bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Researcher's View
Authors: Horowitz Herschel S. 
Published: April 2007

AbstractThe Food and Drug Administration (FDA), by ensuring that the health care products used by Americans are both safe and effective, provides an essential regulatory function. With respect to the regulation of dental drug products, this researcher perceives that the FDA has not changed or modified its position on a number of issues to reflect new scientific information. Reasons for this inflexibility include the size and ponderousness of the agency, inadequate staff with dental expertise, and a failure to keep current with new dental research findings. The FDA must solve these problems if it wishes to regulate intelligently. The acceptance and certification programs of the American Dental Association ensure that products offered to the profession and the public that bear its seal of acceptance are safe and effective. The ADA's Council on Dental Therapeutics has a long history of staying current on issues in dental research and public health and regularly seeks consultation from eminently qualified experts. Overall, it has done an excellent job over the years in conducting an important voluntary regulatory program. Both the FDA and the ADA benefit and help protect the oral health of the public.
The Regulatory Process for Dental Devices: a Researcher's View
Authors: de Rijk Waldemar G. 
Published: April 2007

AbstractComments from the three previous speakers ranged from moderate satisfaction to strong dissatisfaction with the regulatory process. Three different types of research are identified that seem to predict the ease of compliance with the 510(k) process. No one expressed satisfaction with the PMA application. It seems that current evaluation procedures inhibit the developing and marketing of new devices, but foster only enhancements to existing de‐vices. The development of new evaluation methods is advocated to provide fast, inexpensive, but rigorous assessment of the clinical safety and treatment value of new devices.
Legal and Regulatory Developments of the 1990s in Oral Care Products: Learning from What Has Come Before
Authors: O'Reilly James T. 
Published: April 2007

AbstractThe development of oral care products has occurred faster than congressional enactments regulating these products. Terms such as “cosmetic, drug, and new drug” are defined. A history of scientific publications and common acceptance by experts is necessary for the FDA to categorize a product as “generally recognized as safe and effective” (GRASE). The FDA classification process of the numerous over‐the‐counter drugs into a few categories, each of which required a three‐part approval process, is not complete. Delays in the FDA's OTC review resulted in an “OTC moratorium”, which allows new products to enter the market at the owners risk. The relative risks and benefits of marketing an oral care product with or without an approved New Drug Application are discussed. Increased resources at the FDA are recommended to expedite fairness to manufacturers and to eliminate inappropriate oral care products from the market.
Contrasting the abundance, nitrogen, and carbon of epiphytic macrolichen species between host trees and soil types in a sub-boreal forest
Authors: Campbell Jocelyn , Fredeen Arthur L. 
Published: April 2007

Differences in lichen diversity and abundance and lichen N and C pools were examined across the two dominant host tree species ( Picea engelmannii Parry ex Engelm. × Picea glauca (Moench) Voss) and Abies lasiocarpa (Hook.) Nutt.)) and two soil types (fine- and coarse-textured soils) in an old-growth sub-boreal forest in central British Columbia, Canada. Forty-four epiphytic macrolichen species were identified across the study area. Hair lichen species, particularly nonsorediate Bryoria species, were more abundant in spruce on coarse-textured soils, while cyanolichens were most commonly observed in subalpine fir on fine-textured soils. Overall macrolichen biomass and C pools were greatest in subalpine fir trees on coarse-textured soils. The tripartite species Lobaria pulmonaria (L.) Hoffm. was the dominant macrolichen, particularly over fine-textured soils where its stand level biomass was greater than that of all other species combined. The N pools of L. pulmonaria in combination with the less abundant N-rich bipartite cyanolichens amounted to 7.5 ± 1.9 kg N·ha–1on fine-textured soils. These results indicate that epiphytic cyanolichens may make substantial contributions to ecosystem N despite their relatively insignificant contributions to overall forest biomass and C stocks.
A new concept for Dictyostelium sphaerocephalum based on morphology and phylogenetic analysis of nuclear ribosomal internal transcribed spacer region sequences
Authors: Romeralo Maria , Fiz-Palacios Omar , Lado Carlos , Cavender James C. 
Published: April 2007

Three dictyostelid isolates were found in Spain and Argentina that are morphologically different from known species. These isolates have some features similar to Dictyostelium sphaerocephalum (Oudem.) Sacc., Marchal & É.J. Marchal, but differ in size and sorocarp branching pattern. We sequenced the nuclear ribosomal internal transcribed spacer region to explore phylogenetic relationships among this group of species, including the three new isolates and their closest relatives. In all phylogenetic analyses performed, sequences of all three isolates group together with sequences from “typical” D. sphaerocephalum samples. This result supports previous observations of the morphological plasticity in dictyostelids, especially D. sphaerocephalum, leading us to broaden the classical concept of this species.
Decomposition of oak leaf litter is related to initial litter Mn concentrations
Authors: Davey Matthew P. , Berg Björn , Emmett Bridget A. , Rowland Phil 
Published: April 2007

The factors determining the quantity of litter being incorporated into stable organic matter were examined as part of a broader study investigating carbon (C) sequestration in forest ecosystems. Litter was collected from 20 common oak (Quercus robur L.) stands in Wales (UK) and placed in litter-decomposition bags. These bags were installed in an oak stand for 3, 6, 12, 21, and 31 months to study the effect of litter quality on decomposition (mass loss) rates and the limit value for a broad-leaf species. Results indicate that the initial decomposition rate is highly correlated with the manganese content of the litter (P = 0.007, R2 = 0.34). In the final stages of decomposition, limit values ranged between 57% and 95% of initial litter mass. These estimated limit values were not significantly correlated with initial concentrations of other nutrients. However, Ca concentrations gave a significance level of P = 0.067. Estimated rates of C sequestration in soil ranged from 0.93 to 80.22 g C·m–2·year–1.
Density dependence and interspecific interactions between arbuscular mycorrhizal fungi mediated plant growth, glomalin production, and sporulation
Authors: Violi Helen A. , Treseder Kathleen K. , Menge John A. , Wright Sara F. , Lovatt Carol J. 
Published: April 2007

Functional differences between the arbuscular mycorrhizal fungi Glomus intraradices Schenk and Smith and Scutellospora heterogama Nicolson and Gerdemann as they affect Persea americana Mill. growth, glomalin, and fungal sporulation were examined by varying the composition and relative density of the two fungi over a gradient of available phosphorus (P). The plant benefit provided by these mycorrhizal fungi together was not a simple sum of the benefits provided by each fungus in monoculture at its respective density. Glomus intraradices and S. heterogama interacted to reduce plant growth rates and uptake of P, zinc (Zn), and iron (Fe) relative to plants inoculated with G. intraradices alone. Thus, for plant growth and nutrition, no evidence for functional complementarity was detected. Instead, interspecific interactions between mycorrhizal fungi resulted in a negative feedback on plants. Under high available P, fungal functional differences were reduced, whereas the overall difference between mycorrhizal and nonmycorrhizal plants was greatest. Overall, S. heterogama produced more glomalin than did G. intraradices. In a mixture, sporulation of the inferior mutualist, S. heterogama, was lower than that of the superior mutualist, G. intraradices, but interspecific fungal interactions increased the sporulation of both fungi. Despite the negative impact of interspecific interactions on plants, supporting multiple arbuscular mycorrhizal fungi was of greater benefit than being nonmycorrhizal.
Weaning from mechanical ventilation
Authors: Boles J-M. , Bion J. , Connors A. , Herridge M. , Marsh B. , Melot C. , Pearl R. , Silverman H. , Stanchina M. , Vieillard-Baron A. , Welte T. 
Published: April 2007

Weaning covers the entire process of liberating the patient from mechanical support and from the endotracheal tube. Many controversial questions remain concerning the best methods for conducting this process. An International Consensus Conference was held in April 2005 to provide recommendations regarding the management of this process. An 11-member international jury answered five pre-defined questions. 1) What is known about the epidemiology of weaning problems? 2) What is the pathophysiology of weaning failure? 3) What is the usual process of initial weaning from the ventilator? 4) Is there a role for different ventilator modes in more difficult weaning? 5) How should patients with prolonged weaning failure be managed?The main recommendations were as follows. 1) Patients should be categorised into three groups based on the difficulty and duration of the weaning process. 2) Weaning should be considered as early as possible. 3) A spontaneous breathing trial is the major diagnostic test to determine whether patients can be successfully extubated. 4) The initial trial should last 30 min and consist of either T-tube breathing or low levels of pressure support. 5) Pressure support or assist–control ventilation modes should be favoured in patients failing an initial trial/trials. 6) Noninvasive ventilation techniques should be considered in selected patients to shorten the duration of intubation but should not be routinely used as a tool for extubation failure.
Transbronchial decompression of emphysematous bullae: a new therapeutic approach
Authors: Bhattacharyya P. , Sarkar D. , Nag S. , Ghosh S. , Roychoudhury S. 
Published: April 2007

Bullae are common accompaniments of chronic obstructive pulmonary disease especially emphysema. They contribute to increased lung volume and worsen the mechanical disadvantage of the inspiratory muscles by increasing the residual volume (RV) and RV/total lung capacity ratio. Thus effective decompression of a large bulla or bullae is thus important to improve the lung function of affected patients and also to provide symptomatic relief. Surgery and thoracoscopy are two commonly performed procedures used to treat bullae. Although bronchoscopic lung volume reduction has been successfully accomplished for emphysema, isolated decompression of bullae bronchoscopically has not been tried to date.A large emphysematous bulla in the left lower lobe of a surgically unfit patient was bronchoscopically punctured with a transbronchial aspiration needle; the position of the needle inside the bulla was confirmed and the air from the bulla was aspirated slowly to allow collapse. Finally, some autologous blood was instilled into the bulla before the needle was withdrawn.The patient had immediate and sustained symptomatic relief with significant improvement in lung function.Bronchoscopic transbronchial decompression of emphysematous bullae can be an effective therapeutic option and warrants further investigation.
Bronchiolitis obliterans following haematopoietic stem cell transplantation
Authors: Soubani A. O. , Uberti J. P. 
Published: April 2007

The aim of the present article is to review the available clinical data on bronchiolitis obliterans following haematopoietic stem cell transplantation (HSCT).The data sources used were the Medline database and references from the identified articles related to bronchiolitis obliterans, noninfectious pulmonary complications and HSCT.HSCT is an important treatment for a variety of malignant and nonmalignant conditions. However, the procedure is limited by significant complications that may involve every organ of the body. Pulmonary complications are seen in 40–60% of HSCT recipients. The recent advances in prophylaxis and treatment of infectious complications have increased the significance of late noninfectious pulmonary conditions.Currently, bronchiolitis obliterans is one of the most challenging pulmonary complications facing clinicians who are taking care of haematopoietic stem cell transplantation recipients. This article reviews the clinical and pathological features of this condition, sheds some light on potential mechanisms of pathogenesis, and discusses the available management options.
Histamine and tryptase modulate asthmatic airway smooth muscle GM-CSF and RANTES release
Authors: Chhabra J. , Li Y-Z. , Alkhouri H. , Blake A. E. , Ge Q. , Armour C. L. , Hughes J. M. 
Published: April 2007

Degranulating mast cells are increased in the airway smooth muscle (ASM) of asthmatics, where they may influence ASM function. The aim of the present study was to determine whether histamine and tryptase modulate ASM cell granulocyte-macrophage colony-stimulating factor (GM-CSF) and RANTES (regulated on activation, normal T-cell expressed and secreted) release and also to examine which receptors are involved in this release.Confluent, quiescent ASM cells from asthmatic and nonasthmatic donors were treated with histamine (1 μM–100 μM) with and without histamine receptor antagonist pre-treatment, or the protease-activated receptor (PAR)-2 agonists tryptase (0.5–5 nM) and SLIGKV (100 and 400 μM). The cells were then stimulated with interleukin (IL)-1β and/or tumour necrosis factor (TNF)-α (10 ng·mL−1) or left unstimulated for 24 h. Release of GM-CSF and RANTES was determined by ELISA and prostaglandin (PG)E2measured by enzyme immunoassay.Neither histamine nor tryptase induced ASM GM-CSF or RANTES secretion. However, histamine increased IL-1β-induced GM-CSF release and markedly reduced TNF-α-induced RANTES release by both asthmatic and nonasthmatic cells to a similar extent, but did not modulate PGE2release. All changes involved activation of the histamine H1 receptor as they were partially or fully blocked by chlorpheniramine, but not ranitidine. Tryptase,viaits proteolytic activity, also potentiated GM-CSF, but not RANTES, release from asthmatic and nonasthmatic ASM cells induced by both cytokines. PAR-2 involvement in the tryptase potentiation was unlikely because SLIGKV had no effect.In conclusion, mast cells, through histamine and tryptase, may locally modulate airway smooth muscle-induced inflammation in asthma.
Airway smooth muscle dynamics: a common pathway of airway obstruction in asthma
Authors: An S. S. , Bai T. R. , Bates J. H. T. , Black J. L. , Brown R. H. , Brusasco V. , Chitano P. , Deng L. , Dowell M. , Eidelman D. H. , Fabry B. , Fairbank N. J. , Ford L. E. , Fredberg J. J. , Gerthoffer W. T. , Gilbert S. H. , Gosens R. , Gunst S. J. , Halayko A. J. , Ingram R. H. , Irvin C. G. , James A. L. , Janssen L. J. , King G. G. , Knight D. A. , Lauzon A. M. , Lakser O. J. , Ludwig M. S. , Lutchen K. R. , Maksym G. N. , Martin J. G. , Mauad T. , McParland B. E. , Mijailovich S. M. , Mitchell H. W. , Mitchell R. W. , Mitzner W. , Murphy T. M. , Paré P. D. , Pellegrino R. , Sanderson M. J. , Schellenberg R. R. , Seow C. Y. , Silveira P. S. P. , Smith P. G. , Solway J. , Stephens N. L. , Sterk P. J. , Stewart A. G. , Tang D. D. , Tepper R. S. , Tran T. , Wang L. 
Published: April 2007

Excessive airway obstruction is the cause of symptoms and abnormal lung function in asthma.As airway smooth muscle (ASM) is the effecter controlling airway calibre, it is suspected that dysfunction of ASM contributes to the pathophysiology of asthma. However, the precise role of ASM in the series of events leading to asthmatic symptoms is not clear. It is not certain whether, in asthma, there is a change in the intrinsic properties of ASM, a change in the structure and mechanical properties of the noncontractile components of the airway wall, or a change in the interdependence of the airway wall with the surrounding lung parenchyma. All these potential changes could result from acute or chronic airway inflammation and associated tissue repair and remodelling.Anti-inflammatory therapy, however, does not “cure” asthma, and airway hyperresponsiveness can persist in asthmatics, even in the absence of airway inflammation. This is perhaps because the therapy does not directly address a fundamental abnormality of asthma, that of exaggerated airway narrowing due to excessive shortening of ASM.In the present study, a central role for airway smooth muscle in the pathogenesis of airway hyperresponsiveness in asthma is explored.
Light chain deposition disease involving the airways: diagnosis by fibreoptic bronchoscopy
Authors: Colombat M. , Gounant V. , Mal H. , Callard P. , Milleron B. 
Published: April 2007

Light chain deposition disease (LCDD) infrequently affects the lungs and usually causes damage to the parenchyma, while bronchial involvement appears to be very rare. The present authors report the case of a 64-yr-old female with LCDD characterised by asymptomatic airway involvement.Ten months after excision of a poorly differentiated vaginal carcinoma, a routine chest computed tomography (CT) scan revealed two lung cysts, several bilateral nodules and diffuse bronchial thickening. Pulmonary function tests were normal. Fibreoptic bronchoscopy showed marked diffuse mucosal thickening with highly conspicuous vascular plexuses. Nonamyloidal deposits were found in the bronchial wall, but no definite diagnosis could be proposed.On follow-up, the patient was still asymptomatic and the CT scan and endoscopic appearance remained unchanged. The final diagnosis of κ LCDD was established 18 months later by another series of bronchial biopsies with frozen samples. Interestingly, electron microscopy showed dense granular deposits associated with nonamyloidal fibrils. An increased number of lung cysts were observed 32 months after identification of bronchial abnormalities, confirming the progressive nature of the disease. No extrapulmonary deposits or immunoproliferative disorder were found.In conclusion, light chain deposition disease, which may remain latent for several years, can entirely involve large airways and may be diagnosed by bronchial biopsy.
Multiple non-collinear TF-map alignments of promoter regions
Authors: Blanco Enrique , Guigó Roderic , Messeguer Xavier 
Published: April 2007

Abstract

Background
The analysis of the promoter sequence of genes with similar expression patterns is a basic tool to annotate common regulatory elements. Multiple sequence alignments are on the basis of most comparative approaches. The characterization of regulatory regions from co-expressed genes at the sequence level, however, does not yield satisfactory results in many occasions as promoter regions of genes sharing similar expression programs often do not show nucleotide sequence conservation.

Results
In a recent approach to circumvent this limitation, we proposed to align the maps of predicted transcription factors (referred as TF-maps) instead of the nucleotide sequence of two related promoters, taking into account the label of the corresponding factor and the position in the primary sequence. We have now extended the basic algorithm to permit multiple promoter comparisons using the progressive alignment paradigm. In addition, non-collinear conservation blocks might now be identified in the resulting alignments. We have optimized the parameters of the algorithm in a small, but well-characterized collection of human-mouse-chicken-zebrafish orthologous gene promoters.

Conclusion
Results in this dataset indicate that TF-map alignments are able to detect high-level regulatory conservation at the promoter and the 3'UTR gene regions, which cannot be detected by the typical sequence alignments. Three particular examples are introduced here to illustrate the power of the multiple TF-map alignments to characterize conserved regulatory elements in absence of sequence similarity. We consider this kind of approach can be extremely useful in the future to annotate potential transcription factor binding sites on sets of co-regulated genes from high-throughput expression experiments.
A decline in transcript abundance for Heterodera glycines homologs of Caenorhabditis elegans uncoordinatedgenes accompanies its sedentary parasitic phase
Authors: Klink Vincent P , Martins Veronica E , Alkharouf Nadim W , Overall Christopher C , MacDonald Margaret H , Matthews Benjamin F 
Published: April 2007

Abstract

Background

Heterodera glycines (soybean cyst nematode [SCN]), the major pathogen of Glycine max (soybean), undergoes muscle degradation (sarcopenia) as it becomes sedentary inside the root. Many genes encoding muscular and neuromuscular components belong to the uncoordinated (unc) family of genes originally identified in Caenorhabditis elegans. Previously, we reported a substantial decrease in transcript abundance for Hg-unc-87, the H. glycines homolog of unc-87 (calponin) during the adult sedentary phase of SCN. These observations implied that changes in the expression of specific muscle genes occurred during sarcopenia.

Results
We developed a bioinformatics database that compares expressed sequence tag (est) and genomic data of
C

.

e

legans and
H

.

g

lycines (CeHg database). We identify H. glycines homologs of C. elegans unc genes whose protein products are involved in muscle composition and regulation. RT-PCR reveals the transcript abundance of H. glycines unc homologs at mobile and sedentary stages of its lifecycle. A prominent reduction in transcript abundance occurs in samples from sedentary nematodes for homologs of actin, unc-60B (cofilin), unc-89, unc-15 (paromyosin), unc-27 (troponin I), unc-54 (myosin), and the potassium channel unc-110 (twk-18). Less reduction is observed for the focal adhesion complex gene Hg-unc-97.

Conclusion
The CeHg bioinformatics database is shown to be useful in identifying homologs of genes whose protein products perform roles in specific aspects of H. glycines muscle biology. Our bioinformatics comparison of C. elegans and H. glycines genomic data and our Hg-unc-87 expression experiments demonstrate that the transcript abundance of specific H. glycines homologs of muscle gene decreases as the nematode becomes sedentary inside the root during its parasitic feeding stages.