bluuebunny/crossref_metadata_2025_split huggingface dataset:
A probabilistic measure for alignment-free sequence comparison
Authors: Pham Tuan D. , Zuegg Johannes 
Published: July 2004

Abstract
Motivation: Alignment-free sequence comparison methods are still in the early stages of development compared to those of alignment-based sequence analysis. In this paper, we introduce a probabilistic measure of similarity between two biological sequences without alignment. The method is based on the concept of comparing the similarity/dissimilarity between two constructed Markov models.
Results: The method was tested against six DNA sequences, which are the thrA, thrB and thrC genes of the threonine operons from Escherichia coli K-12 and from Shigella flexneri; and one random sequence having the same base composition as thrA from E.coli. These results were compared with those obtained from CLUSTAL W algorithm (alignment-based) and the chaos game representation (alignment-free). The method was further tested against a more complex set of 40 DNA sequences and compared with other existing sequence similarity measures (alignment-free).
Availability: All datasets and computer codes written in MATLAB are available upon request from the first author.
ViTO: tool for refinement of protein sequence–structure alignments
Authors: Catherinot Vincent , Labesse Gilles 
Published: July 2004

Abstract
Summary: ViTO is a graphical application, including an editor, of multiple sequence alignment and a three-dimensional (3D) structure viewer. It is possible to manipulate alignments containing hundreds of sequences and to display a dozen structures. ViTO can handle so-called ‘multiparts’ alignments to allow the visualization of complex structures (multi-chain proteins and/or small molecules and DNA) and the editing of the corresponding alignment. The 3D viewer and the alignment editor are connected together allowing rapid refinement of sequence–structure alignment by taking advantage of the immediate visualization of resulting insertions/deletions and strict conservations in their structural context. More generally, it allows the mapping of informations about the sequence conservation extracted from the alignment onto the 3D structures in a dynamic way. ViTO is also connected to two comparative modelling programs, SCWRL and MODELLER.
These features make ViTO a powerful tool to characterize protein families and to optimize the alignments for comparative modelling.
Availability: http://bioserv.cbs.cnrs.fr/VITO/DOC/
Supplementary information: http://bioserv.cbs.cnrs.fr/VITO/DOC/index.html
Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach
Authors: Siew Joyce Phui Yee , Khan Asif M. , Tan Paul T. J. , Koh Judice L. Y. , Seah Seng Hong , Koo Chuay Yeng , Chai Siaw Ching , Armugam Arunmozhiarasi , Brusic Vladimir , Jeyaseelan Kandiah 
Published: July 2004

Abstract
Motivation: Sequence annotations, functional and structural data on snake venom neurotoxins (svNTXs) are scattered across multiple databases and literature sources. Sequence annotations and structural data are available in the public molecular databases, while functional data are almost exclusively available in the published articles. There is a need for a specialized svNTXs database that contains NTX entries, which are organized, well annotated and classified in a systematic manner.
Results: We have systematically analyzed svNTXs and classified them using structure–function groups based on their structural, functional and phylogenetic properties. Using conserved motifs in each phylogenetic group, we built an intelligent module for the prediction of structural and functional properties of unknown NTXs. We also developed an annotation tool to aid the functional prediction of newly identified NTXs as an additional resource for the venom research community.
Availability: We created a searchable online database of NTX proteins sequences (http://research.i2r.a-star.edu.sg/Templar/DB/snake_neurotoxin). This database can also be found under Swiss-Prot Toxin Annotation Project website (http://www.expasy.org/sprot/)
PCOAT: positional correlation analysis using multiple methods
Authors: Qi Yuan , Grishin Nick V. 
Published: July 2004

Abstract
Summary: PCOAT (Positional COrrelation Analysis Tool) is a program to perform positional correlation analysis for protein multiple sequence alignment in order to identify structurally or functionally important interactions between positions in a protein family. We implement different statistical methods to detect highly correlated position pairs, amino acid pairs, individual positions and networks of correlated positions, and utilize multiple sequence weighting and sampling methods to eliminate background correlations caused by phylogeny and stochastic events. Our program runs relatively fast and is suitable for analyzing alignments containing large number of sequences.
Availability: ftp://iole.swmed.edu/pub/PCOAT/
Supplementary information: The PCOAT ftp site contains a detailed description of the program, and the results of PCOAT analysis on C2H2 alignment and ACT domain alignment.
The Transglabellar Subcranial Approach for Nasal Dermoids with Intracranial Extension
Authors: Kellman Robert M. , Goyal Parul , Rodziewicz Gerard S. 
Published: July 2004

AbstractObjectives/Hypothesis:Nasal dermoids are the most common congenital midline nasal lesions. When a midline nasal pit or cyst is identified, scans should be obtained to look for an intracranial connection. The intracranial portion of the lesions has traditionally been approached by the performance of a frontal craniotomy. The transglabellar subcranial approach is a useful technique to resect these lesions and offers several advantages over a traditional craniotomy approach.Study Design:Retrospective case review.Methods:Records of two patients who underwent excision of nasal dermoids by way of a subcranial approach were analyzed.Results:Two patients underwent successful resection of nasal dermoids with intracranial extension by way of a subcranial approach. The patients were 13 months and 19 months old at the time of excision and have been followed for 7 years and 6 years, respectively. There has not been any recurrence of the lesions. There has been no apparent negative impact on facial growth in either of these cases.Conclusions:The subcranial approach is an effective technique for the resection of nasal dermoids with intracranial extension. These lesions have traditionally been managed with lateral rhinotomy, midface degloving, or external rhinoplasty approaches combined with a frontal craniotomy. The subcranial approach offers excellent exposure, minimizes frontal lobe retraction, reduces the likelihood of cerebrospinal fluid leak, and provides for excellent cosmetic result. This approach was used in two cases with long‐term follow‐up. The lesions were successfully resected in both cases. Long‐term follow‐up has shown no recurrence or negative effect on craniofacial growth.
The Status of the Contralateral Ear in Established Unilateral Menière's Disease
Authors: Perez Ronen , Chen Joseph M. , Nedzelski Julian M. 
Published: July 2004

AbstractObjectives/Hypothesis:To determine the incidence of measurable audiometric changes in the contralateral ear and clinical bilateral Menière's disease in individuals with longstanding established unilateral Menière's disease.Study Design:Analysis of data in an ongoing prospective study.Methods:One hundred and one patients who were treated with intratympanic gentamicin installation for disabling unilateral Menière's disease were followed up for a minimum of 2 years. The mean follow‐up time between the initial diagnosis to the last audiogram conducted was 12 ± 7 (range 2–45) years, and the mean follow‐up between the first and last audiograms conducted in our clinic was 5 ± 3 (range 2–15) years. The incidence of Menière's disease (clinical diagnosis) as compared with audiometric changes in the contralateral ear was analyzed.Results:Compared with several published reports, the development of bilateral Menière's disease in our series within the described observation period was much lower (5%). The incidence of contralateral isolated hearing loss in the low frequencies was 16% (average threshold of .25 and .5 kHz of 25 dB or more). The time interval between the initial diagnosis and the onset of contralateral findings ranged from 0 to 26 years.Conclusion:In our experience, individuals with disabling longstanding unilateral disease are not likely to develop bilateral disease. However, a small but significant percentage of patients have audiometric changes in the low frequencies of the contralateral ear (.25, .5 kHz).
The Utility of Routine Chest Radiography Following Jet Ventilation in Elective Laryngotracheal Surgery
Authors: Merati Albert L. , Sale Keith A. , Toohill Robert J. 
Published: July 2004

AbstractObjectives/Hypothesis: Jet ventilation is a useful mode of airway management for laryngotracheal surgery. The objective of this study is to evaluate the utility of routine chest radiography following jet ventilation for these cases.Study Design: Retrospective chart review.Methods: Thirty‐four elective surgical procedures performed from 1998 to 2002 are reviewed for postoperative airway and pulmonary complications. Data were collected from clinical notes as well as from the results of chest radiographs. This included the need for tracheotomy, reintubation, pneumothorax, pneumomediastinum, and atelectasis.Results: A retrospective chart examination revealed no major complications. Twenty‐nine of the 34 cases had postoperative chest radiography (CXR) performed on a routine basis. Atelectasis was present in 12 of 29 CXR (41%); no intervention was required in these cases.Conclusions: Routine postoperative CXR may not be useful following jet ventilation for elective laryngotracheal surgery. The safety of jet ventilation is discussed.
Surgical Outcomes in Patients with Endolymphatic Sac Tumors
Authors: Hansen Marlan R. , Luxford William M. 
Published: July 2004

AbstractObjective: To determine the surgical outcomes in patients with endolymphatic sac tumors (ELSTs).Study Design: Retrospective review of patients at a referral‐based otology–neurotology practice.Methods: A review of the records from the House Ear Clinic revealed 16 patients treated for ELSTs from 1971 to 2002. This article reports the treatment outcomes for the 14 patients for whom clinical data were available.Results: Sensorineural hearing loss, tinnitus, and dizziness were the most common presenting signs and symptoms. Six patients presented with facial weakness, and three patients had symptoms characteristic of Menière's syndrome. One patient suffered from Von Hippel‐Lindau disease. Patients underwent microsurgical removal and were followed for an average of 59.6 months. Patients that presented with normal facial function maintained excellent postoperative function, and hearing was preserved in two patients with small tumors. Two patients suffered persistent, progressive disease despite multiple attempts at microsurgical removal and radiotherapy. Both had incomplete resections of their initial tumors. A third patient developed a small recurrent tumor that was successfully managed by a second attempt at microsurgical removal.Conclusions: Taken together with other reports, these results suggest that ELSTs are best managed by complete surgical resection. This can generally be accomplished with minimal additional morbidity.
Unbiased Quantification of the Microdissected Human Scarpa's Ganglion Neurons
Authors: Ishiyama Akira , Lopez Ivan , Ishiyama Gail , Tang Yong 
Published: July 2004

AbstractObjective: The objective of the present study was to obtain unbiased estimates of the total number of Scarpa's vestibular ganglion neurons in individuals with normal vestibular function.Study Design: Application of unbiased stereology using microdissected human temporal bone specimens.Methods: Postmortem temporal bones were obtained from five young subjects with no history of audiovestibular disease (age range 42–49 years). The vestibular nerve containing the Scarpa's ganglion was microdissected, embedded in paraffin, and cut into 40 μm serial sections. Unbiased estimates of the total number of neurons were obtained using the optical fractionator technique of stereology.Results: An average of 23,599 (coefficient of variation [CV] = 0.11) vestibular ganglion neurons was obtained. There was no significant difference between the results obtained from the microdissected specimens and results that had been obtained from an age‐matched group derived from a previously published report from our laboratory using archival human temporal bone specimens.Conclusions: This study represents the first report to demonstrate the combination of the microdissection technique and the unbiased stereologic technique in the human temporal bone. This study demonstrates the reliability of the microdissection technique as an alternative method of human temporal bone processing for unbiased stereology. The utility of the microdissection technique is that specimens can be used for quantification, immunohistochemistry, and other powerful applications.
Role of Cytomegalovirus, Epstein‐Barr Virus, and Human Herpes Virus‐8 in Benign Lymphoepithelial Cysts of the Parotid Gland
Authors: Yen Thomas L. , Murr Andrew H. , Rabin Joseph , Mhatre Anand N. , Lalwani Anil K. 
Published: July 2004

AbstractObjective: To provide background and evaluate the role of herpesviruses in benign lymphoepithelial cysts (BLC) of the parotid gland.Study Design: Case series derived from review of pathology specimens.Methods: Radiolabeled polymerase chain reaction (PCR) analysis was used to detect for the presence of cytomegalovirus (CMV), Epstein‐Barr virus (EBV), and human herpes virus 8 (HHV‐8) DNA sequences in 14 paraffin embedded specimens and 1 freshly aspirated BLC specimen. Thirteen normal parotid tissue specimens obtained from paraffin embedded blocks were used as a control group.Results: CMV was detected with nearly equal frequency between the two groups (23% of normal vs. 20% in BLC). HHV‐8 was found in 13% of the BLC group and in none of the normal group (P = .4841). There was significant difference in EBV detection between the normal (0%) and the BLC (33%) groups (P = .0437).Conclusion: CMV and HHV‐8 does not appear to be associated with BLCs. Although EBV is found more frequently in BLC than in normal parotid controls, further studies are needed to elucidate the role of this virus in BLC pathogenesis.
Temporary Intermaxillary Fixation using Individualized Acrylic Splints Permits Image–Data‐Based Surgery of the Lower Jaw and Oropharynx
Authors: Hoffmann Jürgen , Troitzsch Dirk , Westendorff Carsten , Weinhold Octavio , Reinert Siegmar 
Published: July 2004

AbstractObjectives/Hypothesis: Image–data‐based surgical navigation is used as a helpful device in the operating room to localize critical structures with a high degree of accuracy. It also enables physicians to plan therapeutic performance. Because it relies on preoperatively acquired computed tomography (CT) or magnetic resonance imaging (MRI) data, there is restricted access for navigation of surgical instruments in areas that show motion uncorrelated with radiologic data. Thus, in the case of moveable structures, for example the lower jaw, navigational procedures could not yet be applied.Study Design: We introduce a new technique using individualized intermaxillary splints that fix the mandible in a reproducible aboccluded position at the time of image‐data acquisition and surgery.Methods: Different manufacturing processes were investigated. The feasibility of uni‐ and bilateral intermaxillary splints was studied under clinical conditions in four patients during different procedures in the mandibular and oropharyngeal regions.Results: The manufacturing of the splints showed was easily performed in a short time. With bilateral fixation, there was a high anatomic target precision of 1.6 to 2.3 mm.Conclusions: The use of bilateral intermaxillary splints that fix the patient's mandible in a reproducible aboccluded position permits an image–data‐based navigated surgical approach to the oropharyngeal and mandibular regions.
Trichomonas vaginalis‐induced apoptosis in RAW264·7 cells is regulated through Bcl‐xL, but not Bcl‐2
Authors: Chang J.‐H. , Ryang Y.‐S. , Kim S.‐K. , Park J.‐Y. 
Published: July 2004

SUMMARY The purpose of this study was to determine whether anti‐apoptotic proteins of the Bcl‐2 family such as Bcl‐2 and Bcl‐x

L

, proteins that confer resistance to apoptotic death from some stimuli, block apoptotic cell death in RAW264·7 cells upon treatment with Trichomonas vaginalis. In this study, the expression level of Bcl‐2 was unchanged throughout the course of apoptotic cell death, and overexpressed Bcl‐2 did not prevent release of cytochrome c, the significant change of the membrane potential, activation of caspases, and PARP cleavage in T. vaginalis‐treated RAW264·7 cells. On the other hand, Bcl‐xLexpression was decreased after T. vaginalis treatment accompanied with Bax activation. Furthermore, we showed that release of mitochondrial cytochrome c, cleavage of caspase‐9 and PARP during apoptosis in T. vaginalis‐treated RAW264·7 cells were considerably diminished by transfection with overexpressed Bcl‐xL, and overexpressed Bcl‐xLcould inhibit T. vaginalis‐induced apoptosis in RAW264·7 cells. In addition, interestingly, pre‐treatment with caspase inhibitors, Boc‐D‐FMK and Z‐DEVD‐FMK, significantly abolished T. vaginalis‐induced down‐regulation of Bcl‐xL, suggesting that caspase‐3 may play a pivotal role in the process of apoptosis as well as the down‐regulation of Bcl‐xLby T. vaginalis. Therefore, these results suggest that T. vaginalis‐induced apoptosis in RAW264·7 cells can occur via a Bcl‐xL‐dependent apoptotic mechanism.
Gas flux to the atmosphere from mud volcanoes in eastern Romania
Authors: Etiope G. , Baciu C. , Caracausi A. , Italiano F. , Cosma C. 
Published: July 2004

AbstractGas flux measurements have for the first time been taken from vents and soil of eastern Romania mud volcanoes, the largest geological structures in Europe releasing methane into the atmosphere. In the quiescent phase, the methane emission from single vents is up to 28 t yr−1. Diffuse soil microseepage is of the order of 102−105 mg m−2 day−1. A total output of at least 1200 tonnes of CH4per year can be conservatively estimated over the area investigated alone (∼ 2.3 km2). Helium fluxes are up to five orders of magnitude higher than the average flux in a stable continental area, pointing to a close link between mud volcanoes and crustal degassing through faults crossing the deep hydrocarbon reservoirs. These data represent a key contribution towards refining global CH4‐emission estimates, which indicate mud volcanoes as a significant and unavoidable source of greenhouse gases for the atmosphere.
Fracture sealing of quartzite under a temperature gradient: experimental results
Authors: Hilgers Christoph , Tenthorey Eric 
Published: July 2004

AbstractVeined lithologies are formed by fracturing and sealing processes, with the veins representing former fluid conduits through the rock. Although detailed fieldwork and numerical simulations have provided a better understanding of vein growth, few studies have attempted to seal fractures and generate veins experimentally. In this pilot study, we subjected fractured quartzite to temperature gradients of 45–125 °C under hydrothermal conditions in a static fluid, with the aim of precipitating secondary quartz in the cooler portions of the fracture. Results show that secondary quartz precipitates due to the imposed temperature gradient, causing the initial fracture to seal locally. Although no systematic sealing pattern was observed along the fracture, samples subjected to higher temperatures exhibit a smaller fracture width and appear to have reacted more extensively. Electron microprobe mapping visualizes the spatial distribution of secondary quartz, which contains elevated concentrations of aluminium.
From rifting to spreading in the eastern Gulf of Aden: a geophysical survey of a young oceanic basin from margin to margin
Authors: Leroy Sylvie , Gente Pascal , Fournier Marc , D'Acremont Elia , Patriat Philippe , Beslier Marie‐Odile , Bellahsen Nicolas , Maia Marcia , Blais Angelina , Perrot Julie , Al‐Kathiri Ali , Merkouriev Serge , Fleury Jean‐Marc , Ruellan Pierre‐Yves , Lepvrier Claude , Huchon Philippe 
Published: July 2004

AbstractA geophysical survey in the eastern Gulf of Aden, between the Alula–Fartak (52°E) and the Socotra (55°E) transform faults, was carried out during the Encens–Sheba cruise. The conjugate margins of the Gulf are steep, narrow and asymmetric. Asymmetry of the rifting process is highlighted by the conjugate margins (horst and graben in the north and deep basin in the south). Two transfer fault zones separate the margins into three segments, whereas the present‐day Sheba Ridge is divided into two segments by a transform discontinuity. Therefore segmentation of the Sheba Ridge and that of the conjugate margins did coincide during the early stages of oceanic spreading. Extensive magma production is evidenced in the central part of the western segment. Anomaly 5d was identified in the northern and southern parts of the oceanic basin, thus confirming that seafloor spreading in this part of Gulf of Aden started at least 17.6 Ma ago.
Characteristics of the 1912 co‐seismic rupture along the North Anatolian Fault Zone (Turkey): implications for the expected Marmara earthquake
Authors: Altunel Erhan , Meghraoui Mustapha , Akyüz H. Serdar , Dikbas Aynur 
Published: July 2004

AbstractEvidence of right‐lateral offsets associated with the 1912 earthquake (Mw 7.4) along the North Anatolian Fault (Gaziköy–Saros segment) allow us to survey (using DGPS) the co‐seismic and cumulative slip distribution. The damage distribution and surface breaks related with the earthquake show an elongated zone of maximum intensity (X MSK) parallel to the fault rupture on land but this may extend offshore to the north‐east and south‐west. Detailed mapping of the fault using topographic maps and aerial photographs indicates the existence of pull‐apart basins and pressure ridges. At several localities, the average 1912 offset along strike is 3.5–4 m and cumulative slip is 2–6 times that of individual movement. The fault rupture geometry and slip distribution suggest the existence of three subsegments with a combined total length of 110–120 km, a fault length and maximum slip similar to those of the 1999 Izmit earthquake. The amount of slip at the north‐easternmost section and in the coastal region of the Sea of Marmara reaches an average 4 m, thereby implying the offshore extension of the 1912 rupture. The results suggest that the 1912 event generated up to 150 km of surface faulting, which would imply a Mw 7.2–7.4 earthquake and which, added with rupture lengths of the 1999 earthquakes, help to constrain the remaining seismic gap in the Sea of Marmara.