bluuebunny/crossref_metadata_2025_split huggingface dataset:
Degradable star polymers with high “click” functionality
Authors: Wiltshire James T. , Qiao Greg G. 
Published: February 2009

AbstractDegradable polyester‐based star polymers with a high level of functionality in the arms were synthesized via the “arms first” approach using an acetylene‐functional block copolymer macroinitiator. This was achieved by using 2‐hydroxyethyl 2′‐methyl‐2′‐bromopropionate to initiate the ring‐opening polymerization (ROP) of caprolactone monomer followed by an atom transfer radical polymerization (ATRP) of a protected acetylene monomer, (trimethylsilyl)propargyl methacrylate. The hydroxyl end‐group of the resulting block copolymer macroinitiator was subsequently crosslinked under ROP conditions using a bislactone monomer, 4,4′‐bioxepanyl‐7,7′‐dione, to generate a degradable core crosslinked star (CCS) polymer with protected acetylene groups in the corona. The trimethylsilyl‐protecting groups were removed to generate a CCS polymer with an average of 1850 pendent acetylene groups located in the outer block segment of the arms. The increased functionality of this CCS polymer was demonstrated by attaching azide‐functionalized linear polystyrene via a copper (I)‐catalyzed cycloaddition reaction between the azide and acetylene groups. This resulted in a CCS polymer with “brush‐like” arm structures, the grafted segment of which could be liberated via hydrolysis of the polyester star structure to generate molecular brushes. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1485–1498, 2009
Amphiphilic block copolymers containing thermally degradable poly(phthalaldehyde) blocks
Authors: Köstler Stefan , Zechner Barbara , Trathnigg Bernd , Fasl Hubert , Kern Wolfgang , Ribitsch Volker 
Published: February 2009

AbstractIn this study, the preparation of a new class of amphiphilic block copolymers consisting of a poly(phthalaldehyde) (PPA) block and hydrophilic poly(alkylene oxide) blocks is described. PPA was prepared by ionic cyclopolymerization. A telechelic polymer block was prepared by endcapping of the PPA by a bifunctional reagent carrying isocyanate and isothiocyanate groups. As the second block, monoamino‐terminated poly(alkylene oxide)s (Surfonamines®, also known as Jeffamines®) were chosen. These polymers could be readily coupled to the PPA telechel and gave amphiphlic, mainly ABA‐type block copolymers. The PPA block of these products can be selectively depolymerized at moderate temperature. The block copolymers were characterized by dual‐detection size exclusion chromatography, and the defined and stepwise thermal decomposition of the two different block types were shown by thermogravimetric analysis. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1499–1509, 2009
Anionic polymerization of methacrylates by samarium (III) enolate on networked polystyrene: Effects of its sterically confined environment on polymerization behavior
Authors: Nagai Daisuke , Fujii Asuka , Tanaka Masayoshi , Ochiai Bungo , Sudo Atsushi , Endo Takeshi 
Published: February 2009

AbstractAnionic polymerization of methacrylates under sterically confined environment in a spherical beads‐shaped networked polystyrene (NwPS) matrix is described. The initiator used herein is a samarium (Sm) (III) enolate, which was formed by treatment of 2‐bromoisobutylate immobilized in the side chain of NwPS with Sm (II) iodide. By using this NwPS‐bound initiator, polymerization of a series of methacrylates (=solid‐supported polymerization) was studied to find its two aspects: (1) In the early stages, the rate constant for each methacrylate was comparable to that for its conventional solution‐phase polymerization using a Sm (III) enolate, suggesting that methacrylate can be efficiently supplied to the propagating end by its free permeation without any interference by the networked structure of the matrix. (2) After the early stages, the rate constant decreased remarkably, implying that permeation of methacrylate was sterically interfered by the formed poly(methacrylate) that filled the confined space in NwPS, as supported by a SEM image of the resulting beads, of which pores were filled with the formed polymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1510–1521, 2009
Synthesis of polymeric nanocapsules with a crosslinked shell through interfacial miniemulsion polymerization
Authors: Cao Zhihai , Shan Guorong 
Published: February 2009

AbstractA water‐soluble comonomer, N‐isopropylacrylamide (NIPAM), and an oil‐soluble crosslinker, divinylbenzene (DVB), have been combined in a system for the synthesis of nanocapsules with crosslinked shells through interfacial miniemulsion polymerization by encapsulating a liquid nonsolvating hydrocarbon. Oligomers of poly(N‐isopropylacrylamide) (PNIPAM) were dehydrated and separated from the aqueous phase and were adsorbed by the nanodroplets or latex particles and then anchored at their interfaces by means of a crosslinking reaction. Nanocapsules were then formed through encapsulation of the hydrocarbon by the newly produced polymers at the interfaces of the droplets. The crosslinked structure gradually grew to stabilize the shell morphology. The incorporation of NIPAM into the shell copolymers has been verified by FTIR and solid‐state 13C NMR data. The fact that the number of nanocapsules increases with increasing amounts of DVB and NIPAM supports the formation of nanocapsules following interfacial (co)polymerization. Therefore, a mechanism for the formation of nanocapsules through interfacial (co)polymerization induced by NIPAM and DVB is proposed. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1522–1534, 2009
Relationship of psychological characteristics and self‐efficacy in gastrointestinal cancer survivors
Authors: Kohno Yuuta , Maruyama Michio , Matsuoka Yutaka , Matsushita Toshiko , Koeda Michihiko , Matsushima Eisuke 
Published: February 2009

AbstractTo characterize gastrointestinal cancer survivors' ability to psychologically adjust, we examined the relationship between psychological characteristics (quality of life (QOL), anxiety, depression, and post‐traumatic stress symptoms) and self‐efficacy (perceived ability to initiate coping strategies). Forty‐seven subjects (32 males and 15 females) were recruited from outpatient clinics or general surgical wards after readmission for therapy unrelated to cancer. All had undergone treatment for gastrointestinal cancer. Japanese version of the Functional Assessment of Cancer Therapy—General (FACT‐G), Japanese version of Hospital Anxiety and Depression Scale (HADS), Japanese version of Impact of Event Scale—Revised (IES‐R), and The Self‐Efficacy Scale for Advanced Cancer (SEAC) were administered. Correlation analyses revealed a statistically significant positive correlation between three subscales of SEAC and QOL (total of FACT‐G value) and a significant negative correlation between anxiety, depression (the total of HADS value), post‐traumatic stress symptoms (the total of IES‐R value), and SEAC. In multiple regression analysis, the influence from Affect Regulation Efficacy (subscale of SEAC) was the largest in anxiety and post‐traumatic stress symptoms while the influence from Activities of Daily Living Efficacy (subscale of SEAC) was the largest in QOL and depression. Our findings revealed that a strong relationship between self‐efficacy and psychological adjustment, and that there should be several psychological intervention forms performed at various treatment stages to enhance self‐efficacy in this population of gastrointestinal cancer survivors. These results also imply the effectiveness of interventions on self‐efficacy for gastrointestinal cancer survivors and the influence of psychological factors such as QOL, anxiety, depression, and post‐traumatic stress symptoms. Copyright © 2009 John Wiley & Sons, Ltd.
Waist circumference associated with pulmonary function in children
Authors: Chen Yue , Rennie Donna , Cormier Yvon , Dosman James A. 
Published: February 2009

AbstractIn adults abdominal obesity is related to lung dysfunction and waist circumference (WC) predicts pulmonary function. It is not known how WC affects pulmonary function in children. A cross‐sectional study of 718 children 6–17 years of age was conducted in a rural community to determine the predictability of WC for pulmonary function in children. Height, weight, WC, and pulmonary function were measured. Multivariate analysis was conducted. WC was positively associated with FVC and FEV1 and was more strongly associated with FVC than with FEV1. Increase in WC significantly predicted a reduction in FEV1/FVC. After adjustment for sex, age, and height, an increase of 1 cm for WC was associated with an increase of 7 ml of FVC and 4 ml of FEV1, and with an increase of 4 ml of FVC and 2 ml of FEV1 with an additional adjustment for weight. Height and weight were not significantly associated with FEV1/FVC. WC but not body mass index predicted a decline of FEV1/FVC. WC had a larger impact on FVC than FEV1. WC, but not BMI, was negatively associated with FEV1/FVC in children. Pediatr Pulmonol. 2009; 44:216–221. © 2009 Wiley‐Liss, Inc.
Severity of childhood community‐acquired pneumonia and chest radiographic findings
Authors: Kin Key Ng , Araújo‐Neto César Augusto , Nascimento‐Carvalho Cristiana Maria 
Published: February 2009

AbstractTo assess if chest radiographic findings present on admission are associated with severity of childhood community‐acquired pneumonia (CAP), a total of 161 children hospitalized with pulmonary infiltrate were enrolled in the study; 48 (30%) patients were excluded because of presence of bilateral chest radiographic alterations (33; 20%) and presence of underlying diseases (15; 9%). According to WHO and BTS criteria, severe CAP was present in 57 (50%) and in 96 (85%) cases, respectively; 29 (26%) were aged less than 1 year. The median age (months) was 22 (mean 24 ± 14, range 2–58). Overall, radiographic finding was right‐sided in 77 (68%) cases and the upper lobe was compromised in 36 (32%) cases. By analyzing data stratified to age, the frequency of upper lobe involvement was significantly higher among severe cases (WHO criteria) only for those patients aged ≥1 year (13/35 [37%] vs. 7/45 [16%], P = 0.03, OR [95% CI] 3.2 [1.1–9.2]). The specificity and positive predictive value of upper lobe involvement for severity among the latter group of patients were 84% (95% CI 70–93%) and 65% (95% CI 41–84%), respectively. No association was found by using the BTS criteria. The admission chest radiography was useful to predict severity of children aged ≥1 year hospitalized with CAP. Pediatr Pulmonol. 2009; 44:249–252. © 2009 Wiley‐Liss, Inc.
Tricuspid regurgitant jet velocity elevation and its relationship to lung function in pediatric sickle cell disease
Authors: Liem Robert I. , Nevin Mary A. , Prestridge Adrienne , Young Luciana T. , Thompson Alexis A. 
Published: February 2009

AbstractConcerns about the morbidity and mortality associated with tricuspid regurgitant jet velocity (TRJV) elevation, which may indicate pulmonary hypertension (PHT), in adults with sickle cell disease (SCD) have prompted growing interest in screening the pediatric sickle cell population. The goals of our study were to estimate the prevalence of TRJV elevation and determine its relationship to pulmonary function in children and young adults with SCD at baseline. Seventy‐eight subjects (10–24 years old) with SCD underwent prospective screening by Doppler echocardiogram (ECHO), complete lung function evaluation, and laboratory testing as part of standard care at steady state. Tricuspid regurgitation was quantifiable in 68/78 (87%) subjects and peak TRJV was ≥2.5 m/sec in 26/78 (33.3%) evaluated. The frequency of obstruction, restriction, or abnormal gas exchange found on lung function evaluation was not significantly different in subjects with and without TRJV elevation. However, significant inverse correlations were observed between TRJV and both % predicted forced vital capacity (FVC) (r = −0.29, P = 0.022) and oxygen saturation (r = −0.26, P = 0.036). When compared to subjects without TRJV elevation, subjects with TRJV elevation had significantly lower % predicted forced expiratory volume in 1 sec (FEV1) (78.9 ± 14.4 vs. 86.6 ± 13.0%, P = 0.023), FVC (82.8 ± 14.1 vs. 90.7 ± 12.9%, P = 0.017), and oxygen saturation (95.8 ± 3.2 vs. 97.5 ± 2.4%, P = 0.016). We found that the combination of low hemoglobin and low % predicted FVC best predicted TRJV elevation (χ2 = 17.05, P = 0.001) in our cohort, correctly identifying 70% of cases and resulting in positive and negative predictive values of 60 and 74%, respectively. We conclude that in this young population with SCD, TRJV elevation that is not significantly associated with abnormal lung function is common at baseline. Pediatr Pulmonol. 2009; 44:281–289. © 2009 Wiley‐Liss, Inc.
Solution structure of the RNA binding domain in the human muscleblind‐like protein 2
Authors: He Fahu , Dang Weirong , Abe Chikage , Tsuda Kengo , Inoue Makoto , Watanabe Satoru , Kobayashi Naohiro , Kigawa Takanori , Matsuda Takayoshi , Yabuki Takashi , Aoki Masaaki , Seki Eiko , Harada Takushi , Tomabechi Yuri , Terada Takaho , Shirouzu Mikako , Tanaka Akiko , Güntert Peter , Muto Yutaka , Yokoyama Shigeyuki 
Published: February 2009

AbstractThe muscleblind‐like (MBNL) proteins 1, 2, and 3, which contain four CCCH zinc finger motifs (ZF1–4), are involved in the differentiation of muscle inclusion by controlling the splicing patterns of several pre‐mRNAs. Especially, MBNL1 plays a crucial role in myotonic dystrophy. The CCCH zinc finger is a sequence motif found in many RNA binding proteins and is suggested to play an important role in the recognition of RNA molecules. Here, we solved the solution structures of both tandem zinc finger (TZF) motifs, TZF12 (comprising ZF1 and ZF2) and TZF34 (ZF3 and ZF4), in MBNL2 from Homo sapiens. In TZF12 of MBNL2, ZF1 and ZF2 adopt a similar fold, as reported previously for the CCCH‐type zinc fingers in the TIS11d protein. The linker between ZF1 and ZF2 in MBNL2 forms an antiparallel β‐sheet with the N‐terminal extension of ZF1. Furthermore, ZF1 and ZF2 in MBNL2 interact with each other through hydrophobic interactions. Consequently, TZF12 forms a single, compact global fold, where ZF1 and ZF2 are approximately symmetrical about the C2 axis. The structure of the second tandem zinc finger (TZF34) in MBNL2 is similar to that of TZF12. This novel three‐dimensional structure of the TZF domains in MBNL2 provides a basis for functional studies of the CCCH‐type zinc finger motifs in the MBNL protein family.
A summary of the measured pK values of the ionizable groups in folded proteins
Authors: Grimsley Gerald R. , Scholtz J. Martin , Pace C. Nick 
Published: February 2009

AbstractWe tabulated 541 measured pK values reported in the literature for the Asp, Glu, His, Cys, Tyr, and Lys side chains, and the C and N termini of 78 folded proteins. The majority of these values are for the Asp, Glu, and His side chains. The average pK values are Asp 3.5 ± 1.2 (139); Glu 4.2 ± 0.9 (153); His 6.6 ± 1.0 (131); Cys 6.8 ± 2.7 (25); Tyr 10.3 ± 1.2 (20); Lys 10.5 ± 1.1 (35); C‐terminus 3.3 ± 0.8 (22) and N‐terminus 7.7 ± 0.5 (16). We compare these results with the measured pK values of these groups in alanine pentapeptides, and comment on our overall findings.
OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold
Authors: Fazelinia Hossein , Cirino Patrick C. , Maranas Costas D. 
Published: February 2009

AbstractOne of the many challenging tasks of protein design is the introduction of a completely new function into an existing protein scaffold. In this study, we introduce a new computational procedure OptGraft for placing a novel binding pocket onto a protein structure so as its geometry is minimally perturbed. This is accomplished by introducing a two‐level procedure where we first identify where are the most appropriate locations to graft the new binding pocket into the protein fold by minimizing the departure from a set of geometric restraints using mixed‐integer linear optimization. On identifying the suitable locations that can accommodate the new binding pocket, CHARMM energy calculations are employed to identify what mutations in the neighboring residues, if any, are needed to ensure that the minimum energy conformation of the binding pocket conserves the desired geometry. This computational framework is benchmarked against the results available in the literature for engineering a copper binding site into thioredoxin protein. Subsequently, OptGraft is used to guide the transfer of a calcium‐binding pocket from thermitase protein (PDB: 1thm) into the first domain of CD2 protein (PDB:1hng). Experimental characterization of three de novo redesigned proteins with grafted calcium‐binding centers demonstrated that they all exhibit high affinities for terbium (Kd ∼ 22, 38, and 55 μM) and can selectively bind calcium over magnesium.
Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution‐state structure of the nucleocapsid protein from HIV‐1
Authors: Summers Michael F. , Henderson Louis E. , Chance Mark R. , South Terri L. , Blake Paul R. , Perez‐Alvarado Gabriela , Bess Julian W. , Sowder Raymond C. , Arthur Larry O. , Sagi Irit , Hare Dennis R. 
Published: February 2009

AbstractAll retroviral nucleocapsid (NC) proteins contain one or two copies of an invariant 3Cys‐1His array (CCHC = C‐X2‐C‐X4‐H‐X4‐C; C = Cys, H = His, X = variable amino acid) that are essential for RNA genome packaging and infectivity and have been proposed to function as zinc‐binding domains. Although the arrays are capable of binding zinc in vitro, the physiological relevance of zinc coordination has not been firmly established. We have obtained zinc‐edge extended X‐ray absorption fine structure (EXAFS) spectra for intact retroviruses in order to determine if virus‐bound zinc, which is present in quantities nearly stoichiometric with the CCHC arrays (Bess, J.W., Jr., Powell, P.J., Issaq, H.J., Schumack, L.J., Grimes, M.K., Henderson, L.E., & Arthur, L.O., 1992, J. Virol. 66, 840–847), exists in a unique coordination environment. The viral EXAFS spectra obtained are remarkably similar to the spectrum of a model CCHC zinc finger peptide with known 3Cys‐1His zinc coordination structure. This finding, combined with other biochemical results, indicates that the majority of the viral zinc is coordinated to the NC CCHC arrays in mature retroviruses. Based on these findings, we have extended our NMR studies of the HIV‐1 NC protein and have determined its three‐dimensional solution‐state structure. The CCHC arrays of HIV‐1 NC exist as independently folded, noninteracting domains on a flexible polypeptide chain, with conservatively substituted aromatic residues forming hydrophobic patches on the zinc finger surfaces. These residues are essential for RNA genome recognition, and fluorescence measurements indicate that at least one residue (Trp37) participates directly in binding to nucleic acids in vitro. The NC is only the third HIV‐1 protein to be structurally characterized, and the combined EXAFS, structural, and nucleic acid‐binding results provide a basis for the rational design of new NC‐targeted antiviral agents and vaccines for the control of AIDS.
Identification of the posttranslational modifications of bovine lens αB‐crystallins by mass spectrometry
Authors: Smith Jean B. , Sun Yiping , Smith David L. , Green Brian 
Published: February 2009

AbstractA combination of mass spectrometric techniques has been used to investigate the amino acid sequence and post‐translational modifications of αB‐crystallin isolated from bovine lenses by gel filtration chromatography and reversed‐phase high performance liquid chromatography. Chromatographic fractions were analyzed by electrospray ionization mass spectrometry to determine the homogeneity and molecular weights of proteins in the fractions. The αB‐crystallin primary gene product, its mono‐ and diphosphorylated forms, its N‐ and C‐terminal truncated forms, as well as other lens proteins unrelated to the αB‐crystallins were identified by their molecular weights. Detailed information about the sites of phosphorylation, as well as evidence supporting reassignment of Asn to Asp at position 80, was obtained by analyzing proteolytic digests of these proteins by fast atom bombardment mass spectrometry. Results of this investigation indicate that αB‐crystallin is phosphorylated in vivo at Ser 45, Ser 59, and either Ser 19 or 21. From the specificity of phosphorylation of α‐crystallins, it appears that there may be two different kinases responsible for their phosphorylation.
Protein classification artificial neural system
Authors: Wu Cathy , Whitson George , Mclarty Jerry , Ermongkonchai Adisorn , Chang Tzu‐Chung 
Published: February 2009

AbstractA neural network classification method is developed as an alternative approach to the large database search/organization problem. The system, termed Protein Classification Artificial Neural System (ProCANS), has been implemented on a Cray supercomputer for rapid superfamily classification of unknown proteins based on the information content of the neural interconnections. The system employs ann‐gram hashing function that is similar to thek‐tuple method for sequence encoding. A collection of modular back‐propagation networks is used to store the large amount of sequence patterns. The system has been trained and tested with the first 2,148 of the 8,309 entries of the annotated Protein Identification Resource protein sequence database (release 29). The entries included the electron transfer proteins and the six enzyme groups (oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases), with a total of 620 superfamilies. After a total training time of seven Cray central processing unit (CPU) hours, the system has reached a predictive accuracy of 90%. The classification is fast (i.e., 0.1 Cray CPU second per sequence), as it only involves a forward‐feeding through the networks. The classification time on a full‐scale system embedded with all known superfamilies is estimated to be within 1 CPU second. Although the training time will grow linearly with the number of entries, the classification time is expected to remain low even if there is a 10–100‐fold increase of sequence entries. The neural database, which consists of a set of weight matrices of the networks, together with the ProCANS software, can be ported to other computers and made available to the genome community. The rapid and accurate superfamily classification would be valuable to the organization of protein sequence databases and to the gene recognition in large sequencing projects.