bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulmonary fibrosis and other clinical manifestations of small vessel vasculitis in a family with seropositive juvenile rheumatoid arthritis
Authors: Rohayem Julia , Leupold W. , Paul K.‐D. , Gahr M. 
Published: September 2002

AbstractWe report on a family (mother, daughter, and son) suffering from progressive pulmonary fibrosis associated with deforming arthritis, sinusitis, glomerulonephritis, and cutaneous vasculitis. We suggest that these clinical features display the variable expressions of small‐vessel vasculitis in juvenile rheumatoid arthritis. Pediatr Pulmonol. 2002; 33:65–70. © 2002 Wiley‐Liss, Inc.
Automated analysis of paradoxical ribcage motion during sleep in infants
Authors: Brown K.A. , Platt R. , Bates J.H.T. 
Published: September 2002

AbstractIdentification of thoracoabdominal asynchrony (TAS) during breathing is currently detected by visual coding of records of ribcage (RC) and abdominal (AB) movements. There is thus a need to automate this process in order to save time and improve TAS detection accuracy.We studied 15 infants of 39–49 weeks postconceptional age. RC and AB signals were recorded continuously by inductance plethysmography for 4–24 hr immediately after herniorraphy. In our novel analysis approach, the records were divided into 10 sec epochs, and the equation RC = αAB + β was fit to each epoch, using recursive linear regression with an exponential memory time constant of 1 and 2 sec. This yielded 10 sec signals for alpha corresponding to each epoch. The fraction of time that each alpha signal was positive was taken as a measure of synchrony between RC and AB for that epoch, while asynchrony was indicated by the fraction of time the signal was negative. We also assessed synchrony and asynchrony using a conventional measure known as thoracic delay (TD), which is based on the degree to which the peaks in RC and AB are coincident in time. Using TD as the basis of comparison, we found that our new recursive least squares method gave a positive predictive value of 99%.We conclude that our recursive least squares method is able to accurately identify portions of the RC and AB records that correspond to TAS, and we speculate that it may be useful in automating detection of TAS. Pediatr Pulmonol. 2002; 33:38–46. © 2002 Wiley‐Liss, Inc.
Childhood asthma in the United States: Urban issues
Authors: Shapiro Gail G. , Stout James W. 
Published: September 2002

AbstractThe prevalence and morbidity of asthma are growing problems that appear to affect urban populations and particularly impoverished centers disproportionately. Poor children are more likely to be hospitalized for asthma than nonpoor children, and are more likely to experience clinical and social dysfunction due to asthma. While guidelines exist for best care of childhood asthma, the neediest children are least likely to encounter the benefits of these recommendations.The relationship between host and environment in both primary causation and disease exacerbation is an area of research and debate. Allergen exposure in early life appears to correlate with sensitization and expression of atopy and asthma. Impoverished households are more likely to be reservoirs for dust mite and cockroach antigen in high concentrations than more affluent settings. Lifestyle factors, including diet and ambient air quality, may be disease modifiers.Suboptimal systems for delivery of healthcare to high‐risk populations are obvious targets for blame. Poor children are more likely than nonpoor children to receive sick care in emergency rooms that lack a connection to chronic care providers. Besides the method of delivery, the quality of care is questionable, as poor children are less likely to receive the anti‐inflammatory maintenance medications for asthma that evidence‐based guidelines recommend. Efforts to correct these problems must take into account such issues as explaining the nature of the disease and the best intervention strategies to people who have a diverse array of cultural backgrounds, belief systems, and life stressors. Efforts to improve the status quo are underway in many communities. Environmental control measures to reduce dust mite and cockroach exposure have met with some success. Models to improve access to care and acceptance of care may improve community outreach maneuvers that connect the medical establishment with families and patients. Examination and assessment of new approaches to facilitate this sort of communication hold promise and are receiving attention as well as research dollars. Pediatr Pulmonol. 2002; 33:47–55. © 2002 Wiley‐Liss, Inc.
Revisit on congenital bronchopulmonary vascular malformations: A haphazard branching theory of malinosculations and its clinical classification and implication
Authors: Lee Meng‐Luen , Tsao Lon‐Yen , Chaou Wun‐Tsong , Yang Albert D. , Yeh Kun‐Tu , Wang Jou‐Kou , Wu Mei‐Hwan , Lue Hung‐Chi , Chiu Ing‐Sh , Chang Chung‐I 
Published: September 2002

AbstractWe propose a haphazard branching theory to support the concept of bronchopulmonary malinosculations, and we apply this theory to classify congenital bronchopulmonary vascular malformation (BPVM) based on the anatomical results we have found. Between January 1990 and December 1997, a total of 22 pediatric patients (10 male and 12 female), aged 2 days to 14 years (median, 19.6 months), with congenital BPVM were enrolled in this retrospective study. Study modalities include the clinical features and plain chest films (n = 22) plus at least two of the following: echocardiography (n = 13), barium esophagraphy (n = 2), bronchoscopy (n = 4), contrast bronchography (n = 8), high‐resolution direct coronal CT (n = 1) and electron beam or ultrafast CT (n = 1) of the chest, MRI (n = 10), MRA (n = 1), contrast cineangiocardiography (n = 9), surgery (n = 11), or autopsy (n = 2).The salient clinical features were recurrent lung infections in 14 patients, acute respiratory distress in 13, associated cardiovascular malformations in 8, dextroversion in 7, congestive heart failure in 7, dextrocardia in 4, and complex congenital heart diseases in 4. There were abnormal openings (malinosculations) of the pulmonary airway in 20 patients: to an artery in 12, to a vein in 8, and to the lung parenchyma in 9. These 22 patients with congenital BPVM can be classified into bronchial malinosculation (10 cases), arterial malinosculation (2 cases), and bronchoarterial malinosculation (10 cases).Congenital BPVM can be classified in terms of bronchopulmonary malinosculation based upon a haphazard branching theory, in which abnormal communications between two independent systems (primitive foregut system and aortic‐pulmonary arch system) occurred coincidentally rather than causally. Pediatr Pulmonol. 2002; 33:1–11. © 2002 Wiley‐Liss, Inc.
Congenital central hypoventilation syndrome associated with Hirschsprung's disease and neuroblastoma: Case of multiple neurocristopathies
Authors: Rohrer Tilman , Trachsel Daniel , Engelcke Gabriele , Hammer Jürg 
Published: September 2002

AbstractWe report on a male infant with the rare combined occurrence of congenital central hypoventilation syndrome (CCHS or Ondine's curse), Hirschsprung's disease (HD), and neuroblastoma. Current therapeutical options leave no doubt that children with isolated forms of CCHS, HD, or neuroblastoma must be treated, but management decisions and the ethical dilemma become more difficult with the presence of multiple neurocristopathies. Our patient was dependent on mechanical ventilation and total parenteral nutrition, when a neuroblastoma was diagnosed at age 5 months. We initiated an attempt at curative chemotherapy. The tumor failed to respond to recommended chemotherapeutic regimens, and the patient died at 11 months of age. We emphasize the importance of screening CCHS patients for associated illnesses such as neuroblastoma and ganglioneuroblastoma at time of diagnosis. Pediatr Pulmonol. 2002; 33:71–76. © 2002 Wiley‐Liss, Inc.
Permissive hypercapnia in neonates: The case of the good, the bad, and the ugly
Authors: Varughese M. , Patole S. , Shama A. , Whitehall J. 
Published: September 2002

AbstractAdvances in neonatology have resulted in an increase in the absolute number of survivors with chronic lung disease (CLD), though its overall incidence has not changed. Though the single most important high‐risk factor for CLD is prematurity, the focus of attention has recently changed over to minimizing the impact of other two risk factors: baro/volutrauma related to mechanical ventilation, and oxygen toxicity. Permissive hypercapnia (PHC) or controlled ventilation is a strategy that minimizes baro/volutrauma by allowing relatively high levels of arterial CO2, provided the arterial pH does not fall below a preset minimal value. The benefits of PHC are primarily mediated by the reduction of lung stretch that occurs when tidal volumes are minimized. PHC can be a deliberate choice to restrict ventilation in order to avoid overdistention, while application of high airway pressures and large tidal volumes would permit normocapnia, or relative hypocapnia (PaCO2, ≤ 25–30 mmHg), but may result in CLD and be harmful to the developing lung. The current concept that PaCO2 levels of 45–55 mmHg in high‐risk neonates are “safe” and “well tolerated” is based on limited data. Further prospective trials are needed to study the definition, safety and efficacy of PHC in ventilated preterm and term neonates. However, designing disease/gestational‐postnatal age‐specific clinical trials of PHC will be difficult in neonates, given the diverse pathophysiology of their diseases and the various ventilatory modes/variables currently available. The potential benefits and adverse effects of PHC are reviewed, and its relationship to current ventilatory strategies like synchronized mechanical ventilation and high‐frequency ventilation in high‐risk neonates is briefly discussed. Pediatr Pulmonol. 2002; 33:56–64. © 2002 Wiley‐Liss, Inc.
Evaluation of a fast implicit solvent model for molecular dynamics simulations
Authors: Ferrara Philippe , Apostolakis Joannis , Caflisch Amedeo 
Published: September 2002

AbstractA solvation term based on the solvent accessible surface area (SASA) is combined with the CHARMM polar hydrogen force field for the efficient simulation of peptides and small proteins in aqueous solution. Only two atomic solvation parameters are used: one is negative for favoring the direct solvation of polar groups and the other positive for taking into account the hydrophobic effect on apolar groups. To approximate the water screening effects on the intrasolute electrostatic interactions, a distance‐dependent dielectric function is used and ionic side chains are neutralized. The use of an analytical approximation of the SASA renders the model extremely efficient (i.e., only about 50% slower than in vacuo simulations). The limitations and range of applicability of the SASA model are assessed by simulations of proteins and structured peptides. For the latter, the present study and results reported elsewhere show that with the SASA model it is possible to sample a significant amount of folding/unfolding transitions, which permit the study of the thermodynamics and kinetics of folding at an atomic level of detail. Proteins 2002;46:24–33. © 2001 Wiley‐Liss, Inc.
Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low‐resolution models
Authors: de la Cruz Xavier , Sillitoe Ian , Orengo Christine 
Published: September 2002

AbstractPredicting the three‐dimensional structure of proteins is still one of the most challenging problems in molecular biology. Despite its difficulty, several investigators have started to produce consistently low‐resolution predictions for small proteins. However, in most of these cases, the prediction accuracy is still too low to make them useful. In the present article, we address the problem of obtaining better‐quality predictions, starting from low‐resolution models. To this end, we have devised a new procedure that uses these models, together with structure comparison methods, to identify the structural family of the target protein. This would allow, in a second step not described in the present work, to refine the predictions using conserved features of the identified family. In our approach, the structure database is investigated using predictions, at different accuracy levels, for a given protein. As query structures, we used both low‐resolution versions of the native structures, as well as different sets of low accuracy predictions. In general, we found that for predictions with a resolution of ≥5–7 Å, structure comparison methods were able to identify the fold of a protein in the top positions. Proteins 2002;46:72–84. © 2001 Wiley‐Liss, Inc.
Browsing gene banks for Fe2S2 ferredoxins and structural modeling of 88 plant‐type sequences: An analysis of fold and function
Authors: Bertini Ivano , Luchinat Claudio , Provenzani Alessandro , Rosato Antonio , Vasos Paul R. 
Published: September 2002

AbstractOne‐hundred‐and‐seventy‐nine sequences of Fe2S2 ferredoxins and ferredoxin precursors were identified in and retrieved from currently available protein and cDNA databases. On the basis of their cluster‐binding patterns, these sequences were divided into three groups: those containing the CX4CX2CXnC pattern (plant‐type ferredoxins), those with the CX5CX2CXnC pattern (adrenodoxins), and those with a different pattern. These three groups contain, respectively, 139, 36, and 4 sequences. After excluding ferredoxin precursors in the first group, two subgroups were identified, again based on their cluster‐binding patterns: 88 sequences had the CX4CX2CX29C pattern, and 29 had the CX4CX2CXmC (m ≠ 29) pattern. The structures of the 88 ferredoxins with the CX4CX2CX29C pattern were modeled based on the available experimental structures of nine proteins within this same group. The modeling procedure was tested by building structural models for the ferredoxins with known structures. The models resulted, on average, in being within 1 Å of the backbone root‐mean‐square deviation from the corresponding experimental structures. In addition, these structural models were shown to be of high quality by using assessment procedures based on energetic and stereochemical parameters. Thus, these models formed a reliable structural database for this group of ferredoxins, which is meaningful within the framework of current structural genomics efforts. From the analysis of the structural database generated it was observed that the secondary structural elements and the overall three‐dimensional structures are maintained throughout the superfamily. In particular, the residues in the hydrophobic core of the protein were found to be either absolutely conserved or conservatively substituted. In addition, certain solvent‐accessible charged groups, as well as hydrophobic groups, were found to be conserved to the same degree as the core residues. The patterns of conservation of exposed residues identified the regions of the protein that are critical for its function in electron transfer. An extensive analysis of protein—protein interactions is now possible. Some conserved interactions between residues have been identified and related to structural and/or functional features. All this information could not be obtained from the analyses of the primary sequences alone. Finally, the analysis of the sequences of the related subgroup featuring the CX4CX2CXmC (m ≠ 29) cluster‐binding pattern in the light of the structural and functional insights provided by the inspection of the mentioned structural database affords some hints on the functional features of ferredoxins belonging to this subgroup. Proteins 2002;46:110–127. © 2001 Wiley‐Liss, Inc.
A unifold, mesofold, and superfold model of protein fold use
Authors: Coulson Andrew F. W. , Moult John 
Published: September 2002

AbstractAs more and more protein structures are determined, there is increasing interest in the question of how many different folds have been used in biology. The history of the rate of discovery of new folds and the distribution of sequence families among known folds provide a means of estimating the underlying distribution of fold use. Previous models exploiting these data have led to rather different conclusions on the total number of folds. We present a new model, based on the notion that the folds used in biology fall naturally into three classes: unifolds, that is, folds found only in a single narrow sequence family; mesofolds, found in an intermediate number of families; and the previously noted superfolds, found in many protein families. We show that this model fits the available data well and has predicted the development of SCOP over the past 2 years. The principle implications of the model are as follows: (1) The vast majority of folds will be found in only a single sequence family; (2) the total number of folds is at least 10,000; and (3) 80% of sequence families have one of about 400 folds, most of which are already known. Proteins 2002;46:61–71. © 2001 Wiley‐Liss, Inc.
Why are proteins marginally stable?
Authors: Taverna Darin M. , Goldstein Richard A. 
Published: September 2002

AbstractMost globular proteins are marginally stable regardless of size or activity. The most common interpretation is that proteins must be marginally stable in order to function, and so marginal stability represents the results of positive selection. We consider the issue of marginal stability directly using model proteins and the dynamical aspects of protein evolution in populations. We find that the marginal stability of proteins is an inherent property of proteins due to the high dimensionality of the sequence space, without regard to protein function. In this way, marginal stability can result from neutral, non‐adaptive evolution. By allowing evolving protein sub‐populations with different stability requirements for functionality to complete, we find that marginally stable populations of proteins tend to dominate. Our results show that functionalities consistent with marginal stability have a strong evolutionary advantage, and might arise because of the natural tendency of proteins towards marginal stability. Proteins 2002;46:105–109. © 2001 Wiley‐Liss, Inc.
Intrinsic structural disorder and sequence features of the cell cycle inhibitor p57Kip2
Authors: Adkins Joshua N. , Lumb Kevin J. 
Published: September 2002

AbstractThe cell cycle inhibitor p57Kip2 induces cell cycle arrest by inhibiting the activity of cyclin‐dependent kinases. p57, although active as a cyclin A‐CDK2 inhibitor, is largely unfolded or intrinsically disordered as shown by circular dichroism and fluorescence spectra characteristic of an unfolded protein and a hydrodynamic radius consistent with an unfolded structure. In addition, the N‐terminal domain of p57 is both functionally independent as a cyclin A‐CDK2 inhibitor and unstructured, as demonstrated by circular dichroism and fluorescence spectra indicative of unfolded proteins, a lack of 1H chemical shift dispersion and a hydrodynamic radius consistent with a highly unfolded structure. The amino acid compositions of full‐length p57 and the excised QT domain of p57 exhibit significant deviations from the average composition of globular proteins that are consistent with the observed intrinsic disorder. However, the amino acid composition of the CDK inhibition domain of p57 does not exhibit such a striking deviation from the average values observed for proteins, implying that a general low level of hydrophobicity, rather than depletion or enrichment in specific amino acids, contributes to the intrinsic disorder of the excised p57 CDK inhibition domain. Proteins 2002;46:1–7. © 2001 Wiley‐Liss, Inc.
Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model
Authors: Liu Yongxing , Beveridge D. L. 
Published: September 2002

AbstractA theoretical and computational approach to ab initio structure prediction for polypeptides in water is described and applied to selected amino acid sequences for testing and preliminary validation. The method builds systematically on the extensive efforts applied to parameterization of molecular dynamics (MD) force fields, employs an empirically well‐validated continuum dielectric model for solvation, and an eminently parallelizable approach to conformational search. The effective free energy of polypeptide chains is estimated from AMBER united atom potential functions, with internal degrees of freedom for both backbone and amino acid side chains explicitly treated. The hydration free energy of each structure is determined using the Generalized Born/Solvent Accessibility (GBSA) method, modified and reparameterized to include atom types consistent with the AMBER force field. The conformational search procedure employs a multiple copy, Monte Carlo simulated annealing (MCSA) protocol in full torsion angle space, applied iteratively on sets of structures of progressively lower free energy until a prediction of a structure with lowest effective free energy is obtained. Calibration tests for the effective energy function and search algorithm are performed on the alanine dipeptide, selected protein crystal structures, and united atom decoys on barnase, crambin, and six examples from the Rosetta set. Specific demonstration cases of the method are provided for the 8‐mer sequence of Ala residues, a 12‐residue peptide with longer side chains QLLKKLLQQLKQ, a de novo designed 16 residue peptide of sequence (AAQAA)3Y, a 15‐residue sequence with a β sheet motif, GEWTWDATKTFTVTE, and a 36 residue small protein, Villin headpiece. The Ala 8‐mer readily formed an α‐helix. An α‐helix structure was predicted for the 16‐mer, consistent with observed results from IR and CD spectroscopy and with the pattern in ψ/ϕ angles of known protein structures. The predicted structure for the 12‐mer, composed of a mix of helix and less regular elements of secondary structure, lies 2.65 Å RMS from the observed crystal structure. Structure prediction for the 8‐mer β‐motif resulted in form 4.50 Å RMS from the crystal geometry. For Villin, the predicted native form is very close to the crystal structure, RMS values of 3.5 Å (including sidechains), and 1.01 Å (main chain only). The methodology permits a detailed analysis of the molecular forces which dominate various segments of the predicted folding trajectory. Analysis of the results in terms of internal torsional, electrostatic and van der Waals and the electrostatic and non‐electrostatic contributions to hydration, including the hydrophobic effect, is presented. Proteins 2002;46:128–146. © 2001 Wiley‐Liss, Inc.