bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data Assimilation as Synchronization of Truth and Model: Experiments with the Three-Variable Lorenz System*
Authors: Yang Shu-Chih , Baker Debra , Li Hong , Cordes Katy , Huff Morgan , Nagpal Geetika , Okereke Ena , Villafañe Josue , Kalnay Eugenia , Duane Gregory S. 
Published: September 2006

Abstract
The potential use of chaos synchronization techniques in data assimilation for numerical weather prediction models is explored by coupling a Lorenz three-variable system that represents “truth” to another that represents “the model.” By adding realistic “noise” to observations of the master system, an optimal value of the coupling strength was clearly identifiable. Coupling only the y variable yielded the best results for a wide range of higher coupling strengths. Coupling along dynamically chosen directions identified by either singular or bred vectors could improve upon simpler chaos synchronization schemes. Generalized synchronization (with the parameter r of the slave system different from that of the master) could be easily achieved, as indicated by the synchronization of two identical slave systems coupled to the same master, but the slaves only provided partial information about regime changes in the master. A comparison with a standard data assimilation technique, three-dimensional variational analysis (3DVAR), demonstrated that this scheme is slightly more effective in producing an accurate analysis than the simpler synchronization scheme. Higher growth rates of bred vectors from both the master and the slave anticipated the location and size of error spikes in both 3DVAR and synchronization. With less frequent observations, synchronization using time-interpolated observational increments was competitive with 3DVAR. Adaptive synchronization, with a coupling parameter proportional to the bred vector growth rate, was successful in reducing episodes of large error growth. These results suggest that a hybrid chaos synchronization–data assimilation approach may provide an avenue to improve and extend the period for accurate weather prediction.
Observed Boundary Layer Wind Structure and Balance in the Hurricane Core. Part II: Hurricane Mitch
Authors: Kepert Jeffrey D. 
Published: September 2006

Abstract
Part I of this paper presented a detailed analysis of the boundary layer of Hurricane Georges (1998), based mainly on the newly available high-resolution GPS dropsonde data. Here, similar techniques and data are used to study Hurricane Mitch (1998). In contrast to Hurricane Georges, the flow in the middle to upper boundary layer near the eyewall is found to be strongly supergradient, with the imbalance being statistically significant. The reason for the difference is shown to be the different radial structure of the storms, in that outside of the radius of maximum winds, the wind decreases much more quickly in Mitch than in Georges. Hurricane Mitch was close to inertially neutral at large radius, with a strong angular momentum gradient near the radius of maximum winds. Kepert and Wang predict strongly supergradient flow in the upper boundary layer near the radius of maximum winds in this situation; the observational analysis is thus in good agreement with their theory. The wind reduction factor (i.e., ratio of a near-surface wind speed to that at some level further aloft) is found to increase inward toward the radius of maximum winds, in accordance with theoretical predictions and the analysis by Franklin et al. Marked asymmetries in the boundary layer wind field and in the eyewall convection are shown to be consistent with asymmetric surface friction due to the storm’s proximity to land, rather than to motion. The boundary layer flow was simulated using Kepert and Wang’s model, forced by the observed storm motion, radial profile of gradient wind, and coastline position; and good agreement with the observations was obtained.
Hypusination of eukaryotic initiation factor 5A (eIF5A): a novel therapeutic target in BCR-ABL–positive leukemias identified by a proteomics approach
Authors: Balabanov Stefan , Gontarewicz Artur , Ziegler Patrick , Hartmann Ulrike , Kammer Winfried , Copland Mhairi , Brassat Ute , Priemer Martin , Hauber Ilona , Wilhelm Thomas , Schwarz Gerold , Kanz Lothar , Bokemeyer Carsten , Hauber Joachim , Holyoake Tessa L. , Nordheim Alfred , Brümmendorf Tim H. 
Published: September 2006

AbstractInhibition of BCR-ABL tyrosine kinase with imatinib represents a major breakthrough in the treatment of patients with chronic myeloid leukemia (CML). However, resistance to imatinib develops frequently, particularly in late-stage disease. To identify new cellular BCR-ABL downstream targets, we analyzed differences in global protein expression in BCR-ABL–positive K562 cells treated with or without imatinib in vitro. Among the 19 proteins found to be differentially expressed, we detected the down-regulation of eukaryotic initiation factor 5A (eIF5A), a protein essential for cell proliferation. eIF5A represents the only known eukaryotic protein activated by posttranslational hypusination. Hypusination inhibitors (HIs) alone exerted an antiproliferative effect on BCR-ABL–positive and –negative leukemia cell lines in vitro. However, the synergistic dose-response relationship found for the combination of imatinib and HI was restricted to Bcr-Abl–positive cells. Furthermore, this synergistic effect was confirmed by cytotoxicity assays, cell-cycle analysis, and CFSE labeling of primary CD34+ CML cells. Specificity of this effect could be demonstrated by cotreatment of K562 cells with imatinib and siRNA against eIF5. In conclusion, through a comparative proteomics approach and further functional analysis, we identified the inhibition of eIF5A hypusination as a promising new approach for combination therapy in BCR-ABL–positive leukemias.
CD33 responses are blocked by SOCS3 through accelerated proteasomal-mediated turnover
Authors: Orr Selinda J. , Morgan Nuala M. , Elliott Joanne , Burrows James F. , Scott Christopher J. , McVicar Daniel W. , Johnston James A. 
Published: September 2006

AbstractCD33 is a member of the sialic acid–binding immunoglobulin-like lectin (Siglec) family of inhibitory receptors and a therapeutic target for acute myeloid leukemia (AML). CD33 contains a cytoplasmic immunoreceptor tyrosine-based inhibitory motif (ITIM), which can recruit SHP-1 and SHP-2. How CD33 expression is regulated is unclear. Suppressor of cytokine signaling 3 (SOCS3) is expressed in response to cytokines, LPS, and other PAMPs, and competes with SHP-1/2 binding to ITIMs of cytokine receptors, thereby inhibiting signaling. In this study, using peptide pull-down experiments, we found that SOCS3 can specifically bind to the phosphorylated ITIM of CD33. Additionally, following cross-linking SOCS3 can recruit the ECS E3 ligase resulting in accelerated proteasomal degradation of both CD33 and SOCS3. Our data suggest that the tyrosine motifs in CD33 are not important for internalization, while they are required for degradation. Moreover, SOCS3 inhibited the CD33-induced block on cytokine-induced proliferation. This is the first receptor shown to be degraded by SOCS3 and where SOCS3 and its target protein are degraded concomitantly. Our findings clearly suggest that during an inflammatory response, the inhibitory receptor CD33 is lost by this mechanism. Moreover, this has important clinical implications as tumors expressing SOCS3 may be refractory to α-CD33 therapy.
Parental smoking increases exhaled nitric oxide in young children
Authors: Franklin P. J. , Turner S. , Mutch R. , Stick S. M. 
Published: September 2006

The present study investigated the association between reported parental smoking and exhaled nitric oxide fraction (FeNO) in young children.In total, 78 children (24 females, mean age 51.3 weeks) were recruited. Fourteen lived with one smoking parent and eight with two smoking parents.FeNOwas measured using the modified single-breath technique.Mean±sdFeNOlevels were 33.0±18.9, 38.3±15.0 and 48.3±14.7 ppb for children with no, one and two smoking parents, respectively. There was a significant linear trend across the groups and, after controlling for other relevant factors, a significant difference between the groups.In the present study, exposure to environmental tobacco smoke was associated with increased exhaled nitric oxide fraction in young children. Furthermore, there was evidence of a dose–response relationship between childhood exhaled nitric oxide fraction and the number of smoking parents.
Advances in the diagnosis and management of chronic pulmonary aspiration in children
Authors: Boesch R. P. , Daines C. , Willging J. P. , Kaul A. , Cohen A. P. , Wood R. E. , Amin R. S. 
Published: September 2006

Chronic pulmonary aspiration (CPA) in children is an important cause of recurrent pneumonia, progressive lung injury, respiratory disability and death. It is sporadic, intermittent and variable, and often occurs in children with complicated underlying medical conditions and syndromes that produce symptoms indistinguishable from CPA. For most types of aspiration there is no gold-standard diagnostic test. The diagnosis of CPA is currently made clinically with some supporting diagnostic evaluations, but often not until significant lung injury has been sustained. Despite multiple diagnostic techniques, the diagnosis or exclusion of CPA in children is challenging. This is of particular concern given the outcome of unrecognised progressive lung injury and the invasiveness of definitive therapies.Although new techniques have been introduced since the 1990s and significant advances in the understanding of dysphagia and gastro-oesophageal reflux have been made, characterisation of the aspirating child remains elusive.
Massive cavitary pulmonary rheumatoid nodules in a patient with HIV
Authors: Khazeni N. , Homer R. J. , Rubinowitz A. N. , Chupp G. L. 
Published: September 2006

The case of a 52-yr-old female with rheumatoid arthritis and HIV who developed massive, progressive, cavitary pulmonary nodules is described.Multiple diagnostic bronchoscopies and lung biopsies failed to demonstrate the presence of any microorganisms. Pathological analysis showed palisading histiocytes with necrobiosis consistent with rheumatoid nodules.The effect of co-existing HIV infection on the course and prognosis of rheumatoid arthritis is discussed, and it is concluded that the complex relationship between these two disease processes warrants further investigation.
Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data
Authors: Kim Seon-Young , Kim YongSung 
Published: September 2006

AbstractBackgroundA complete understanding of the regulatory mechanisms of gene expression is the next important issue of genomics. Many bioinformaticians have developed methods and algorithms for predicting transcriptional regulatory mechanisms from sequence, gene expression, and binding data. However, most of these studies involved the use of yeast which has much simpler regulatory networks than human and has many genome wide binding data and gene expression data under diverse conditions. Studies of genome wide transcriptional networks of human genomes currently lag behind those of yeast.ResultsWe report herein a new method that combines gene expression data analysis with promoter analysis to infer transcriptional regulatory elements of human genes. The Z scores from the application of gene set analysis with gene sets of transcription factor binding sites (TFBSs) were successfully used to represent the activity of TFBSs in a given microarray data set. A significant correlation between the Z scores of gene sets of TFBSs and individual genes across multiple conditions permitted successful identification of many known human transcriptional regulatory elements of genes as well as the prediction of numerous putative TFBSs of many genes which will constitute a good starting point for further experiments. Using Z scores of gene sets of TFBSs produced better predictions than the use of mRNA levels of a transcription factor itself, suggesting that the Z scores of gene sets of TFBSs better represent diverse mechanisms for changing the activity of transcription factors in the cell. In addition, cis-regulatory modules, combinations of co-acting TFBSs, were readily identified by our analysis.ConclusionBy a strategic combination of gene set level analysis of gene expression data sets and promoter analysis, we were able to identify and predict many transcriptional regulatory elements of human genes. We conclude that this approach will aid in decoding some of the important transcriptional regulatory elements of human genes.
Evaluation of BacLite Rapid MRSA, a rapid culture based screening test for the detection of ciprofloxacin and methicillin resistant S. aureus (MRSA) from screening swabs
Authors: Johnson Gemma , Millar Michael R , Matthews Stuart , Skyrme Margaret , Marsh Peter , Barringer Emma , O'Hara Stephen , Wilks Mark 
Published: September 2006

Abstract

Background
Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen worldwide. The need for accurate and rapid screening methods to detect MRSA carriers has been clearly established. The performance of a novel assay, BacLite Rapid MRSA (Acolyte Biomedica, UK) for the rapid detection (5 h) and identification of hospital associated ciprofloxacin resistant strains of MRSA directly from nasal swab specimens was compared to that obtained by culture on Mannitol salt agar containing Oxacillin (MSAO) after 48 h incubation.

Results
A total of 1382 nasal screening swabs were tested by multiple operators. The BacLite Rapid MRSA test detected 142 out of the 157 confirmed MRSA that were detected on MSAO giving a diagnostic sensitivity of 90.4, diagnostic specificity of 95.7% and a negative predictive value of 98.7%. Of the 15 false negatives obtained by the BacLite Rapid MRSA test, seven grew small amounts (< 10 colonies of MRSA) on the MSAO culture plate and five isolates were ciprofloxacin sensitive. However there were 13 confirmed BacLite MRSA positive samples, which were negative by the direct culture method, probably due to overgrowth on the MSAO plate. There were 53 false positive results obtained by the BacLite Rapid MRSA test at 5 h and 115 cases where MRSA colonies were tentatively identified on the MSAO plate when read at 48 h, and which subsequently proved not to be MRSA.

Conclusion
The Baclite MRSA test is easy to use and provides a similar level of sensitivity to conventional culture for the detection of nasal carriage of MRSA with the advantage that the results are obtained much more rapidly.
Analysis of in vitro replicated human hepatitis C virus (HCV) for the determination of genotypes and quasispecies
Authors: Revie Dennis , Alberti Michael O , Braich Ravi S , Chelyapov Nickolas , Bayles David , Prichard John G , Salahuddin S Zaki 
Published: September 2006

Abstract
Isolation and self-replication of infectious HCV has been a difficult task. However, this is needed for the purposes of developing rational drugs and for the analysis of the natural virus. Our recent report of an in vitro system for the isolation of human HCV from infected patients and their replication in tissue culture addresses this challenge. At California Institute of Molecular Medicine several isolates of HCV, called CIMM-HCV, were grown for over three years in cell culture. This is a report of the analysis of CIMM-HCV isolates for subtypes and quasispecies using a 269 bp segment of the 5'UTR. HCV RNA from three patients and eleven CIMM-HCV were analyzed for this purpose. All isolates were essentially identical. Isolates of HCV from one patient were serially transmitted into fresh cells up to eight times and the progeny viruses from each transmission were compared to each other and also to the primary isolates from the patient's serum. Some isolates were also transmitted to different cell types, while others were cultured continuously without retransmission for over three years. We noted minor sequence changes when HCV was cultured for extended periods of time. HCV in T-cells and non-committed lymphoid cells showed a few differences when compared to isolates obtained from immortalized B-cells. These viruses maintained close similarity despite repeated transmissions and passage of time. There were no subtypes or quasispecies noted in CIMM-HCV.
Plasma levels of leptin and mammographic density among postmenopausal women: a cross-sectional study
Authors: Stuedal Anne , Ursin Giske , Veierød Marit B , Bremnes Yngve , Reseland Janne E , Drevon Christian A , Gram Inger T 
Published: September 2006

Abstract
Introduction
Obesity has been linked to increased risk of breast cancer in postmenopausal women. Increased peripheral production of estrogens has been regarded as the main cause for this association, but other features of increased body fat mass may also play a part. Leptin is a protein produced mainly by adipose tissue and may represent a growth factor in cancer. We examined the association between leptin plasma levels and mammographic density, a biomarker for breast cancer risk.

Methods
We included data from postmenopausal women aged 55 and older, who participated in a cross-sectional mammography study in Tromsø, Norway. Mammograms, plasma leptin measurements as well as information on anthropometric and hormonal/reproductive factors were available from 967 women. We assessed mammographic density using a previously validated computer-assisted method. Multiple linear regression analysis was applied to investigate the association between mammographic density and quartiles of plasma leptin concentration. Because we hypothesized that the effect of leptin on mammographic density could vary depending on the amount of nondense or fat tissue in the breast, we also performed analyses on plasma leptin levels and mammographic density within tertiles of mammographic nondense area.

Results
After adjusting for age, postmenopausal hormone use, number of full-term pregnancies and age of first birth, there was an inverse association between leptin and absolute mammographic density (Ptrend = 0.001). When we additionally adjusted for body mass index and mammographic nondense area, no statistically significant association between plasma leptin and mammographic density was found (Ptrend = 0.16). Stratified analyses suggested that the association between plasma leptin and mammographic density could differ with the amount of nondense area of the mammogram, with the strongest association between leptin and mammographic absolute density in the stratum with the medium breast fat content (Ptrend = 0.003, P for interaction = 0.05).

Conclusion
We found no overall consistent association between the plasma concentration of leptin and absolute mammographic density. Although weak, there was some suggestion that the association between leptin and mammographic density could differ with the amount of fat tissue in the breast.
Facial nerve problems: Including Remarks on Bell's Palsy.
Authors: Deweese David D. 
Published: September 2006

AbstractParalysis of the facial nerve, whether spontaneous or traumatic, can be improved in the majority of instances with proper management.Traumatic injury of the facial nerve is caused most often by operations on the temporal bone. Injury of the facial nerve during operation can usually be avoided by recognition of well‐established anatomic landmarks. The most important of these are: 1. the horizontal semicircular canal of the labyrinth; 2. the digastric crest; 3. the stylomastoid foramen.Continuity of the injured facial nerve can be re‐established successfully in a large percentage of patients by means of end‐to‐end suture or with a fresh graft. The length of the graft is of less importance than precise approximation. Function following repair is usually better when the injury has occurred outside the temporal bone than when it has taken place inside the temporal bone.In Bell's palsy the percentage of complete recoveries and the degree of partial recovery can be improved by surgical decompression of the facial nerve. The rate of recovery, or lack of it, plus results of electrical tests, assist the physician in determining when or whether decompression should be undertaken. In certain patients the best final results can be achieved only by surgical decompression.
Subarachnoid shunt for drainage of endolymphatic hydrops. a preliminary report.
Authors: House William F. 
Published: September 2006

AbstractExcessive endolymphatic pressure, established as a feature of Ménière's disease by recent experiments and probably due to disturbed absorption, may be corrected by drainage of the endolymphatic sac. By use of the operating microscope, diamond dental drill and continuous irrigation, the endolymphatic sac can be accurately identified and opened under direct vision. Continuous drainage of endolymph is maintained by creating a shunt into the subarachnoid space through a silicone rubber tube inserted into the sac.Seven patients, observed for two to six months, showed relief of most symptoms of Ménière's disease, with improvement of hearing in the majority. Although a larger series of patients and a longer follow‐up period will be required for conclusive evaluation, these early results indicate that continuous drainage of endolymph is an effective treatment of Ménière's disease.
From draining ear to tympanoplasty.
Authors: Kramer Bernard M. 
Published: September 2006

AbstractInasmuch as the preferred candidate for tympanoplasty has a dry ear, the object of all preoperative care is to control infection and drainage before definitive surgery is undertaken. In our desire to perform this exacting surgery, we must realize that not all patients with chronic otitis media are candidates nor can they all be converted to candidates despite our best efforts. If we are as careful in our preoperative care and selection of tympanoplasty candidates as we are when performing the surgery, then this most valuable procedure will attain the status we feel it deserves. Specific reference is made to para‐otitic disease, tubal disease, and middle ear and mastoid disease.
Tympanic grafts: Personal experiences with surgical repair of tympanic perforations
Authors: Guilford Frederick R. 
Published: September 2006

AbstractThe complications that occur after use of split‐thickness and full‐thickness postauricular skin for tympanic grafts are discussed and the results stated. The use of the vein graft, the combination of canal skin and vein grafts, and vein graft stapediopexy are discussed, and the improved results with these measures are noted. Attention is called to the difficulties in complete reporting of any subject as complex as tympanoplasty.