bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternate pathways for NADH oxidation in Thermus thermophilus using type 2 NADH dehydrogenases
Authors: Venkatakrishnan Padmaja , Lencina Andrea M. , Schurig-Briccio Lici A. , Gennis Robert B. 
Published: February 2013

Abstract
Type 2 NADH dehydrogenase (NDH-2) is a single-subunit membrane-associated flavoenzyme that is part of the respiratory chain of many prokaryotes. The enzyme catalyzes the electron transfer from NADH to quinone but is not directly coupled to the generation of a proton motive force. The purpose of the current work is to compare two different NDH-2s that are encoded in strains of Thermus thermophilus. The aerobic T. thermophilus HB27 strain expresses one NDH-2 that has been previously isolated and characterized. In this work it is shown that a gene, which is misannotated as an NADH oxidase, encodes this enzyme. Unlike HB27, strain NAR1 of T. thermophilus is capable of partial denitrification, and in addition its genome contains the nrcN gene that encodes a second putative NDH-2. Of particular interest is the fact that nrcN is part of an operon (nrcDEFN) that is proposed to encode a protein complex specifically required for nitrate reduction. In this work, the nrcN gene has the activity expected of a NDH-2, and functions independently of other components of the putative Nrc complex. The biochemical properties of the two NDH-2 enzymes are compared. Efforts to demonstrate that NrcN is part of a multiprotein complex were not successful. However, the NrcE protein was expressed in Escherichia coli and shown to be a membrane-bound protein containing heme B.
Mechanistic aspects of sodium-binding sites in LeuT-like fold symporters
Authors: Perez Camilo , Ziegler Christine 
Published: February 2013

Abstract
Secondary active transporters are of paramount biological impact in all living cells, facilitating the movement of many different substrates across the membrane against a concentration gradient. The uphill transport of one substrate is coupled to the downhill transport of another and driven by the electrochemical gradient. In the last decade, an increasing number of atomic structures of secondary transporters have been reported, confirming a very fundamental mechanistic concept known as the alternating-access cycle. The wealth of structures of transporters sharing the so-called LeuT-like fold that is characterized by two five-transmembrane-helix repeats sharing a 2-fold inverted pseudo symmetry has raised big hopes to finally describe alternating access on a molecular level. Although comparing the individual transporter states of different LeuT-like fold transporters revealed striking similarities, the coupling process, which represents the heart of secondary transport, is far from being understood. Here, we review the structural, functional, and biophysical validation of sodium-binding sites in four different LeuT-like fold transporters. The conservation of sodium sites is discussed in light of their role as key elements connecting symmetry-related structural domains, which are involved in substrate translocation. Moreover, we highlight their crucial roles in conformational changes of LeuT-like fold transporters and their implication on a unifying mechanism in secondary transport.
Hydrolysis of dipeptide derivatives reveals the diversity in the M49 family
Authors: Jajčanin-Jozić Nina , Abramić Marija 
Published: February 2013

Abstract
Dipeptidyl peptidase III, a metallopeptidase of the M49 family, was first identified (in the pituitary) by its specific cleavage of diarginyl arylamides, which have been used as preferred assay substrates until now. Here we examined the activity of the yeast and human dipeptidyl peptidase III in parallel. The human enzyme preferred Arg2-β-naphthylamide and showed 620-fold higher k
cat/K
m for this substrate. In contrast, the yeast enzyme did not display a preference for any of the X-Arg-β-naphthylamide analyzed. The replacement of Gly505 with Asp, resulted in a less active, but more selective, yeast enzyme form. These results indicate diversity in cleavage specificity in the M49 family.
Heparan sulfate: a key regulator of embryonic stem cell fate
Authors: Kraushaar Daniel C. , Dalton Stephen , Wang Lianchun 
Published: February 2013

Abstract
Heparan sulfate (HS) belongs to a class of glycosaminoglycans and is a highly sulfated, linear polysaccharide. HS biosynthesis and modification involves numerous enzymes. HS exists as part of glycoproteins named HS proteoglycans, which are expressed abundantly on the cell surface and in the extracellular matrix. HS interacts with numerous proteins, including growth factors, morphogens, and adhesion molecules, and thereby regulates important developmental processes in invertebrates and vertebrates. Embryonic stem cells (ESCs) are distinguished by their characteristics of self-renewal and pluripotency. Self-renewal allows ESCs to proliferate indefinitely in their undifferentiated state, whereas pluripotency implies their capacity to differentiate into the three germ layers and ultimately all cell types of the adult body. Both traits are tightly regulated by numerous cell signaling pathways. Recent studies have highlighted the importance of HS in the modulation of ESC functions, specifically their lineage fate. Here, we review the current advances that have been made in understanding the structural changes of HS during ESC differentiation and in deciphering the molecular mechanisms by which HS modulates cell fate. Finally, we discuss the applications of heparinoids and chemical inhibitors of HS biosynthesis for the manipulation of ESC culture and directed differentiation.
Crystal structure of μ3-fluoro-tri-μ2-fluoro-tris(tetramethylethylenediamine nickel(II)) fluoride trihydrate, [Ni3(tmen)3F5]+·F–·3H2O, C18H54F6N6Ni3O3
Authors: Ishikawa Yuki , Miyamoto Keiko , Horn Ernst 
Published: February 2013

Abstract C18H54F6N6O3Ni3, triclinic, P1̄ (no. 2), a = 8.6908(7) Å, b = 13.717(1) Å, c = 14.281(1) Å, α = 72.997(1)°, β = 89.459(1)°, γ = 75.718(1)°, V = 1574.1(2) Å3, Z = 2, Rgt(F) = 0.0355, wRref(F2) = 0.0433, T = 273,2 K.
Liquid meal composition, postprandial satiety hormones, and perceived appetite and satiety in obese women during acute caloric restriction
Authors: Heden Timothy D , Liu Ying , Sims Lauren , Kearney Monica L , Whaley-Connell Adam T , Chockalingam Anand , Dellsperger Kevin C , Fairchild Timothy J , Kanaley Jill A 
Published: February 2013

ObjectiveThe purpose of this study was to compare postprandial satiety regulating hormone responses (pancreatic polypeptide (PP) and peptide tyrosine tyrosine (PYY)) and visual analog scale- (VAS) assessed perceived appetite and satiety between liquid high-protein (HP) and high-carbohydrate (HC) meals in obese women during acute (24-h) caloric restriction.DesignEleven obese premenopausal women completed two conditions in random order in which they consumed 1500 calories as six 250-calorie HP meals or six 250-calorie HC meals over a 12-h period. Blood samples were taken at baseline and every 20 min thereafter and analyzed for PP and PYY concentrations. At these same points, perceived hunger and fullness were assessed with a VAS. The incremental area under the curve (iAUC) was used to compare postprandial responses.ResultsThe 12-h PP and PYYiAUC were greater (P≤0.05) during the HP condition (PP: 4727±1306 pg/ml×12 h, PYY: 1373±357 pg/ml×12 h) compared with the HC condition (PP: 2300±528 pg/ml×12 h, PYY: 754±246 pg/ml×12 h). Perceived hunger and fullness were not different between conditions (P>0.05). The greatest changes in PYY and perceived fullness occurred after the morning meals during both conditions.ConclusionsThese data suggest that in obese women during acute caloric restriction before weight loss, i) liquid HP meals, compared with HC meals, result in greater postprandial PP and PYY concentrations, an effect not associated with differential appetite or satiety responses, and ii) meal-induced changes in PYY and satiety are greatest during the morning period, regardless of dietary macronutrient composition.
Electrocatalyis for PEFCs: Oxygen Reduction on Nanoparticles and Extended Surfaces
Authors: Schmidt Thomas J. , Rabis Annett , Schwanitz Bernhard , Scherer Günther G. 
Published: February 2013

ABSTRACTThis work makes an attempt to correlate experimentally observed Tafel slopes from the oxygen reduction reaction in both model rotating disk electrode and polymer electrolyte fuel cell measurements, respectively, with the kinetic description of a coverage dependent current-potential relationship. It is shown that the potential dependent OHadcoverage can be used as a descriptor of potential dependent Tafel slopes, pointing to the validity of underlying Temkin-Frumkin adsorption properties in combination with the Butler-Volmer approach.
Coverage of Isolated, Severe Gingival Recession: A Modified Technique
Authors: Tsourounakis Ioannis , Sweidan Caesar , Palaiologou Angela A. , Maney Pooja 
Published: February 2013

Introduction: Gingival recession (GR) presents a major concern for patients, especially when associated with tooth sensitivity or esthetic concerns.Case Presentation: This report describes a modified technique for the treatment of isolated, severe GR combining a full‐thickness/split‐thickness coronally positioned flap with a subepithelial connective tissue graft. After treatment of severe GR of the maxillary right and left canines (5 and 6 mm, respectively), there was almost complete coverage of both canines and an increase in keratinized gingiva.Conclusion: A promising technique is presented, yielding 84% to 100% of defect coverage and gingival tissue enhancement on single teeth.
The Role of Implant Position on Long‐Term Success
Authors: Su Chuan‐Yi , Fu Jia‐Hui , Wang Hom‐Lay 
Published: February 2013

Focused Clinical Question: In the past, implants were placed where the bone was. This mode of treatment often led to implant‐related complications, such as peri‐implant soft‐tissue recession, esthetic challenges, and fractured implants and/or associated suprastructures. Therefore, advances in soft‐tissue and bone augmentation techniques have enabled implants to be placed in an ideal three‐dimensional position, thus ensuring adequate peri‐implant soft tissue and bone thickness for a stable and successful long‐term treatment outcome. The present report aims to answer the question: What are the clinical guidelines for implant placement to achieve long‐term success?Summary: In the maxillary anterior region where esthetics is of paramount importance, 2 mm of buccal bone anterior to the implant is preferred. This ensures stability of the buccal bone plate, minimizing peri‐implant mucosal recession. To achieve an esthetic emergence profile, the implant platform is generally placed 3 to 4 mm apical to the cemento‐enamel junction (CEJ) of the adjacent teeth and 1.5 to 2 mm away from the adjacent roots. In the posterior region, a minimum of 1 mm of buccal bone around the implant ensures stability of the buccal plate. Generally, implants with a polished collar are preferred because the collar can be placed supracrestally to compensate for any vertical ridge deficiency and yet not compromise the esthetics of the restoration. The implant is placed 1.5 to 3 mm apical to the CEJ of the adjacent teeth and 3 to 4 mm away from adjacent roots to create a smooth transition from implant platform to occlusal plane.Conclusion: Ideal three‐dimensional implant positioning ensures a long‐term stable esthetic and functional treatment outcome.
A Comparative Study of Reduced-Variables-Based Flash and Conventional Flash
Authors: Michelsen Michael L. , Yan Wei , Stenby Erling H. 
Published: February 2013

Summary
For compositional transient simulations including compositional reservoir simulations, phase-equilibrium calculation, often formulated as a flash problem, can be time consuming. It is therefore important to speed up the calculation of phase equilibrium to improve the efficiency of the simulator. The reduced-variables methods, or the reduction methods, reformulate the original phase equilibrium problem with a smaller set of independent variables. Various versions of the reduced-variables methods have been proposed since the mid-1980s. The methods were first proposed for cubic equations of state (EOSs) with zero binary-interaction parameters (BIPs) and later generalized to situations with nonzero-BIP matrices. Most of the studies in the last decade suggest that the reduced-variables methods are much more efficient than the conventional flash method. However, Haugen and Beckner (2011) questioned the advantages of the reduced-variables methods in their recent paper. A fair comparison between the reduced-variables-based flash and the conventional flash is not straightforward because it is difficult to formulate the former as unconstrained minimization problems, and the flash calculation time is also related to the implementation quality. With the recent formulations by Nichita and Graciaa (2011), it is possible to code the reduced-variables methods without extensive modifications of Michelsen's conventional flash algorithm. A minimization-based reduced-variables algorithm was coded and compared with the conventional minimization-based flash. A test with the use of the SPE 3 example (Kenyon and Behie 1987) showed that the best reduction in time was less than 20% for the extreme situation of 25 components and just one row/column with nonzero BIPs. A better performance can be achieved by a simpler implementation directly using the sparsity of the BIP matrix.
Investigation of Emulsion Flow in Steam-Assisted Gravity Drainage
Authors: Ezeuko C.C.. C. , Wang J.. , Gates I.D.. D. 
Published: February 2013

Summary
We present a numerical simulation approach that allows incorporation of emulsion modeling into steam-assisted gravity-drainage (SAGD) simulations with commercial reservoir simulators by means of a two-stage pseudochemical reaction. Numerical simulation results show excellent agreement with experimental data for low-pressure SAGD, accounting for approximately 24% deficiency in simulated oil recovery, compared with experimental data. Incorporating viscosity alteration, multiphase effect, and enthalpy of emulsification appears sufficient for effective representation of in-situ emulsion physics during SAGD in very-high-permeability systems. We observed that multiphase effects appear to dominate the viscosity effect of emulsion flow under SAGD conditions of heavy-oil (bitumen) recovery. Results also show that in-situ emulsification may play a vital role within the reservoir during SAGD, increasing bitumen mobility and thereby decreasing cumulative steam/oil ratio (cSOR). Results from this work extend understanding of SAGD by examining its performance in the presence of in-situ emulsification and associated flow of emulsion with bitumen in porous media.
On Some Characteristic Features of Fractured-Horizontal Wells and Conclusions Drawn Thereof
Authors: Chen C.. , Raghavan R.. 
Published: February 2013

Summary
The model developed by Raghavan et al. (1997) is used to examine the characteristics of horizontal wells produced through multiple, transverse vertical fractures. The features of models of horizontal wells that drain a reservoir through multiple fractures are highlighted from the viewpoint of the use of commonly used approximate models. Rigorous and approximate predictions are compared. It is shown that scaling is needed to ensure that volumes drained by approximate models are indeed correct. To that end, information on volumes drained by individual fractures is noted.
Gingival Biotype Assessement: Visual Inspection Relevance And Maxillary Versus Mandibular Comparison
Authors: Cuny-Houchmand Madline , Renaudin Stéphane , Leroul Mustapha , Planche Lucie , Guehennec Laurent Le , Soueidan Assem 
Published: February 2013

Objective:This clinical study was aimed at evaluating the accuracy of gingival visual inspection procedures during clinical examination and determining whether differences existed between the maxillary and mandibular gingival biotypes.Materials and Methods:The study included 53 patients and 124 clinicians. The clinicians were asked to assign to each subject, using photographic documents, one of three biotypes: thin-scalloped, thick-scalloped, or thick-flat gingival biotype. A total of 19716 responses were collected for statistical analysis.Results:Identification accuracy of the gingival biotype and the intra-examiner repeatability presented poor highlighting of the limited relevance of visual inspection. In addition, the percent of agreement between classifications based on the global view of both the maxilla and mandible and the classification based on the individual mandibular or maxillary anterior teeth was not statistically significant.Conclusion:Based on the above results, it can be concluded that a simple visual inspection is not effective for the identification of gingival biotype. Furthermore, evidence suggests that a difference of biotype between the maxilla and the mandible in the same patient is conceivable. Therefore, orthodontic clinical examination should incorporate a reproducible method of determining the individualized gingival biotype for each group of teeth that will be moved.
Comparison of Sequencing Utility Programs
Authors: Aronesty Erik 
Published: February 2013

High throughput sequencing (HTS) has resulted in extreme growth rates of sequencing data. At our lab, we
generate terabytes of data every day. It is usually seen as required for data output to be “cleaned” and processed in various
ways prior to use for common tasks such as variant calling, expression quantification and assembly.
Two common tasks associated with HTS are adapter trimming and paired-end joining. I have developed two tools at
Expression Analysis, Inc. to address these common tasks. The names of these programs are fastq-mcf and fastq-join. I
compared the performance of these tools to similar open-source utilities, both in terms of resource efficiency, and
effectiveness.
Documentation and Management of CKD in Rural Primary Care
Authors: Rao Maya K. , Morris Cynthia D. , O’Malley Jean P. , Davis Melinda M. , Mori Motomi , Anderson Sharon 
Published: February 2013

SummaryBackground and objectivesRecognition of CKD by primary care practitioners is essential in rural communities where nephrology access is limited. This study determined the prevalence of undocumented CKD in patients cared for in rural primary care practices and evaluated characteristics associated with undocumented CKD as well as CKD management.Design, setting, participants, & measurementsA retrospective cohort study, conducted within the Oregon Rural Practice Based Research Network, consisted of 865 CKD patients with serum creatinine≥1.5 mg/dl in males and ≥1.3 mg/dl in females and an estimated GFR<60 ml/min per 1.73 m2. Documentation of a CKD diagnosis and laboratory values were abstracted by chart review.ResultsOf CKD patients, 51.9% had no documentation of CKD. Undocumented CKD occurred more frequently in female patients (adjusted odds ratio=2.93, 95% confidence interval=2.04, 4.21). The association of serum creatinine reporting versus automating reporting of estimated GFR on CKD documentation was dependent on patient sex, years of practitioner experience, and practitioner clinical training. Hypertensive patients with documented CKD were more likely to have a BP medication change than patients with undocumented CKD (odds ratio=2.07, 95% confidence interval=1.15, 3.73). Only 2 of 449 patients with undocumented CKD were comanaged with a nephrologist compared with 20% of patients with documented CKD (odds ratio=53.20, 95% confidence interval=14.90, 189.90).ConclusionsUndocumented CKD in a rural primary care setting is frequent, particularly in female patients. Depending on practitioner characteristics, automatic reporting of estimated GFR might improve documentation of CKD in this population.
Preemptive Deceased Donor Kidney Transplantation
Authors: Grams Morgan E. , Chen B. Po-Han , Coresh Josef , Segev Dorry L. 
Published: February 2013

Summary

Background and objectives
There exists gross disparity in national deceased donor kidney transplant availability and practice: waiting times exceed 6 years in some regions, but some patients receive kidneys before they require dialysis. This study aimed to quantify and characterize preemptive deceased donor kidney transplant recipients and compare their outcomes with patients transplanted shortly after dialysis initiation.

Design, setting, participants, & measurements
Using the Scientific Registry of Transplant Recipients database, first-time adult deceased donor kidney transplant recipients between 1995 and 2011 were classified as preemptive, early (on dialysis≤1 year), or late recipients. Random effects logistic regression and multivariate Cox proportional hazards regression were used to identify characteristics of preemptive deceased donor kidney transplant and evaluate survival in preemptive and early recipients, respectively.

Results
Preemptive recipients were 9.0% of the total recipient population. Patients with private insurance (adjusted odds ratio=3.15, 95% confidence interval=3.01–3.29, P<0.001), previous (nonkidney) transplant (adjusted odds ratio=1.94, 95% confidence interval=1.67–2.26, P<0.001), and zero-antigen mismatch (adjusted odds ratio=1.45, 95% confidence interval=1.37–1.54, P<0.001; Caucasians only) were more likely to receive preemptive deceased donor kidney transplant, even after accounting for center-level clustering. African Americans were less likely to receive preemptive deceased donor kidney transplant (adjusted odds ratio=0.44, 95% confidence interval=0.41–0.47, P<0.001). Overall, patients transplanted preemptively had similar survival compared with patients transplanted within 1 year after initiating dialysis (adjusted hazard ratio=1.06, 95% confidence interval=0.99–1.12, P=0.07).

Conclusions
Preemptive deceased donor kidney transplant occurs most often among Caucasians with private insurance, and survival is fairly similar to survival of recipients on dialysis for <1 year.
Two-Year Outcome of the ISKDC Regimen and Frequent-Relapsing Risk in Children with Idiopathic Nephrotic Syndrome
Authors: Nakanishi Koichi , Iijima Kazumoto , Ishikura Kenji , Hataya Hiroshi , Nakazato Hitoshi , Sasaki Satoshi , Honda Masataka , Yoshikawa Norishige 
Published: February 2013

Summary

Background and objectives
Early identification of frequently relapsing children with idiopathic nephrotic syndrome is desirable.

Design, setting, participants, & measurements
The relapse status and clinical data of patients previously registered (January of 1993 to December of 2001) in a multicenter prospective study of the International Study of Kidney Disease in Children regimen were analyzed for risk of frequent relapsers over a 2-year follow-up period.

Results
Of 166 children with nephrotic syndrome (113 boys and 53 girls; median age=5.1 years), 145 (87.3%, median age=5.5 years) children were steroid-sensitive, and 21 (12.7%, median age=2.9 years) children were steroid-resistant. Of 145 children with steroid-sensitive nephrotic syndrome, 32 (22.1%, median age=4.2 years) children experienced frequent relapses over 2 years. The time to initial response was significantly longer (10 versus 7 days, P<0.001, log-rank test) in the 32 frequent relapsers than in the 106 nonfrequent relapsers. The time from start of initial treatment to first relapse was significantly shorter (2.6 versus 6.1 months, P<0.001, log-rank test) in the 32 frequent relapsers than in the 57 infrequent relapsers. In a Cox regression model, the time to initial response ≥9 days and the duration from start of initial treatment to first relapse <6 months were significant predictors of frequent relapses (unadjusted and adjusted).

Conclusions
Initial remission time ≥9 days and first relapse within 6 months were associated with frequent relapses. These findings may also be useful also in selecting potential frequent relapsers for clinical trials.