides. Future development of compounds that seek to utilize MtDppA as a drug delivery mechanism, will likely require a tri- or tetrapeptide component with a hydrophobic -non-acidic peptide sequence.
Effective nutrition from conception to adulthood (2014)

This article summarises presentations at the plenary session of the Annual Meeting of the British Fertility Society, on Effective nutrition from conception to adulthood, held in Sheffield, UK in January 2014. It highlights the pivotal role of the late David Barker (1938-2014) in revolutionising our understanding of the influence of maternal, gamete, embryo, foetal and infant nutrition on the health of the offspring in later life.
Genomic Sequence of a Calnexin Homolog from Arabidopsis thaliana (1994)

Calnexin is a membrane-bound protein of the ER in animal cells (Wada et al., 1991). It shows considerable similarity to the major calcium-sequestering protein of the ER lumen, calreticulin, with two calcium-binding regions--a high-affinity, low-capacity region in the ER lumen and a low-affinity, high-capacity region in the cytoplasm. The protein is postulated to act as a calcium-regulated chaperone during protein maturation (Ou et al., 1993). We have isolated a genomic sequence showing significant homology to the animal gene over the predicted coding sequence (Table I). A partial cDNA from Zea mays was isolated from an expression library made from 6-d coleoptiles (Clontech, Palo Alto, CA). The library was screened using a monoclonal antibody raised against a small number of microsomal proteins resulting from a partial purification of plasma membrane Ca2+ ATPase (Briars et al., 1988). The partial cDNA showed sequence homology to the calcium-binding region common to calreticulin and calnexin. The fragment was used to screen a genomic library constructed from Arabidopsis thaliana (cv Larasbonerecta), and a 15-kb fragment was isolated and subcloned and the relevant subfragments were sequenced. The coding region contains five introns, two in the N-terminal region and three in the C-terminal region. The predicted amino acid sequence shows a high level of homology with the animal calnexin, although the terminal highly acidic calcium-binding region is shorter. A cDNA for a putative homolog of calnexin was isolated from A. thaliana (cv Columbia) by Huang et al.(1993); our coding sequence shows 85% identity and 92% similarity determined by FASTA (Wisconsin Genetics Computer Group package); however, the differences are greater than would be expected between cultivars of the same species. A Southern blot probed with DNA from the central calcium-binding region shows multiple bands. This, combined with the sequence heterogeneity, suggests that calnexin belongs to a family of related genes.
Generation of Electricity and Analysis of Microbial Communities in Wheat Straw Biomass-Powered Microbial Fuel Cells (2009)

Electricity generation from wheat straw hydrolysate and the microbial ecology of electricity-producing microbial communities developed in two-chamber microbial fuel cells (MFCs) were investigated. The power density reached 123 mW/m(2) with an initial hydrolysate concentration of 1,000 mg chemical oxygen demand (COD)/liter, while coulombic efficiencies ranged from 37.1 to 15.5%, corresponding to the initial hydrolysate concentrations of 250 to 2,000 mg COD/liter. The suspended bacteria found were different from the bacteria immobilized in the biofilm, and they played different roles in electricity generation from the hydrolysate. The bacteria in the biofilm were consortia with sequences similar to those of Bacteroidetes (40% of sequences), Alphaproteobacteria (20%), Bacillus (20%), Deltaproteobacteria (10%), and Gammaproteobacteria (10%), while the suspended consortia were predominately Bacillus (22.2%). The results of this study can contribute to improving understanding of and optimizing electricity generation in microbial fuel cells.
Influences of age, sex, and LDL-C change on cardiovascular risk reduction with pravastatin treatment in elderly Japanese patients: A post hoc analysis of data from the Pravastatin Anti-atherosclerosis Trial in the Elderly (PATE) (2006)

The results from this post hoc analysis suggest that pravastatin 5 to 20 mg/d might elicit CVE risk reduction by mechanisms other than cholesterol-lowering effects alone. They also suggest that pravastatin treatment might be effective in reducing the risk for CVEs in both female and male patients aged ⩾75 years.
Unequal Weight Planar Prediction and Weighted Angular Prediction (2018)

This paper describes two modifications to intra prediction methods in the developing video coding standard, JVET. The first mode, unequal weight planar prediction modifies planar mode by using lifting process to improve accuracy of bottom row and right column references calculation. Moreover, unequal weights are used to combine horizontal and vertical prediction samples in the final prediction generation step. The second mode, weighted angular prediction, modifies angular prediction process such that prediction pixels are generated using pixels at projected position on both top reference row and left reference column. Simulation results show that unequal weight planar prediction provides average BD-rate gain of 0.1% gain over JEM-7.0 anchor. Similar coding performance is observed for weighted angular prediction. Combining unequal weight planar prediction and weighted angular prediction increases average BD-rate gain to 0.2%, with larger coding improvement (0.3%) for larger resolution video (class A sequences).
Pharmacokinetics (PK) of 2 dosing regimens of palifermin in patients (Pts) with hematologic malignancies (HM) undergoing high-dose chemoradiotherapy and hematopoietic stem cell transplantation (HSCT) (2006)

For patients (pts) with HM undergoing HSCT, oral mucositis (OM) is a frequent and debilitating complication that negatively impacts treatment outcomes, patient quality of life, and healthcare resources. Palifermin reduces the incidence and duration of severe OM in the HSCT setting. This phase 1 open-label study assessed the PK of 2 palifermin dosing regimens. Methods: Pts were 18 to 76 years old with HM and a Karnofsky performance score ≥70%. Palifermin was administered intravenously once daily as follows: 60 mcg/kg/day for 3 consecutive days on day −11, day −10, and day −9 before conditioning (total body irradiation [TBI] + etoposide + cyclophosphamide) and following HSCT on days 0, 1, and 2 (part A) and a single dose of 180 mcg/kg (part B) before conditioning on day −11 and after HSCT on d 0. In part A (6 total doses), PK parameters were assessed after the first, third, fourth, and sixth doses. In part B (2 total doses), assessments were made after each dose administration (day −11 and day 0). Results: In part A, 13 pts received palifermin; in part B, 12 pts received the single dose on day −11 and 11 pts received the single dose on day 0. For both dosing regimens, palifermin concentrations declined rapidly (≥98% decrease) in the first 30 minutes postdose, followed by a slight increase in mean concentrations between 1 and 4 hours and then a terminal decay phase. Respective mean (SD) PK parameter values for the 2 dosing regimens are shown in Table 1. In part A, mean AUC0-t values were comparable between doses 1 and 3 (within 15%) and 1 and 4 (within 1%). In part B, mean PK parameter values were similar (within 10% of each other) between doses 1 and 2. The mean AUC after the first 180 mcg/kg dose in part B was approximately 4-fold higher than that after the first 60 mcg/kg dose in part A. Mean half-life values ranged between 3.3 to 5.7 hours in part A and the value was 5.4 hours in part B. Conclusions: The PK data in pts receiving HSCT were consistent with approximately dose-linear PK in the dose range of 60 and 180 mcg/kg, with no observed accumulation, based on AUC, after 3 daily doses of 60 mcg/kg in this pt population in the HSCT setting (Table1).Table 1DosingRegimen(Dosing Day)nAUC0-t (hr × ng/mL) Mean (SD)Clearance (mL/hr/kg) Mean (SD)Vss (mL/kg) Mean (SD)Part A - 60 mcg/kg/day × 3 consecutive days1st dose (day −11)9 to 1334.3 (15.9)1730 (497)5320 (2330)3rd dose (day −9)1339.8 (36.4)--4th dose (day 0)11 to 1334.8 (22.5)2030 (862)3870 (2080)6th dose (day 2)1321.2 (15.1)--Part B - 180 mcg/kg/day × 1 day1st dose (day −11)12140 (50.9)1460 (600)4290 (3270)2nd dose (day 0)11143 (71.8)1770 (1290)4270 (4700)Accurate computations of clearance (CL) and volume of distribution at steady state (Vss) were not possible for some concentration-time profiles. Open table in a new tab Accurate computations of clearance (CL) and volume of distribution at steady state (Vss) were not possible for some concentration-time profiles.
Multilevel modelling of the incidence of visceral leishmaniasis in Teresina, Brazil (2006)

Epidemics of visceral leishmaniasis (VL) in major Brazilian cities are new phenomena since 1980. As determinants of transmission in urban settings probably operate at different geographic scales, and information is not available for each scale, a multilevel approach was used to examine the effect of canine infection and environmental and socio-economic factors on the spatial variability of incidence rates of VL in the city of Teresina. Details on an outbreak of greater than 1200 cases of VL in Teresina during 1993-1996 were available at two hierarchical levels: census tracts (socio-economic characteristics, incidence rates of human VL) and districts, which encompass census tracts (prevalence of canine infection). Remotely sensed data obtained by satellite generated environmental information at both levels. Data from census tracts and districts were analysed simultaneously by multilevel modelling. Poor socio-economic conditions and increased vegetation were associated with a high incidence of human VL. Increasing prevalence of canine infection also predicted a high incidence of human VL, as did high prevalence of canine infection before and during the epidemic. Poor socio-economic conditions had an amplifying effect on the association between canine infection and the incidence of human VL. Focusing interventions on areas with characteristics identified by multilevel analysis could be a cost-effective strategy for controlling VL. Because risk factors for infectious diseases operate simultaneously at several levels and ecological data usually are available at different geographical scales, multilevel modelling is a valuable tool for epidemiological investigation of disease transmission.
Remarkable Ability of Horse Spleen Apoferritin To Demetallate Hemin and To Metallate Protoporphyrin IX as a Function of pH (1997)

In previous studies it has been shown that reaction of crystalline horse spleen apoferritin with hemin leads to a protoporphyrin IX-apoferritin complex [Précigoux et al. (1994) Acta Crystallogr. D50, 739-743]. We show here the following. (i) Hemin binds to two classes of sites in horse spleen apoferritin at pH 8, each with a binding stoichiometry of 0.5 hemin/subunit; protoporphyrin IX also binds to horse spleen apoferritin with an apparent binding stoichiometry of 1 molecule of protoporphyrin IX/subunit. (ii) When Fe(III)-protoporphyrin IX binds to apoferritin, there is a pH-dependent loss of the metal ion, extremely slow at alkaline pH values (half-time of weeks) and much more rapid at acidic pH values (half-time of seconds below pH 5.0); maximum rates of demetallation are found at pH 4.0, and at lower pH values they decrease. (iii) Chemical modification of 11 carboxyl groups/subunit in horse spleen apoferritin does not affect hemin binding at alkaline pH values; however, it prevents hemin demetallation at acidic pH values. (iv) Hemin that has been demetallated at acidic pH values can be remetallated by increasing the pH; the rate of remetallation is greater at more alkaline pH values. (v) When around 20 atoms of iron/molecule are incorporated into horse spleen apoferritin and protoporphyrin IX is then bound, iron can subsequently be transferred to the porphyrin at pH 8.0. A mechanism is proposed to explain demetallation of heme, involving attack on the tetrapyrrole nitrogens of the protoporphyrin IX-Fe by protons derived from protein carboxylic acid groups and subsequent complexation of the iron by the corresponding carboxylates and binding of protoporphyrin IX to a preformed pocket in the inner surface of the apoferritin protein shell. The cluster of carboxylates involved is situated at the entrance to the pocket in which the protoporphyrin IX molecule is bound and has been previously identified as the site of iron incorporation into L-chain apoferritins. This appears to be the first example of iron removal and incorporation into porphyrins under relatively mild physiological conditions.
2P2-H09 Development of Surgical Cockpit for Brain Tumor Removal Robot System(Surgical Robotics and Mechatronics) (2011)

In this paper, a surgical cockpit for brain tumor removal surgery is presented. The surgical cockpit was developed to be used with a neurosurgical intelligent surgical robot. As a concept of the surgical cockpit, the cockpit system can be intuitively used by introducing a similar manner of conventional neurosurgical procedure. Therefore, the presented surgical cockpit was designed to perform the motions of conventional neurosurgical procedure in tumor removal. In addition, the installability of the system in operation room was taken into account.
Scanning Tunneling Microscopy under Polar Solvents with Uncoated Tips (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTScanning Tunneling Microscopy under Polar Solvents with Uncoated TipsP. G. Van Patten, J. D. Noll, M. L. McLester, Y.-G. Kim, and M. L. MyrickView Author Information Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208 Cite this: Langmuir 1997, 13, 2, 365–368Publication Date (Web):January 22, 1997Publication History Received5 August 1996Revised27 September 1996Published online22 January 1997Published inissue 1 January 1997https://pubs.acs.org/doi/10.1021/la960768qhttps://doi.org/10.1021/la960768qbrief-reportACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views90Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Algorithms,Imaging,Scanning tunneling microscopy,Solvents Get e-Alerts
Selective quenching of species that produce sonoluminescence (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective quenching of species that produce sonoluminescenceC. Sehgal, R. G. Sutherland, and R. E. VerrallCite this: J. Phys. Chem. 1980, 84, 5, 529–531Publication Date (Print):March 1, 1980Publication History Published online1 May 2002Published inissue 1 March 1980https://pubs.acs.org/doi/10.1021/j100442a016https://doi.org/10.1021/j100442a016research-articleACS PublicationsRequest reuse permissionsArticle Views69Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Percutaneous lines for delivering intravenous antibiotics in people with cystic fibrosis (2010)

There is some evidence to support the use of long intravenous lines rather than short intravenous lines, in terms of lifespan of the line and patient satisfaction. There is no evidence to suggest that any one type of long intravenous line is superior, and currently choice of line should be determined by operator and patient preference. There are numerous devices available which are used in cystic fibrosis. Further research is required to identify clinically important differences between these devices.
Anycast Rendevous Point (RP) mechanism using Protocol Independent Multicast (PIM) and Multicast Source Discovery Protocol (MSDP) (2003)

This document describes a mechanism to allow for an arbitrary number of Rendevous Points (RPs) per group in a single shared-tree Protocol Independent Multicast-Sparse Mode (PIM-SM) domain.
Predictive Value of Somatosensory Evoked Potentials for Long-lasting Pain Relief after Spinal Cord Stimulation: Practical Use for Patient Selection (2003)

Preoperative SSEPs provide an objective prediction of patient outcome after SCS. We suggest that if a patient's CCT is abolished or significantly altered, the patient should not undergo SCS.
Software-reconfigurable universally-applicable microfluidic platform (2010)

Reference EPFL-CONF-178692View record in Web of Science Record created on 2012-06-25, modified on 2017-12-17
Strapped-down accelerometer effects on NDBO wave measurements (1982)

Equations for wave displacement measurements by buoys equipped with strapped-down accelerometers are derived and used for computer simulations of wave measurements for a variety of sea states. Use of strapped-down accelerometers causes measured acceleration to be a sea state dependent time varying combination of buoy vertical acceleration, buoy horizontal acceleration, and acceleration due to gravity. As a result of the nonlinear equations that describe strapped-down accelerometer measurements, measured wave spectra have excess low frequency energy. Buoy responses to waves are considered to quantify error levels of operational NOAA Data Buoy Office buoys with strapped-down accelerometers. Simulations of several thousand buoy measured wave records and processing of these records in a manner similar to operational processing indicate that strapped-down accelerometers introduce significant wave height errors that are generally less than 5%, but that effects on low frequency swell measurements are at times substantial.