bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jump start exit criterion: Exploring a new model of service delivery for the treatment of childhood feeding problems
Authors: Pizzo Bianca , Williams Keith E. , Paul Candace , Riegel Katherine 
Published: April 2009

AbstractWhile the literature on the assessment and treatment of childhood feeding disorders continues to grow, little research has focused on developing new forms of service delivery. This study demonstrates the effectiveness of a brief, intensive intervention for the treatment of food selectivity in three boys who had failed to progress in traditional outpatient treatment. The implications of this model of service delivery are discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Detecting changes in simulated events II: Using variations of momentary time‐sampling to measure changes in duration events
Authors: Carroll Regina A. , Rapp John T. , Colby‐Dirksen Amanda M. , Lindenberg Ally M. 
Published: April 2009

AbstractThe extent to which a greater proportion of small behavior changes could be detected with momentary time‐sampling (MTS) was evaluated by (a) combining various interval sizes of partial‐interval recording (PIR) with 20 s, 30 s, 1 min MTS and (b) using variable interval sizes of MTS that were based on means of 20 s and 1 min. For each targeted percentage, low, moderate, and high inter‐response times (IRTs) to event‐run ratios were compared with reversal designs to determine whether sensitivity increased with either variation of MTS. The results showed that (a) combinations of 30 s and 1 min MTS/PIR yielded increased sensitivity over MTS alone; however, the increased sensitivity was offset by an increased probability of generating false positives and (b) variable‐interval MTS produced comparable sensitivity to fixed‐interval MTS. Thus, none of the methods increased detection of small behavior changes (decreased false negatives) without also increasing false positives. Copyright © 2009 John Wiley & Sons, Ltd.
Conformational preferences and cis–trans isomerization of L‐3,4‐dehydroproline residue
Authors: Kang Young Kee , Park Hae Sook 
Published: April 2009

AbstractThe conformational study of N‐acetyl‐N′‐methylamide of L‐3,4‐dehydroproline (Ac‐Dhp‐NHMe, the Dhp dipeptide) is carried out using hybrid density functional methods with the self‐consistent reaction field method in the gas phase and in solution (chloroform and water). The incorporation of a double bond between Cβ and Cγ into the prolyl ring results in the puckering, backbone population, and barriers to prolyl cis–trans isomerization different from those of the Pro dipeptide. For local minima of the Dhp dipeptide in the gas phase and in water, the CβCγ bonds become shorter by ∼0.2 Å and the bond angles CαCβCγ and CβCγCδ are widened by ∼8° than those of the Pro dipeptide, and the puckering amplitude is computed to be 0.01–0.07 Å, indicating that the 3,4‐dehydroprolyl ring is quite less puckered. However, polyproline‐like conformations become preferred and the relative stability of the conformation tC with a C7 intramolecular hydrogen bond decreases as the solvent polarity increases, as found for the Pro dipeptide. The barriers to cis–trans isomerization of the Ac−Dhp peptide bond increase with the increase of solvent polarity and the isomerization is likely to proceed through the clockwise rotation in water, as found for the prolyl peptide bond. The hydrogen bond between the prolyl nitrogen and the following amide NH group seems to contribute in stabilizing the transition state structures. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 387–398, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Mapping the stability clusters in bovine pancreatic ribonuclease A
Authors: Vilà Roger , Benito Antoni , Ribó Marc , Vilanova Maria 
Published: April 2009

AbstractIn the present work, we have thermodynamically characterized the thermally induced unfolding of 20 variants of bovine pancreatic ribonuclease A (RNase A) to experimentally describe the residues and the regions that are critical for the stability of the enzyme. The achieved results, complemented with previous studies by our group, allowed us to define the significance of the two hydrophobic nuclei present in the RNase A structure, as well as the contribution of the participating residues within each nucleus, to the global enzyme stability. We propose a structural model for the major and the minor hydrophobic nuclei of RNase A. The major nucleus is composite and located in the cavity delimited by α‐helices 1 and 3, and the β‐sheet that is formed by strands 2, 3, 5, and 6. It consists of a central tight packed part constituted by residues Phe8, Met13, Val54, Val57, Ile106, Val108, and Phe120. This central part is surrounded by a layer formed by residues Val63, Tyr73, Met79, Ile107, Val116, and Val118. The minor nucleus, although less complex, is also constituted by a tight packing that involves the side chains of residues Tyr25, Met29, Met30, Leu35, Phe46, and Tyr97, which fill the cavity that originates the β‐sheet formed by β‐strands 1, 4, and 5 together with α‐helix2. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1038–1047, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Descriptively quantitative relationship between mutated N‐acetylgalactosamine‐6‐sulfatase and mucopolysaccharidosis IVA
Authors: Yan Shaomin , Wu Guang 
Published: April 2009

AbstractTo study the quantitative relationship between the mutant N‐acetylgalactosamine‐6‐sulfatase and the occurrence of mucopolysaccharidosis IVA, the human N‐acetylgalactosamine‐6‐sulfatase with 117 mutations was quantified using the amino‐acid distribution probability, then the mutations and clinical outcomes were coupled using the cross‐impact analysis. The results show that a patient has 0.94 chance of being mucopolysaccharidosis IVA when a new mutation occurs in N‐acetylgalactosamine‐6‐sulfatase. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 399–404, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins
Authors: Merlino Antonello , Vitagliano Luigi , Howes Barry D. , Verde Cinzia , di Prisco Guido , Smulevich Giulietta , Sica Filomena , Vergara Alessandro 
Published: April 2009

AbstractRecent studies have demonstrated that hemoglobins isolated from Antarctic fish undergo peculiar oxidation processes. Here we show, by combining crystallographic and spectroscopic data, that the oxidation pathway of Trematomus bernacchii hemoglobin (HbTb) is distinct from that observed for the major component of Trematomus newnesi (Hb1Tn), despite the high sequence identity of the two proteins and structural similarity of their ferrous and fully oxidized states. Resonance Raman analysis of HbTb autoxidation upon air‐exposure reveals the absence of the oxidized pentacoordinated state that was observed for Hb1Tn. The HbTb oxidation pathway is characterized by two ferric species: an aquo hexacoordinated high spin state and a bis‐histidyl hexacoordinated low spin form, which appear in the early stages of the oxidation process. The high resolution structure of an intermediate along the oxidation pathway has been determined at 1.4 Å resolution. The analysis of the electron density of the heme pocket shows, for both the α and the β iron, the coexistence of multiple binding states. In this partially oxidized form, HbTb exhibits significant deviations from the canonical R state both at the local and global level. The analysis of these modifications highlights the structural correlation between key functional regions of the protein. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1117–1125, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Conformations of heterochiral and homochiral proline‐pseudoproline segments in peptides: Context dependent cis–trans peptide bond isomerization
Authors: Kantharaju  , Raghothama Srinivasarao , Raghavender Upadhyayula Surya , Aravinda Subrayashastry , Shamala Narayanaswamy , Balaram Padmanabhan 
Published: April 2009

AbstractThe pseudoproline residue (ΨPro, L‐2,2‐dimethyl‐1,3‐thiazolidine‐4‐carboxylic acid) has been introduced into heterochiral diproline segments that have been previously shown to facilitate the formation of β‐hairpins, containing central two and three residue turns. NMR studies of the octapeptide Boc‐Leu‐Phe‐Val‐DPro‐ΨPro‐Leu‐Phe‐Val‐OMe (1), Boc‐Leu‐Val‐Val‐DPro‐ΨPro‐Leu‐Val‐Val‐OMe (2), and the nonapeptide sequence Boc‐Leu‐Phe‐Val‐DPro‐ΨPro‐DAla‐Leu‐Phe‐Val‐OMe (3) established well‐registered β‐hairpin structures in chloroform solution, with the almost exclusive population of the trans conformation for the peptide bond preceding the ΨPro residue. The β‐hairpin conformation of 1 is confirmed by single crystal X‐ray diffraction. Truncation of the strand length in Boc‐Val‐DPro‐ΨPro‐Leu‐OMe (4) results in an increase in the population of the cis conformer, with a cis/trans ratio of 3.65. Replacement of ΨPro in 4 by LPro in 5, results in almost exclusive population of the trans form, resulting in an incipient β‐hairpin conformation, stabilized by two intramolecular hydrogen bonds. Further truncation of the sequence gives an appreciable rise in the population of cis conformers in the tripeptide Piv‐DPro‐ΨPro‐Leu‐OMe (6). In the homochiral segment Piv‐Pro‐ΨPro‐Leu‐OMe (7) only the cis form is observed with the NMR evidence strongly supporting a type VIa β‐turn conformation, stabilized by a 4→1 hydrogen bond between the Piv (CO) and Leu (3) NH groups. The crystal structure of the analog peptide 7a (Piv‐Pro‐ΨH,CH3Pro‐Leu‐NHMe) confirms the cis peptide bond geometry for the Pro‐ΨH,CH3Pro peptide bond, resulting in a type VIa β‐turn conformation. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 405–416, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Rat mitochondrial manganese superoxide dismutase: Amino acid positions involved in covalent modifications, activity, and heat stability
Authors: Castellano Immacolata , Cecere Francesca , De Vendittis Alberto , Cotugno Roberta , Chambery Angela , Di Maro Antimo , Michniewicz Andzelika , Parlato Giuseppe , Masullo Mariorosario , Avvedimento Enrico Vittorio , De Vendittis Emmanuele , Ruocco Maria Rosaria 
Published: April 2009

AbstractThe role of three amino acid residues (Q143, Y34, S82) of rat mitochondrial superoxide dismutase (ratSOD2) in the enzymatic activity, thermostability, and post‐translational modification of the enzyme was investigated through site‐directed mutagenesis studies. Six recombinant forms of the enzyme were produced, carrying the Q143 or H143 residue with or without the Y34F or S82A replacement. All proteins bound manganese as active cofactor and were organized as homotetramers. The greatest effect on the activity (sixfold reduction) was observed in ratSOD2 forms containing the H143 variant, whereas Y34F and S82A substitutions moderately reduced the enzymatic activity compared to the Q143 form. Heat inactivation studies showed the high thermo‐tolerance of ratSOD2 and allowed an evaluation of the related activation parameters of the heat inactivation process. Compared to Q143, the H143 variant was significantly less heat stable and displayed moderately lower enthalpic and entropic factors; the Y34F substitution caused a moderate reduction of heat stability, whereas the S82A replacement slightly improved the thermo‐tolerance of the Q143 variant; both substitutions significantly increased enthalpic and entropic factors of heat inactivation, the greatest effect being observed with S82A substitution. All recombinant forms of ratSOD2 were glutathionylated in Escherichia coli, a feature pointing to the high reactivity of ratSOD2 toward glutathione. Moreover, the S82 position of the enzyme was phosphorylated in an in vitro system containing human mitochondrial protein extracts as source of protein kinases. These data highlight the role played by some residues in ratSOD2 and suggest a fine regulation of the enzyme occurring in vivo. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1215–1226, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Single‐molecule pair studies of the interactions of the α‐GalNAc (Tn‐antigen) form of porcine submaxillary mucin with soybean agglutinin
Authors: Sletmoen Marit , Dam Tarun K. , Gerken Thomas A. , Stokke Bjørn T. , Brewer Curtis Fred 
Published: April 2009

AbstractMucins form a group of heavily O‐glycosylated biologically important glycoproteins that are involved in a variety of biological functions, including modulating immune response, inflammation, and adhesion. Mucins are also involved in cancer and metastasis and often express diagnostic cancer antigens. Recently, a modified porcine submaxillary mucin (Tn‐PSM) containing GalNAcα1‐O‐Ser/Thr residues was shown to bind to soybean agglutinin (SBA) with ∼106‐fold enhanced affinity relative to GalNAcα1‐O‐Ser, the pancarcinoma carbohydrate antigen. In this study, dynamic force spectroscopy is used to investigate molecular pairs of SBA and Tn‐PSM. A number of force jumps that demonstrate unbinding or rebinding events were observed up to a distance equal to 2.0 μm, consistent with the length of the mucin chain. The unbinding force increased from 103 to 402 pN with increasing force loading rate. The position of the activation barrier in the energy landscape of the interaction was 0.1 nm. The lifetime of the SBA–TnPSM complex in the absence of applied force was determined to be in the range 1.3–1.9 s. Kinetic parameters describing the rate of dissociation of other sugar lectin interactions are in the range 3.3 × 10−3–2.5 × 10−3 s. The long lifetime of the SBA‐TnPSM complex is compatible with a binding model in which lectin molecules “bind and jump” from α‐GalNAc residue to α‐GalNAc residue along the polypeptide chain of Tn‐PSM before dissociating. These findings have important implications for the molecular recognition properties of mucins. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 719–728, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Decreased secretion and unfolded protein response up‐regulation are correlated with intracellular retention for single‐chain antibody variants produced in yeast
Authors: Xu Ping , Robinson Anne Skaja 
Published: April 2009

AbstractHeterologous protein expression can easily overwhelm a cell's capacity to properly fold protein, initiating the unfolded protein response (UPR), and resulting in a loss of protein expression. In the current model of the UPR, the chaperone BiP modulates the activation of the UPR due to its interactions with the signaling protein Ire1p and newly synthesized proteins. In this research, 4‐4‐20 scFv variants were generated by rational design to alter BiP binding to newly synthesized scFv proteins or via directed evolution aimed at improved secretion. Interestingly, the predicted BiP binding ability did not correlate significantly with the UPR. However, pulse‐chase analysis of scFv fate revealed that mutants with a decreased ER residence time were more highly secreted, indicating that improved protein folding was more likely the cause for improved secretion. In fact, decreased secretion correlated with increased binding by BiP, as determined by co‐immune precipitation studies. This suggests that the algorithm is not useful for in vivo prediction of variants, and that in vivo screens are more effective for finding variants with improved properties. Biotechnol. Bioeng. 2009; 104: 20–29 © 2009 Wiley Periodicals, Inc.
Targeted gene delivery to CD117‐expressing cells in vivo with lentiviral vectors co‐displaying stem cell factor and a fusogenic molecule
Authors: Froelich Steven , Ziegler Leslie , Stroup Katie , Wang Pin 
Published: April 2009

AbstractThe development of a lentiviral system to deliver genes to specific cell types could improve the safety and the efficacy of gene delivery. Previously, we have developed an efficient method to target lentivectors to specific cells via an antibody–antigen interaction in vitro and in vivo. We report herein a targeted lentivector that harnesses the natural ligand–receptor recognition mechanism for targeted modification of c‐KIT receptor‐expressing cells. For targeting, we incorporate membrane‐bound human stem cell factor (hSCF), and for fusion, a Sindbis virus‐derived fusogenic molecule (FM) onto the lentiviral surface. These engineered vectors can recognize cells expressing surface CD117, resulting in efficient targeted transduction of cells in an SCF‐receptor dependent manner in vitro, and in vivo in xenografted mouse models. This study expands the ability of targeting lentivectors beyond antibody targets to include cell‐specific surface receptors. Development of a high titer lentivector to receptor‐specific cells is an attractive approach to restrict gene expression and could potentially ensure therapeutic effects in the desired cells while limiting side effects caused by gene expression in non‐target cells. Biotechnol. Bioeng. 2009; 104: 206–215 © 2009 Wiley Periodicals, Inc.
Metabolic and transcriptional response of recombinant Escherichia coli to elevated dissolved carbon dioxide concentrations
Authors: Baez Antonino , Flores Noemí , Bolívar Francisco , Ramírez Octavio T. 
Published: April 2009

AbstractThe effect of dissolved carbon dioxide (dCO2) concentration on the stoichiometric and kinetic constants and by‐product accumulation was determined for Escherichia coli cells producing recombinant green fluorescent protein (GFP). Constant dCO2, in the range of 20–300 mbar, was maintained during batch cultures by manipulating the inlet gas composition. As dCO2 increased, specific growth rate (µ) decreased, and acetate accumulation and the time for onset of GFP production increased. Maximum biomass yield on glucose and GFP concentration were affected for dCO2 above 70 and 150 mbar, respectively. Expression analysis of 16 representative genes showed that E. coli can respond at the transcriptional level upon exposure to increasing dCO2, and revealed possible mechanisms responsible for the detrimental effects of high dCO2. Genes studied included those involved in decarboxylation reactions (aceF, icdA, lpdA, sucA, sucB), genes from pathways of production and consumption of acetate (ackA, poxB, acs, aceA, fadR), genes from gluconeogenic and anaplerotic metabolism (pckA, ppc), genes from the acid resistance (AR) systems (adiA, gadA, gadC), and the heterologous gene (gfp). The transcription levels of tricarboxylic acid (TCA) cycle genes (icdA, sucA, sucB) and glyoxylate shunt (aceA) decreased as dCO2 increased, whereas fadR (that codes for a negative regulator of the glyoxylate operon) and poxB (that codes for PoxB which is involved in acetate production from pyruvate) were up‐regulated as dCO2 increased up to 150 mbar. Furthermore, transcription levels of genes from the AR systems increased as dCO2 increased up to 150 mbar, indicating that elevated dCO2 triggers an acid stress response in E. coli cells. Altogether, such results suggest that the increased acetate accumulation and reduction in µ, biomass yield and maximum GFP concentration under high dCO2 resulted from a lower carbon flux to TCA cycle, the concomitant accumulation of acetyl‐CoA or pyruvate, and the acidification of the cytoplasm. Biotechnol. Bioeng. 2009; 104: 102–110 © 2009 Wiley Periodicals, Inc.
Faecal calprotectin or lactoferrin can identify postoperative recurrence in Crohn's disease
Authors: Lamb C A , Mohiuddin M K , Gicquel J , Neely D , Bergin F G , Hanson J M , Mansfield J C 
Published: April 2009

Abstract

Background
Identifying Crohn's disease recurrence in symptomatic patients after ileocaecal resection is difficult. The aim of this study was to evaluate faecal concentrations of granulocyte degradation products in this setting.

Methods
A postoperative cohort of 13 patients was followed prospectively for 1 year with regular faecal calprotectin (FC) and lactoferrin (FL) measurements. A second postoperative cohort (median 24 months after resection) of 104 patients provided a single stool sample. Faecal measurements were compared with symptom diaries, the Harvey Bradshaw Index, endoscopic examination, C-reactive protein and platelet measurement.

Results
In the uncomplicated course, both markers normalized within 2 months. Both FC and FL correlated significantly with Harvey Bradshaw Index (P &lt; 0·001). Twenty-eight patients with severely clinically active disease had high mean(s.e.) levels of FC (661·1(119·1) µg/g) and FL (116·6(32·2) µg/g); and 43 with clinically inactive disease had low levels of FC (70·2(27·1) µg/g) and FL (5·9(2·4) µg/g). In patients with mild to moderately clinically active disease, FC and FL identified individuals with and without recurrent inflammatory disease. Faecal markers were more accurate at predicting clinical disease activity than C-reactive protein, platelet count or endoscopic appearance.

Conclusion
FC and FL are non-invasive tests that can help to identify disease recurrence in symptomatic postoperative patients.
Quantitative determination of a novel enantiomeric tropane analog, (−)‐satropane, in biological fluids using liquid chromatography/tandem mass spectrometry
Authors: Fu Jun , Fang Chao , Cui Yong‐Yao , Yang Li‐Min , Zhu Liang , Feng Xue‐Mei , Zheng Pei‐Li , Lu Yang , Chen Hong‐Zhuan 
Published: April 2009

AbstractA sensitive, accurate and precise liquid chromatography–tandem mass spectrometry method was developed for the determination of (−)‐satropane (3α‐paramethyl‐benzenesulfonyloxy‐6β‐acetoxy‐tropane) in rabbit aqueous humor. Since (−)‐satropane may be absorbed from the aqueous humour with resultant systemic side effects, the LC‐MS/MS method was also evaluated for its applicability in analyzing plasma samples containing this compound. (−)‐Satropane and phentolamine (the internal standard, represented as IS) were detected by multiple reaction monitoring using the transitions m/z 354–182 and 282–212, respectively. The calibration curve was linear over the ranges 2–500 and 5–1000 ng/mL, and the values of the lower limit of quantification were 2 and 5 ng/mL for the microdialysis dialysate and rat plasma samples, respectively. The intra‐day and inter‐day precision and accuracy were better than 8.6 and 6.00%, respectively, in both matrices investigated. The absolute recovery of the plasma samples was more than 76.30%. The average matrix effects of (−)‐satropane were 91.72 and 83.05% in the microdialysis dialysate and plasma samples, respectively. The validated method was successfully applied to analyze (−)‐satropane in microdialysis dialysate and rat plasma samples, and this assay has been used to quantify (‐)‐satropane in the pharmacokinetic and toxicokinetic studies in our laboratory. Copyright © 2009 John Wiley & Sons, Ltd.