bluuebunny/crossref_metadata_2025_split huggingface dataset:
Twist‐dependent stacking energy of base‐pair steps in B‐DNA geometry: A density functional theory approach
Authors: Samanta Sudipta , Kabir Mukul , Sanyal Biplab , Bhattacharyya Dhananjay 
Published: January 2008

AbstractStacking energy of all the 10 unique DNA base‐pair steps (bp step) are calculated using density functional theory within the ultrasoft pseudopotential plane wave method and local density approximation for the exchange‐correlation functional. We have studied the dependence of stacking energy on twist angle, an aspect found difficult to explain using classical theory. We have found that the twist angle for different bp steps at stacking energy minimum matches extremely well with the values of average twist obtained from B‐DNA crystal structure data. This indicates that the use of a proper quantum chemical method to calculate the π‐π electronic interactions may explain stacking energy without incorporating hydrophobic interaction through solvent or effect of backbone through pseudobond. From the twist angle‐dependent stacking energy profile, we have also generated the probability distributions of twist for all the bp steps and calculated the variance of the distribution. Our calculated variances show similar trend to that of the experimental data for which sufficient numbers of data are available. The TA, AT, and CG doublets show large variances among the 10 possible bp steps, indicating their maximum flexibility. This might be the case of unusual deformation observed at the TATA‐box while binding to TBP protein. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Hydrogen bonding characterization of XH2NH2···HNO(X = B, Al, Ga) complexes: A theoretical investigation
Authors: Liu Ying 
Published: January 2008

AbstractThe complexes of XH2NH2···HNO(X = B, Al, Ga) are characterized as head to tail with hydrogen bonding interactions. The structural characteristics can be confirmed by atoms in molecules (AIM) analysis, which also provide comparisons of hydrogen bonds strengths. The calculated interaction energies at G2MP2 level show that stability of complexes decrease as BH2NH2···HNO > AlH2NH2···HNO > GaH2NH2···HNO. On the basis of the vibrational frequencies calculations, there are red‐shifts for ν(X1H) and blue‐shifts for ν(NH) in the complexes on dihydrogen bonding formations (X1H···HN). On hydrogen bonding formations (NH···O), there are red‐shifts for ν(NH) compared to the monomers. Natural bond orbital (NBO) analysis is used to discuss the reasons for the ν(X1H) and ν(NH) stretching vibrational shifts by hyperconjugation, electron density redistribution, and rehybridization. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
ONIOM investigation of nucleotide selectivity in phosphodiesterases 3 and 4
Authors: Salter E. A. , O'Brien Kerrie A. , Edmunds R. Wesley , Wierzbicki A. 
Published: January 2008

AbstractThe cyclic nucleotide phosphodiesterases (PDEs) are drug‐targeted enzymes that down regulate cyclic nucleotide concentrations in the cell by catalyzing the hydrolysis of the O3′‐phosphorous bond, yielding the noncyclic nucleotides. Selectivity for cAMP versus cGMP (cyclic 3′,5′‐adenosine/‐guanosine monophosphate) as the favored substrate is primarily attributed to the orientation of a conserved glutamine residue which binds to the adenine/guanine ring. We use ONIOM hybrid quantum methods to accurately describe substrate binding within the catalytic sites of the cAMP‐specific PDE4 and the cGMP‐inhibited, dual‐specific PDE3 in order to understand subtle aspects of substrate selectivity. We estimate PDE4's net preference for cAMP binding to be about 16 kcal/mol; the cause of cAMP's known preference resides both in its fixed glutamine orientation (Gln 369 in PDE4D) and in the differential free energy of solvation, which disfavors the binding of cGMP relative to cAMP by about 15 kcal/mol. Also, we discuss the contributing role played by Asn 321, held in place by a partner Asp 167, in the deselection of cGMP by PDE4. PDE3's conserved glutamine (Gln 988 in PDE3B) is free to take on either a cGMP‐favorable or cAMP‐favorable orientation. We find that enthalpies of binding favor cGMP for PDE3, but only by the same amount as free energies of solvation disfavor cGMP binding. Comparison of the PDE3‐cAMP and ‐cGMP complexes and energetics reveals cAMP to be more susceptible to the attack of the hydroxide nucleophile in PDE3. We identify a key threonine residue (Thr 952) as responsible for PDE3's kinetic relative disfavor of cGMP hydrolysis by causing Gln 988 to tilt out of cGMP's purine plane. Our results are consistent with the PDE3's kinetic specificity for cAMP hydrolysis and the known competitive inhibition of PDE3 by cGMP. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
The design, enactment, and experience of inquiry‐based instruction in undergraduate science education: A case study
Authors: Park Rogers Meredith A. , Abell Sandra K. 
Published: January 2008

AbstractThe purpose of this study was to understand one case of undergraduate inquiry‐based instruction through the words and actions of students and instructors. The data sources included fieldnotes from 16 of 29 classes, two sets of student and instructor interviews (beginning and end of the semester), and a collection of artifacts, such as the laboratory manual, lecture handouts, and the course syllabus. The participants for this study included four faculty instructors and two purposively selected student groups, totaling eight students. We found the instructors' two course goals, (a) teaching students how scientists do science and (b) using an interdisciplinary approach to develop students' content knowledge of the big ideas in science, were consistent with our observations and the students' descriptions of their experience in the course. However, we observed, and the students also noted, an important feature of the course that the instructors did not describe as a course goal was its reliance on the social nature of learning. This telling case demonstrates that inquiry‐based instruction is achievable in undergraduate science education. Implications are discussed for college science instructors interested in inquiry teaching. © 2008 Wiley Periodicals, Inc. Sci Ed 92:591–607, 2008
Analysis of UDP‐galactose 4′‐epimerase mutations associated with the intermediate form of type III galactosaemia
Authors: Chhay J. S. , Vargas C. A. , McCorvie T. J. , Fridovich‐Keil J. L. , Timson D. J. 
Published: January 2008

SummaryType III galactosaemia is a hereditary disease caused by reduced activity in the Leloir pathway enzyme, UDP‐galactose 4′‐epimerase (GALE). Traditionally, the condition has been divided into two forms—a mild, or peripheral, form and a severe, or generalized, form. Recently it has become apparent that there are disease states which are intermediate between these two extremes. Three mutations associated with this intermediate form (S81R, T150M and P293L) were analysed for their kinetic and structural properties in vitro and their effects on galactose‐sensitivity of Saccharomyces cerevisiae cells that were deleted for the yeast GALE homologue Gal10p. All three mutations result in impairment of the kinetic parameters (principally the turnover number, kcat) compared with the wild‐type enzyme. However, the degree of impairment was mild compared with that seen with the mutation (V94M) associated with the generalized form of epimerase deficiency galactosaemia. None of the three mutations tested affected the ability of the protein to dimerize in solution or its susceptibility to limited proteolysis in vitro. Finally, in the yeast model, each of the mutated patient alleles was able to complement the galactose‐sensitivity of gal10Δ cells as fully as was the wild‐type human allele. Furthermore, there was no difference from control in metabolite profile following galactose exposure for any of these strains. Thus we conclude that the subtle biochemical and metabolic abnormalities detected in patients expressing these GALE alleles likely reflect, at least in part, the reduced enzymatic activity of the encoded GALE proteins.
Viscero‐somatic reflexes in referred pain areas evoked by capsaicin stimulation of the human gut
Authors: Arendt‐Nielsen Lars , Schipper Klaus‐Peter , Dimcevski Georg , Sumikura Hiroyuki , Krarup Anne Lund , Giamberardino Maria Adele , Drewes Asbjørn Mohr 
Published: January 2008

AbstractThe interaction between visceral pain and the sympathetic nervous system is only sparsely investigated in quantitative human studies. Referred visceral pain can be evoked experimentally by application of substances such as capsaicin (the pungent substance of chilli pepper) to the gut. The aim of the present study was to induce referred visceral pain from the small and large intestine in 32 volunteers via the stomal opening in patients with ileo‐ or colostomy and quantify the viscero‐somatic reflex responses in these referred pain areas by thermography and laser doppler flowmetry.Capsaicin evoked pain and referred pain areas in all subjects. In the referred pain area, the temperature increased by approximately 0.6°C (P<0.001) and the blood flow by approximately 35AU (P<0.001). Saline was used in a control experiment, and no temperature and blood flow changes were found.The present quantitative human study of viscero‐somatic reflexes showed dramatic sympathetic responses in the referred pain areas after experimentally induced gut pain.
Clinical value of anthropometric estimates of leg lean volume in nutritionally depleted and non-depleted patients with chronic obstructive pulmonary disease
Authors: Villaça Débora Strose , Lerario Maria Cristina , Corso Simone dal , Nápolis Lara , Albuquerque André Luiz Pereira de , Lazaretti-Castro Marize , Sachs Anita , Nery Luiz Eduardo , Neder Jose Alberto 
Published: January 2008

This study aimed to investigate the clinical usefulness of an anthropometrically based method for estimating leg lean volume (LLV) in patients with chronic obstructive pulmonary disease (COPD) who presented or not with nutritional depletion. We prospectively evaluated a group of forty-eight patients (thirty-eight males) with moderate to severe COPD (Global Initiative for Chronic Obstructive Lung disease stages II–IV) who underwent a 6 min walking test and knee isokinetic dynamometry. Leg lean mass (muscle mass plus bone) was determined by dual-energy X-ray absorptiometry (DEXA) with derivation of its respective volume: these values were compared with those obtained by the truncated cones method first described by Jones and Pearson in 1969. As expected, depleted patients (n 19) had reduced exercise capacity and impaired muscle performance as compared to non-depleted subjects (P < 0·01). The mean bias of the LLV differences between anthropometry and DEXA were 0·40 litre (95 % CI − 0·59, 1·39) and 0·50 litre (95 % CI − 1·08, 2·08) for depleted and non-depleted patients, respectively. Anthropometrically and DEXA-based estimates correlated similarly with muscle functional attributes. A ROC curve analysis revealed that leg height-corrected LLV values had acceptable sensitivity and specificity to identify depleted patients (area under the curve 0·93 (range 0·86–1·00); P < 0·001). Moreover, patients with LLV ≤ 9·2 litres/m (the best cut-off value according to the ROC curve) had significantly lower exercise capacity and muscle performance than their counterparts (P < 0·05). In conclusion, an anthropometrically based method of estimating LLV (Jones and Pearson method) was shown to present with clinically acceptable accuracy and external validity in depleted and non-depleted patients with stable COPD.
The Nixon Administration and the Cienfuegos crisis of 1970: crisis-management of a non-crisis?
Authors: SINIVER ASAF 
Published: January 2008

AbstractThis article employs newly declassified documents from the National Archives in Washington and London to re-examine foreign policymaking of the Nixon Administration during the Cienfuegos crisis of 1970. The article seeks to answer two fundamental questions with regard to policy decision-making during the crisis: why did the Administration pursue a public policy of ‘business as usual’ while cloaking the crisis in extreme secrecy, and how was this achieved? Answers to these questions can be found in the unique situation the Administration found itself during the ‘Autumn of Crises’, and in Kissinger’s manipulation of NSC mechanisms and procedures, respectively.
Fluctuation history of the interior East Antarctic Ice Sheet since mid-Pliocene
Authors: Huang Feixin , Liu Xiaohan , Kong Ping , Fink David , Ju Yitai , Fang Aimin , Yu Liangjun , Li Xiaoli , Na Chunguang 
Published: January 2008

AbstractCosmogenic 10Be and 26Al measurements from bedrock exposures in East Antarctica provide indications of how long the rock surface has been free from glacial cover. Samples from the crests of Zakharoff Ridge and Mount Harding, two typical nunataks in the Grove Mountains, show minimum 10Be ages of 2.00 ± 0.22 and 2.30 ± 0.26 Ma, respectively. These ages suggest that the crests were above the ice sheet at least since the Plio–Pleistocene boundary. Adopting a ‘reasonable’ erosion rate of 5–10 cm Ma-1 increases the exposure ages of these two samples to extend into the mid-Pliocene. The bedrock exposure ages steadily decrease with decreasing elevation on the two nunataks, which indicates ~200 m decrease of the ice sheet in the Grove Mountains since mid-Pliocene time. Seven higher elevation samples exhibit a simple exposure history, which indicates that the ice sheet in the Grove Mountains decreased only ~100 m over a period as long as 1–2 Ma. This suggests that the East Antarctic Ice Sheet (EAIS) was relatively stable during the Pliocene warm interval. Five lower elevation samples suggest a complex exposure history, and indicate that the maximum subsequent increase of the EAIS was only 100 m higher than the present ice surface. Considering the uncertainties, their total initial exposure and subsequent burial time could be later than mid-Pliocene, which may not conflict with the stable mid-Pliocene scenario.
Continuous positive airway pressure increases heart rate variability in heart failure patients with obstructive sleep apnoea
Authors: Gilman Matthew P. , Floras John S. , Usui Kengo , Kaneko Yasuyuki , Leung Richard S. T. , Bradley T. Douglas 
Published: January 2008

Patients with heart failure or OSA (obstructive sleep apnoea) have reduced HF-HRV (high-frequency heart rate variability), indicating reduced cardiac vagal modulation, a marker of poor prognosis. CPAP (continuous positive airway pressure) abolishes OSA in patients with heart failure, but effects on daytime HF-HRV have not been determined. We hypothesized that, in patients with heart failure, treatment of coexisting OSA by CPAP would increase morning HF-HRV. In 19 patients with heart failure (left ventricular ejection fraction &lt;45%) and OSA (≥20 apnoeas and hypopnoeas/h of sleep), HF-HRV was quantified before and 1 month after randomization to a control or CPAP-treated group. In the control group (n=7), there were no changes in HF-HRV over the 1 month study during wakefulness in the morning. In the CPAP-treated group (n=12) HF-HRV increased significantly during wakefulness in the morning [from 2.43±0.55 to 2.82±0.50 log(ms2/Hz); P=0.002] due to an increase in transfer function between changes in lung volume and changes in HF-HRV (92.37±96.03 to 219.07±177.14 ms/l; P=0.01). In conclusion, treatment of coexisting OSA by nocturnal CPAP in patients with heart failure increases HF-HRV during morning wakefulness, indicating improved vagal modulation of heart rate. This may contribute to improved prognosis.
Normal-sodium diet compared with low-sodium diet in compensated congestive heart failure: is sodium an old enemy or a new friend?
Authors: Paterna Salvatore , Gaspare Parrinello , Fasullo Sergio , Sarullo Filippo M. , Di Pasquale Pietro 
Published: January 2008

The aim of the present study was to evaluate the effects of a normal-sodium (120 mmol sodium) diet compared with a low-sodium diet (80 mmol sodium) on readmissions for CHF (congestive heart failure) during 180 days of follow-up in compensated patients with CHF. A total of 232 compensated CHF patients (88 female and 144 male; New York Heart Association class II–IV; 55–83 years of age, ejection fraction &lt;35% and serum creatinine &lt;2 mg/dl) were randomized into two groups: group 1 contained 118 patients (45 females and 73 males) receiving a normal-sodium diet plus oral furosemide [250–500 mg, b.i.d. (twice a day)]; and group 2 contained 114 patients (43 females and 71 males) receiving a low-sodium diet plus oral furosemide (250–500 mg, b.i.d.). The treatment was given at 30 days after discharge and for 180 days, in association with a fluid intake of 1000 ml per day. Signs of CHF, body weight, blood pressure, heart rate, laboratory parameters, ECG, echocardiogram, levels of BNP (brain natriuretic peptide) and aldosterone levels, and PRA (plasma renin activity) were examined at baseline (30 days after discharge) and after 180 days. The normal-sodium group had a significant reduction (P&lt;0.05) in readmissions. BNP values were lower in the normal-sodium group compared with the low sodium group (685±255 compared with 425±125 pg/ml respectively; P&lt;0.0001). Significant (P&lt;0.0001) increases in aldosterone and PRA were observed in the low-sodium group during follow-up, whereas the normal-sodium group had a small significant reduction (P=0.039) in aldosterone levels and no significant difference in PRA. After 180 days of follow-up, aldosterone levels and PRA were significantly (P&lt;0.0001) higher in the low-sodium group. The normal-sodium group had a lower incidence of rehospitalization during follow-up and a significant decrease in plasma BNP and aldosterone levels, and PRA. The results of the present study show that a normal-sodium diet improves outcome, and sodium depletion has detrimental renal and neurohormonal effects with worse clinical outcome in compensated CHF patients. Further studies are required to determine if this is due to a high dose of diuretic or the low-sodium diet.
Water Transport by Aquaporins in the Extant Plant Physcomitrella patens
Authors: Liénard David , Durambur Gaëlle , Kiefer-Meyer Marie-Christine , Nogué Fabien , Menu-Bouaouiche Laurence , Charlot Florence , Gomord Véronique , Lassalles Jean-Paul 
Published: January 2008

Abstract
Although aquaporins (AQPs) have been shown to increase membrane water permeability in many cell types, the physiological role of this increase was not always obvious. In this report, we provide evidence that in the leafy stage of development (gametophore) of the moss Physcomitrella patens, AQPs help to replenish more rapidly the cell water that is lost by transpiration, at least if some water is in the direct vicinity of the moss plant. Three AQP genes were cloned in P. patens: PIP2;1, PIP2;2, and PIP2;3. The water permeability of the membrane was measured in protoplasts from leaves and protonema. A significant decrease was measured in protoplasts from leaves and protonema of PIP2;1 or PIP2;2 knockouts but not the PIP2;3 knockout. No phenotype was observed when knockout plants were grown in closed petri dishes with ample water supply. Gametophores isolated from the wild type and the pip2;3 mutant were not sensitive to moderate water stress, but pip2;1 or pip2;2 gametophores expressed a water stress phenotype. The knockout mutant leaves were more bent and twisted, apparently suffering from an important loss of cellular water. We propose a model to explain how the AQPs PIP2;1 and PIP2;2 delay leaf dessication in a drying atmosphere. We suggest that in ancestral land plants, some 400 million years ago, APQs were already used to facilitate the absorption of water.
Evaluation of Association Constants from Fluorescence Data: A Corrected Method*
Authors: Lissit E. A. , Gunthe G. , Zanocco A. L. 
Published: January 2008

ABSTRACTAn equation is proposed for the evaluation of partition or association constants from fluorescence properties (such as spectrum shape or anisotropy) whose values are not linearly related to the solute distribution. The proposed procedure is applied to the binding of pyrene to β‐cyclodextrin (employing the I1/I3 relationship and fluorescence anisotropy) and to the association of pyrene to dioctadecyldimethylammonium small unilamellar vesicles (sonicated) and large unilamellar vesicles (injected). The results obtained in the latter system indicate that the pyrene partition constant between the vesicles and the aqueous medium is nearly 10 times larger in the small vesicles.
Larval Tenebrio molitor (Coleoptera: Tenebrionidae) Fat Body Extracts Catalyze Firefly D‐Luciferin‐ and ATP‐Dependent Chemiluminescence: A Luciferase‐like Enzyme*
Authors: Viviani Vadim R. , Bechara Eteivino J. H. 
Published: January 2008

ABSTRACTUltraweak light emission was detected upon injection of firefly luciferin into live Tenebrio larvae. A chemilumi‐nescent enzymatic activity dependent on molecular oxygen, D‐luciferin and MgATP was then isolated from larval fat body extracts by precipitation with 70% ammonium sulfate. D‐Luciferin and ATP can be replaced by luciferyl‐adenylate. Pyrophosphate is a main product from the chemiluminescent reaction. The in vitro chemiluminescence intensity was not affected by peroxidase inhibitors such as N3−‐ (0.5 mM) and CN− (1 mM), attesting to its nonperoxidatic nature but was strongly inhibited by AMP (1 mM), luciferin 6′‐ethyl ether (1 mM) and sodium pyrophosphate (2 mM), well‐known firefly lucifer‐ase inhibitors. Some physical‐chemical properties of this enzymatic activity were similar to those of firefly lucif‐erase (KMATP = 195 μM; K0.5 luciferin ‐ 0.8 mM; optimum pH 8.5; δmax= 610 nm at pH 8.5; firefly lucifer‐ase: δmax= 565 nm at pH 8.0 and 619 mm at pH 6.0), but the chemiluminescence was not affected by addition of polyclonal antibodies raised against Photinus pyralis luciferase. These data suggest that this chemiluminescence results from a ligase with luciferase activity.
Investigations of Cylindrical Reaction Cavities from Ordered Phases of Alkyl Alkanoates and Their Influence on Some Norrish‐Yang and Photo‐Fries Reactions*
Authors: Baldvins Jon E. , Cui Changxing , Weisst Richard G. 
Published: January 2008

ABSTRACTThe Norrish‐Yang photochemistry of three isomeric p‐alkyl alkanophenones (p‐propyl nonadecanophenone, p‐pentyl heptadecanophenone and p‐octyl tetradecano‐phenone) and the photo‐Fries reactions of 2‐naphthyl myristate have been investigated in the ordered (layered) phases of three isomeric alkyl alkanoates. Comparisons of photoproduct selectivity for irradiation of one substrate in the isotropic and ordered phases of one host ester provide information concerning the influence of the cylindrically shaped reaction cavities on the relative motions and conformational changes necessary to convert the reactants to products. Comparisons of photoproduct distributions from one substrate in comparable phases of two or more esters provide details concerning the “wall stiffness” and importance of functional group interactions of the reaction cavities. Finally, comparisons using one substrate and two ordered phases of the same ester indicate the role of wall stiffness on photoproduct selectivity. The results show that the course of the photochemical reactions can be controlled effectively within the ordered media and provide an indication of how to design and select ordered media to effect other photochemical transformations selectively.