bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting “reverse hydrophobic effect”: Applicable only to coil mutations at the surface
Authors: Gromiha M. Michael 
Published: March 2009

AbstractIn a seminal paper, Pakula and Sauer (Nature, 1990, 344, 363–364) demonstrated that the increase in side‐chain hydrophobicity has a reverse relationship with protein stability. We have addressed this problem with several examples of mutants that span at different locations in protein structure based on secondary structure and solvent accessibility. We confirmed that the stability change upon single coil mutation at exposed region is reversely correlated with hydrophobicity with a single exception. In addition, we found the existence of such relationship in partially buried coil mutants. The stability of exposed helical mutants is governed by conformational properties. In buried and partially buried helical and strand mutants properties reflecting hydrophobicity have direct relationship with stability, whereas an opposite relationship was obtained with entropy and flexibility. The structural analysis of partially buried/exposed mutants showed that the surrounding residues are important for the stability change upon mutation. These results provide insights to understand the general behavior for the stability of proteins upon amino acid substitutions. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 591–599, 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
Outcomes following Turnbull–Cutait abdominoperineal pull-through compared with coloanal anastomosis
Authors: Remzi F H , El Gazzaz G , Kiran R P , Kirat H T , Fazio V W 
Published: March 2009

Abstract

Background
The Turnbull–Cutait abdominoperineal pull-through procedure (T-C) is used as a last resort to avoid permanent diversion in patients with complex anorectal conditions. The aim was to evaluate short- and long-term outcomes after T-C.

Methods
Patients undergoing T-C from 1996 to 2007 were reviewed retrospectively in terms of demographics, diagnosis, indications and postoperative complications. Patients were contacted to obtain functional outcomes using a standardized questionnaire. Functional outcomes were compared with those in a matched group of patients undergoing handsewn coloanal anastomosis (CAA) for rectal cancer.

Results
Sixty-seven patients (40 men) underwent T-C. Postoperative complications included stricture in 11 patients (16 per cent), fistula in five (7 per cent), prolapse of the colon in five (7 per cent) and leak in two (3 per cent). Mean follow-up was 5·6 (s.d. 3·2) years. The operation failed in 17 patients (25 per cent). Among 44 patients (66 per cent) who completed questionnaires, faecal (P = 0·121) and urinary (P = 0·073) incontinence, and sexual function (P = 0·063) were comparable to those in patients who had CAA.

Conclusion
T-C is an option for patients with complex anorectal conditions that might otherwise require permanent diversion. Functional outcomes are comparable to those of CAA.
Endocavitary contact radiation therapy for ultrasonographically staged T1 N0 and T2 N0 rectal cancer
Authors: Christoforidis D , McNally M P , Jarosek S L , Madoff R D , Finne C O 
Published: March 2009

Abstract

Background
The purpose of this study was to determine the long-term outcomes of patients undergoing endocavitary contact radiation therapy (ECR) for stage I rectal cancer.

Methods
A database of patients treated with ECR for biopsy-proven rectal adenocarcinoma from July 1986 to June 2006 was reviewed retrospectively. Only patients with primary, non-metastatic, ultrasonographically staged T1 N0 and T2 N0 cancer who had no adjuvant treatment were included. Patients received a median of 90 (range 60–190) Gy contact radiation, delivered transanally by a 50-kV X-ray tube in two to five fractions.

Results
Of 149 patients, 77 (40 T1, 37 T2) met the inclusion criteria. Median age was 74 (range 38–104) years, and median follow-up 69 (range 10–219) months. ECR failed in 21 patients (27 per cent) (persistent disease, four; recurrence, 17), of whom ten remained disease free after salvage therapy. The estimated 5-year disease-free survival rate was 74 (95 per cent confidence interval 63 to 83) per cent after ECR alone, and 87 (76 to 93) per cent when survival after salvage therapy for recurrence was included.

Conclusion
ECR is a minimally invasive treatment option for early-stage rectal cancer. However, similar to other local therapies, ECR has a worse oncological outcome than radical surgery.
Randomized clinical trial of concomitant or sequential phlebectomy after endovenous laser therapy for varicose veins
Authors: Carradice D , Mekako A I , Hatfield J , Chetter I C 
Published: March 2009

Abstract

Background
The management of residual varicosities following endovenous laser therapy (EVLT) for varicose veins is contentious. Ambulatory phlebectomy may be performed concomitantly with the initial EVLT, or sequentially as a secondary procedure. This randomized trial compared these two approaches.

Methods
Fifty patients with great saphenous varicose veins were randomized to EVLT alone or EVLT with concomitant ambulatory phlebectomies (EVLTAP). Principal outcomes were procedure duration, pain scores, requirement for secondary procedures and quality of life after 3 months.

Results
EVLTAP took longer, but significantly decreased the requirement for subsequent interventions. There was no impairment in immediate postprocedural pain, Short Form 36 or EuroQol 5D scores with EVLTAP. Median (i.q.r.) Venous Clinical Severity Score (VCSS) at 3 months was lower for EVLTAP than for EVLT alone (0 (0–1) versus 2 (0–2); P &lt; 0·001), with lower Aberdeen Varicose Vein Questionnaire (AVVQ) scores at 6 weeks (7·9 (4·1–10·7) versus 13·5 (10·9–18·1); P &lt; 0·001) and 3 months (2·0 (0·4–7·7) versus 9·6 (2·2–13·8); P = 0·015). At 1 year, there were no differences in VCSS or AVVQ scores.

Conclusion
Concomitant phlebectomy with EVLT prolonged the procedure, but reduced the need for secondary procedures and significantly improved quality of life and the severity of venous disease.
Branch duct intraductal papillary mucinous neoplasms in a retrospective series of 190 patients
Authors: Woo S M , Ryu J K , Lee S H , Yoon W J , Kim Y-T , Yoon Y B 
Published: March 2009

Abstract

Background
A consensus conference has recommended close observation of branch duct intraductal papillary mucinous neoplasms (BD-IPMNs) smaller than 30 mm, without symptoms or mural nodules. This study investigated whether these recommendations could be validated in a single-centre experience of BD-IPMNs.

Methods
Some 190 patients with radiological imaging or histological findings consistent with BD-IPMN were enrolled between 1998 and 2005. Those with less than 6 months' follow-up and no histological confirmation were excluded.

Results
BD-IPMN was diagnosed by computed tomography and pancreatography in 105 patients and pathologically in 85. Eighteen patients had adenoma, 53 borderline malignancy, five carcinoma in situ and nine invasive carcinoma. Findings associated with malignancy were the presence of radiologically suspicious features (P &lt; 0·001) and a cyst size of at least 30 mm (P = 0·001). Had consensus guidelines been applied, 54 patients would have undergone pancreatic resection, whereas only 28 of these patients actually had a resection; 12 of the latter patients had a malignancy compared with none of the 26 patients who were treated conservatively.

Conclusion
A simple increase in cyst size is not a reliable predictor of malignancy. Observation is recommended for patients with a BD-IPMN smaller than 30 mm showing no suspicious features on imaging.
Interactions of HIV‐1 Antibodies 2F5 and 4E10 with a gp41 Epitope Prebound to Host and Viral Membrane Model Systems
Authors: Veiga Ana S. , Pattenden Leonard K. , Fletcher Jordan M. , Castanho Miguel A. R. B. , Aguilar Marie Isabel 
Published: March 2009

AbstractPoint of recognition: Surface plasmon resonance was used to study the role of the viral membrane in HIV immunogen recognition by the monoclonal antibodies 2F5 and 4E10. The different behaviour of the antibodies towards membranes and immunogens embedded within membranes, provide insight into the emerging membrane‐based or membrane‐conformation strategies of immunogen design.magnified imageTwo HIV‐1 recognition domains for the human monoclonal antibodies (MAb) 2F5, which recognises the core sequence ELDKWA, and 4E10, which recognises the core sequence NWFNIT, serve as promising models for immunogens in vaccine development against HIV‐1. However, the failure of these recognition domains to generate broadly reactive neutralizing antibodies, and the putative membrane‐binding properties of the antibodies raised to these recognition domains, suggest that additional features or recognition motifs are required to form an efficient immunogen, which could possibly include the membrane components. In this study we used an extended peptide epitope sequence derived from the gp41 native sequence (H‐NEQELLELDKWASLWNWFNITNWLWYIK‐NH), which contains the two recognition domains for 2F5 and 4E10, to examine the role of model cell (POPC) and viral (POPC/cholesterol/sphingomyelin) membranes in the recognition of these two antibodies. By using a surface plasmon resonance biosensor, the binding of 2F5 and 4E10 to membranes was compared and contrasted in the presence and absence of prebound peptide epitope. The recognition of the peptide epitope by each MAb was found to be distinct; 2F5 exhibited strong and almost irreversible binding to both membranes in the presence of the peptide, but bound weakly in the absence of the peptide epitope. In contrast, 4E10 exhibited strong membrane binding in the presence or absence of the peptide epitope, and the binding was essentially irreversible in the presence of the peptide epitope. Overall, these results demonstrate that both 2F5 and 4E10 can bind to membranes prior to epitope recognition, but that high‐affinity recognition of gp41‐derived epitope sequences by 2F5 and 4E10 occurs in a membrane context. Moreover, 4E10 might utilise the membrane to access and bind to gp41; such membrane properties of 2F5 and 4E10 could be exploited in immunogen design.
Comparing long‐term outcomes between drug‐eluting and bare‐metal stents in the treatment of cardiac allograft vasculopathy
Authors: Nfor Tonga , Ansaarie Imran , Gupta Anjan , Bajwa Tanvir , Allaqaband Suhail 
Published: March 2009

AbstractBackground: Cardiac allograft vasculopathy (CAV) is the leading cause of death after the first year following heart transplantation. We compared restenosis rates, mortality, and other major adverse cardiac events (MACE) between transplant recipients treated with DES and BMS for CAV. Methods: All patients from our heart transplant registry undergoing PCI with stenting for CAV were identified. Procedural data, baseline clinical characteristics, yearly coronary angiography, cardiac events and death were prospectively collected. Primary outcome was in‐stent restenosis (ISR). Secondary outcomes were in‐segment restenosis, target vessel revascularization (TVR), all‐cause mortality and combined MACE. Results: 36 lesions in 25 patients treated with DES were compared with 31 BMS‐treated lesions in 19 patients. There were no significant differences in baseline characteristics. 12‐month incidence of ISR was 0% with DES vs. 12.9% with BMS, P = 0.03. Over mean (±standard error) follow‐up of 51.1 ± 7.5 months this difference was significant for vessels ≤3 mm in diameter, hazard ratio (HR) DES vs. BMS 0.37 (95% CI 0.11 to 0.95) P = 0.037; but not for vessels >3 mm P = 0.45. However, there was no difference in overall longterm patency because of similar rates of in‐segment restenosis between DES and BMS, HR 1.13 (95% CI 0.43 to 2.97) P = 0.81. Also, the rates of TVR, death from any cause and combined MACE were similar; log rank P 0.88, 0.67, and 0.85, respectively. Conclusion: This study suggests that after PCI for cardiac allograft vasculopathy, despite a lower in‐stent restenosis rate in DES compared with BMS, in‐segment restenosis and clinical cardiac endpoints are similar. © 2009 Wiley‐Liss, Inc.
Experimental evaluation of a new articulated Amplatzer® ductal occluder device without fabric
Authors: Gruenstein Daniel H. , Bass John L. 
Published: March 2009

AbstractObjectives: To describe a new percutaneous PDA device. Background: The ADO II was developed by AGA Medical for closure of small‐moderate sized PDAs via a small delivery catheter from an antegrade or retrograde catheter approach. The objective of this study was to evaluate the technical feasibility, safety, and efficacy of the ADO II in a canine PDA model. Methods: The ADO‐II consists of multi‐layer nitinol wire braid with symmetric retention disks and an articulating connecting center waist, without sewn‐in polyester, that can be delivered though a 4‐5F catheter. A PDA was surgically created in nine dogs. Transcatheter occlusion of the PDA was performed using the ADO II. Angiographic and hemodynamic data were obtained at 7, 30, 60, and 90 days post‐procedure. The devices were then harvested for pathology. Results: Devices were placed transarterially (n = 8) and transvenously (n = 1). All PDAs were occluded and there were no significant pressure gradients (P > 0.05) at the immediate and 90 post‐implant evaluations. Pathology found endothelial coverage on all aortic and pulmonary disks, except at the tip of the microscrew. There were no procedural complications. One canine was euthanized 4 hr after device implant because of a clinical deterioration. The staff veterinarian and pathologist concluded that the animal's illness was not device related. Conclusions: The Amplatzer ADO II devices can be safely deployed in animal models of PDAs, with complete resolution of the PDA shunt. The lower profile and symmetry of the ADO II allows for venous or arterial approach and smaller delivery catheter size. The ADO‐II is expected to be a preferred alternative for closure of small‐moderate PDAs. © 2009 Wiley‐Liss, Inc.
Kinetics of Primary Nanoparticle Agglomeration in Precipitation of Silver
Authors: Manteghian M. , Ghader S. 
Published: March 2009

AbstractThe precipitation kinetics of silver was studied using a lab‐scale batch crystallizer with special attention to characterization of agglomeration of primary nanoparticles. The vessel was operated at different feed concentrations, molar ratios, and stirrer speed. Nucleation, volume average crystal growth rates, and agglomeration kernels were determined. Empirical relations were obtained between the rates of the different crystallization steps with supersaturation, magma density, and energy dissipation rate. The results show that larger crystals will be obtained at high supersaturation due to dominance of agglomeration, because the rate of agglomeration also increases with supersaturation, thereby suppressing the primary nucleation rate and enhancing the observed average volume growth rate.
Electrochemical Oxidation of Phenol on Metal‐Impregnated Zeolite Electrodes
Authors: Mojović Z. , Milutinović‐Nikolić A. , Mentus S. , Jovanović D. 
Published: March 2009

AbstractNanodispersed metallic clusters of platinum, silver and cobalt were incorporated into NaX zeolite cavities by impregnation with acetone solution of corresponding acetylacetonates and solvent evaporation followed by acetylacetonate thermal decomposition. The mixture of modified zeolites and 10 wt % of carbon black, in the form of a thin layer, was pasted onto a glassy carbon surface by Nafion. With such electrode materials, the phenol oxidation in neutral, alkaline and acid solution was studied by cyclovoltammetry. Deactivation of all electrodes in both neutral and alkaline medium was observed, indicating that polymerization reaction might be the main reaction pathway of phenol at higher pH values. Formation of quinine‐type structures was obtained during electro‐oxidation at lower pH values, being more significant in acidic solutions.
Retracted: Effects of the Operating Conditions and Geometry Parameter on the Filtration Performance of the Fibrous Filter
Authors: Qian F. , Zhang J. , Huang Z. 
Published: March 2009

AbstractThe gas‐solid two‐phase flows in fibrous filters were simulated by computational fluid dynamics (CFD) technology. The pressure drops and filter efficiencies with different operating conditions and geometry parameter, including face velocity, particle size, and solid volume fraction (SVF) were calculated. The effects of the operating conditions and geometry parameter on the filter performance of the fibrous filter were obtained. The results indicate that the pressure drop increases linearly with the face velocity and the predicted values of the pressure drops are in excellent agreement with the experimental correlation. Filtration efficiency decreases with the face velocity for submicrometer particles (0.1 μm) and, for larger particles (1 μm) the tendency is just the opposite. The filtration mechanism is different for different particle sizes. For the filter in this paper, when the particle size is smaller than 0.2 μm, Brownian diffusion plays a significant role in the filtration process. When the particle size is greater than 0.5 μm, inertial impaction becomes an important capture mechanism. For particle sizes in the range of 0.2–0.5 μm, the Brownian diffusion and inertial impaction are both relatively weak and, therefore, the filtration efficiency has the least value in this range. Additionally, the SVF distribution is an important geometry parameter in the filter. The filtration efficiency of the filter with a decreased SVF (geometry B) along the thickness of the filter is higher than that of the filter with the even SVF (geometry A), while maintaining a low pressure drop.
Extraction of Uranium from Aqueous Solutions by Using Ionic Liquid and Supercritical Carbon Dioxide in Conjunction
Authors: Wang Joanna Shaofen , Sheaff Chrystal N. , Yoon Byunghoon , Addleman R. Shane , Wai Chien M. 
Published: March 2009

AbstractSuper powers! Uranium(VI) ions can be extracted from aqueous solutions into supercritical CO2 (sc‐CO2) via an ionic liquid phase that contained tri‐n‐butyl phosphate (TBP) as a complexing agent (see figure). This process has potential applications in the nuclear industry for removing actinides from nuclear waste.magnified imageUranyl ions [UO2]2+ in aqueous nitric acid can be extracted into supercritical CO2 (sc‐CO2) by using an imidazolium‐based ionic liquid with tri‐n‐butyl phosphate (TBP) as a complexing agent. The transfer of uranium from the ionic liquid to the supercritical fluid phase was monitored by UV/Vis spectroscopy using a high‐pressure fiber‐optic cell. The form of the uranyl complex extracted into the sc‐CO2 phase was identified to be [UO2(NO3)2(TBP)2]. The extraction results were confirmed by fluorescence spectroscopy and by neutron activation analysis. This technique has potential applications in the field of nuclear waste management for extracting other actinides.
Halogen Bonding between an Isoindoline Nitroxide and 1,4‐Diiodotetrafluorobenzene: New Tools and Tectons for Self‐Assembling Organic Spin Systems
Authors: Hanson Graeme R. , Jensen Paul , McMurtrie John , Rintoul Llew , Micallef Aaron S. 
Published: March 2009

AbstractRadical assembly: Halogen bonding has been observed for the first time between an isoindoline nitroxide and an iodoperfluorocarbon (see figure), which cocrystallize to form a discrete 2:1 supramolecular compound in which NO.⋅⋅⋅I halogen bonding is the dominant intermolecular interaction. This illustrates the potential use of halogen bonding and isoindoline nitroxide tectons for the assembly of organic spin systems.magnified imageThe isoindoline nitroxide 1,1,3,3‐tetramethylisoindolin‐2‐yloxyl (TMIO) and 1,4‐diiodotetrafluorobenzene readily form a discrete 2:1 complex that shows evidence of relatively strong NO.⋅⋅⋅I halogen bonding. This interaction was characterized in the solid state by single‐crystal X‐ray analysis, thermal analysis, and vibrational spectroscopy (IR and Raman), backed by density functional theory calculations. EPR spectroscopy performed on a solution of TMIO in pentafluoroiodobenzene, a halogen‐bonding donor, indicates that halogen bonding induces an increase in electron density at the nitroxide nitrogen nucleus and an increase in the nitroxide rotational correlation time. Our findings demonstrate the potential of utilizing halogen‐bonding interactions to promote the self‐assembly of new isoindoline nitroxide tectons for the preparation of organic spin systems.
A C‐linked Glycomimetic in the Gas Phase and in Solution: Synthesis and Conformation of the Disaccharide Manα(1,6)‐C‐ManαOPh
Authors: Drouin Ludovic , Stanca‐Kaposta E. Cristina , Saundh Priptal , Fairbanks Antony J. , Kemper Sebastian , Claridge Timothy D. W. , Simons John P. 
Published: March 2009

AbstractThe effect of carbon is subtle but sweet: The flexible C‐linkage in the newly synthesised C‐glycosyl mimetic, Manα(1,6)‐C‐ManαOPh allows OHπ bonding, both in the gas phase and in aqueous solution. This interaction is absent in the O‐linked disaccharide (see figure).magnified imageThe intrinsic conformational preference of a newly synthesised glycomimetic, the C‐linked disaccharide Manα(1,6)‐C‐ManαOPh (1), has been determined in the gas phase at about 10 K by infrared ion dip spectroscopy coupled with density functional theory and ab initio calculations, and compared with its dynamical conformation in aqueous solution at 298 K by NMR spectroscopy. Comparisons are also made between these conformations and those of the corresponding O‐linked disaccharide 2 in the gas phase and the C‐linked disaccharide Manα(1,6)‐C‐ManαOMe (3) in the gas phase and in aqueous solution. The C‐ and O‐linked disaccharides 1 and 2 present quite distinct conformational preferences in the gas phase: inter‐glycosidic hydrogen bonding, seen in one of the two conformers populated in 2, is not seen in 1 which adopts a conformation (not populated in 2) with glycosidic dihedral angles (ϕ, ψ, ω) of −72°, 52° and 66°; supported in part by an OHπ hydrogen bond. This conformer is also strongly populated in an aqueous solution of 1 (and very weakly, of 3) together with a second conformer, with dihedral angles (ϕ, ψ, ω) of about −60°, 180° and 60°, not seen in the gas phase but by far the dominant conformer in an aqueous solution of 3. The C‐disaccharide 1 was tested as a potential inhibitor, but displayed no significant inhibitory activity against Jack Bean α‐mannosidase.
Intramolecular Alkynylogous Mukaiyama Aldol Reaction Starting from Bicyclic Alkanones Tethered to Alkynyl Esters: Formal Total Synthesis of (±)‐Hamigeran B
Authors: Miesch Laurence , Welsch Tania , Rietsch Vincent , Miesch Michel 
Published: March 2009

AbstractSelecting the ring: tert‐Butyldimethylsilyltriflate (TBSOTf)/NEt3 treatment of alkynyl esters tethered to bicycloalkanones leads to the formation of tricyclic allenoates with total diasteroselectivity at the ring junction. An intramolecular alkynylogous Mukaiyama aldol reaction promoted by a TBSOTf/NEt3 dual activation is involved. This novel methodology was illustrated by a formal total synthesis of (±)‐hamigeran B.magnified imagetert‐Butyldimethylsilyltriflate (TBSOTf)/NEt3 treatment of alkynyl esters tethered to bicycloalkanones led to tricyclic allenoates with total diastereoselectivity for the ring junction. The allenoates result from an intramolecular alkynylogous Mukaiyama aldol reaction promoted by a TBSOTf/NEt3 dual activation, with key intermediates of silylalkynylketene acetals. This novel methodology was illustrated by a formal total synthesis of (±)‐hamigeran B.