bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Oxide Film Containing Fluorine Ion on Enhancing the Initial Osseointegration of Titanium-Based Alloy
Authors: Shih Yung H. , Tsai Ming H. , Ou Keng-Liang L. 
Published: December 2007

The effects of nano-γ-TiH phase on formation of nanoporous	titanium oxide by anodization with HF pretreatment have been investigated by optical microscopy, x-ray photoelectron spectroscopy, thin film x-ray diffractometry, scanning electron	microscopy, transmission electron microscopy and secondary ion mass spectroscopy. Furthermore, nanostructural titanium oxide was formed after anodization under various current densities. The γ-TiH is formed by HF pretreatments before anodization. The nano-γ-TiH phase is directly dissolved after anodization. Furthermore, the nanoporous Ti formed by dissolution of nano-titanium hydrides was changed to	nanoporous TiO2. The nano-γ-TiH phase plays an important role in forming nanoporous TiO2. The anodization with HF pretreatment not only produces titanium hydride layer, but also results in formation of nanostructural titanium oxide. The	bioactive nanoporous titanium oxide film presented in the prese nt study is believed to result in enhancing cell differentiation, thereby providing stable fixation to bone and rapid osseointegration.
Novel Hybrid Abrasive Particles for Oxide CMP Applications
Authors: Mudhivarthi Subrahmanya R. , Coutinho Cecil , Kumar Ashok , Gupta Vinay 
Published: December 2007

In the present research, novel abrasive particles are investigated in order to carry out CMP at relatively low down force (low	mechanical stress) yet achieve desirable removal rates and superior post CMP surface quality (reduced scratches). Hybrid abrasives	are developed where the composition of the polymeric particles formed via colloidal precipitation is modified with inorganic	segments to reduce surface damage during CMP. The composition is controlled by changing the time for condensation and	hydrolysis of the inorganic oxide. Characterization of these particles is performed by FTIR spectroscopy, dynamic light scattering, and electron microscopy (TEM/SEM). Tribological characteristics during polishing employing these novel particles are studied on a bench-top CMP tester. Surface roughness and defectivity are estimated using Atomic Force Microscopy (AFM).
Analysis of Pre- and Post-Conditioned Polyurethane CMP Pad Surfaces as a Function of Conditioning Temperature
Authors: Prasad Abaneshwar , Xiang Hongqi , Wang Jianhua , Remsen Edward E. 
Published: December 2007

The investigation of water diffusion in polyurethane CMP pads via hydrogen-deuterium (H-D) exchange, measured by attenuated total reflectance/FT-IR (ATR/FT-IR), is reported. Significant differences in the kinetics of H-D exchange for a	thermoplastic polyurethane (TPU) pad and a conventional cross- linked polyurethane (PU) pad were found. These differences were attributed to the intrinsic chemical and physical	differences between the polymeric materials constituting the pads that were characterized by liquid chromatography/mass spectrometry (LCMS) and 1H NMR spectroscopy. Extraction kinetics for low molecular weight compounds in the pads are reported.	H-D exchange kinetics for both TPU and PU pads show a strong dependence on temperature and were unique to the specific pad type. Pad conditioning also influenced the kinetics. These findings suggest a re-organization of chain segments at or near the surface during pad conditioning. Additiona l studies are proposed to characterize the nature of the molecular changes modulating water diffusion in the pads.
Composite Polymer Core - Silica Shell Abrasive Particles During Oxide CMP: A Defectivity Study
Authors: Armini Silvia , Whelan Caroline M. , Maex Karen 
Published: December 2007

Chemical Mechanical Planarization (CMP) is a triboelectrochemical process dominated by mechanical and chemical-assisted wear. The choice of the abrasive is of fundamental importance. Oxide CMP results using two different 350 nm polymer-core / 30 nm colloidal silica-shell composite	abrasive particles are compared with oxide CMP performances of 30 nm and 90 nm colloidal silica abrasives in terms of removal rate and surface finishing. The composites are achieved by	either creating chemical bonds by silane coupling agents or tuning the pH in order to form electrostatic attractive	interactions between core and shell. Oxide CMP is considered as an easy test vehicle for defectivity characterization and comparison between different abrasives providing the same oxide	thickness removed. Due to the higher complexity of the	composite abrasive with respect to the simple silica particle- wafer system, we combine different surface analysis techniques with m ethods of defect quantification and enhancement. Fewer	and shallower scratches are detected for the composites with	respect to colloidal silica.
The effects of NaCl concentration and pH on the stability of hyperthermophilic protein Ssh10b
Authors: Mao Yong-Jin , Sheng Xiang-Rong , Pan Xian-Ming 
Published: December 2007

Abstract

Background
Hyperthermophiles constitute a group of microorganisms with an optimum growth temperature of between 80°C and 100°C. Although the molecular underpinnings of protein thermostabilization have been the focus of many theoretical and experimental efforts, the properties leading to the higher denaturation temperature of hyperthermophilic proteins are still controversial. Among the large number of factors identified as responsible for the thermostability of hyperthermophilic proteins, the electrostatic interactions are thought to be a universally important factor.

Results
In this study, we report the effects of pH and salt concentration on the urea-induced denaturation of the protein Ssh10b from a hyperthermophile in low ionic strength buffer. In the absence of NaCl, the unfolding ΔG of the protein increased from about 33 kJ/mol at pH 3 to about 78 kJ/mol at pH 10. At all values of pH, the ΔG increased with increasing NaCl concentration, indicating that salt stabilizes the protein significantly.

Conclusion
These findings suggests that the increased number of charged residues and ion pairs in the protein Ssh10b from hyperthermophiles does not contribute to the stabilization of the folded protein, but may play a role in determining the denatured state ensemble and also in increasing the denaturation temperature.
A mixture of feature experts approach for protein-protein interaction prediction
Authors: Qi Yanjun , Klein-Seetharaman Judith , Bar-Joseph Ziv 
Published: December 2007

Abstract

Background
High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false negative rates. A number of researchers have recently presented methods for integrating direct and indirect data for predicting interactions. These methods utilize a common classifier for all pairs. However, due to missing data and high redundancy among the features used, different protein pairs may benefit from different features based on the set of attributes available. In addition, in many cases it is hard to directly determine which of the data sources contributed to a prediction. This information is important for biologists using these predications in the design of new experiments.

Results
To address these challenges we propose a Mixture-of-Feature-Experts method for protein-protein interaction prediction. We split the features into roughly homogeneous sets of feature experts. The individual experts use logistic regression and their scores are combined using another logistic regression. When combining the scores the weighting of each expert depends on the set of input attributes available for that pair. Thus, different experts will have different influence on the prediction depending on the available features.

Conclusion
We applied our method to predict the set of interacting proteins in yeast and human cells. Our method improved upon the best previous methods for this task. In addition, the weighting of the experts provides means to evaluate the prediction based on the high scoring features.
Accurate splice site prediction using support vector machines
Authors: Sonnenburg Sören , Schweikert Gabriele , Philips Petra , Behr Jonas , Rätsch Gunnar 
Published: December 2007

Abstract

Background
For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to solve these tasks.

Results
In this work we consider Support Vector Machines for splice site recognition. We employ the so-called weighted degree kernel which turns out well suited for this task, as we will illustrate in several experiments where we compare its prediction accuracy with that of recently proposed systems. We apply our method to the genome-wide recognition of splice sites in Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Danio rerio, and Homo sapiens. Our performance estimates indicate that splice sites can be recognized very accurately in these genomes and that our method outperforms many other methods including Markov Chains, GeneSplicer and SpliceMachine. We provide genome-wide predictions of splice sites and a stand-alone prediction tool ready to be used for incorporation in a gene finder.

Availability
Data, splits, additional information on the model selection, the whole genome predictions, as well as the stand-alone prediction tool are available for download at http://www.fml.mpg.de/raetsch/projects/splice.
The expression of HSP27 is associated with poor clinical outcome in intrahepatic cholangiocarcinoma
Authors: Romani Antonello A , Crafa Pellegrino , Desenzani Silvia , Graiani Gallia , Lagrasta Costanza , Sianesi Mario , Soliani Paolo , Borghetti Angelo F 
Published: December 2007

Abstract

Background
The heat shock proteins (HSPs) 27-kDa (HSP27) and 72-kDa (HSP72), are ubiquitous chaperone molecules inducible in cells exposed to different stress conditions. Increased level of HSPs are reported in several human cancers, and found to be associated with the resistance to some anticancer treatments and poor prognosis. However, there is no study of the relationship between HSPs expression and patient's prognosis in intrahepatic cholangiocarcinoma (IHCCA). In this exploratory retrospective study, we investigated the expressions of HSP27 and HSP72 as potential prognostic factors in IHCCA.

Methods
Thirty-one paraffin-embedded samples were analyzed by immunohistochemical methods using HSP27 and HSP72 monoclonal antibodies. Proliferation rate was assessed in the same specimens by using monoclonal antibody against phosphorylated histone H3 (pHH3). Fisher's exact test was used to assess the hypothesis of independence between categorical variables in 2 × 2 tables. The ANOVA procedure was used to evaluate the association between ordinal and categorical variables. Estimates of the survival probability were calculated using the Kaplan-Meier method, and the log rank test was employed to test the null hypothesis of equality in overall survival among groups. The hazard ratio associated with HSP27 and HSP72 expression was estimated by Cox hazard-proportional regression.

Results
The expression of HSP27 was related to mitotic index, tumor greatest dimension, capsular and vascular invasion while the expression of HSP72 was only related to the presence of necrosis and the lymphoid infiltration. Kaplan-Maier analysis suggested that the expression of HSP27 significantly worsened the patients' median overall survival (11 ± 3.18 vs 55 ± 4.1 months, P-value = 0.0003). Moreover HSP27-positive patients exhibited the worst mean survival (7.0 ± 3.2 months) in the absence of concomitant HSP72 expression.

Conclusion
The expression of HSP27, likely increasing cell proliferation, tumor mass, vascular and capsular invasion, might promote aggressive tumor behaviour in IHCCA and decrease patients' survival. Immunohistochemical detection of HSP27 on routine sections may provide a reliable prognostic marker for IHCCA able to influence the therapeutic strategies for this cancer.
Correlation between the progressive cytoplasmic expression of a novel small heat shock protein (Hsp16.2) and malignancy in brain tumors
Authors: Pozsgai Eva , Gomori Eva , Szigeti Andras , Boronkai Arpad , Gallyas Ferenc , Sumegi Balazs , Bellyei Szabolcs 
Published: December 2007

Abstract

Background
Small heat shock proteins are molecular chaperones that protect proteins against stress-induced aggregation. They have also been found to have anti-apoptotic activity and to play a part in the development of tumors. Recently, we identified a new small heat shock protein, Hsp16.2 which displayed increased expression in neuroectodermal tumors. Our aim was to investigate the expression of Hsp16.2 in different types of brain tumors and to correlate its expression with the histological grade of the tumor.

Methods
Immunohistochemistry with a polyclonal antibody to Hsp16.2 was carried out on formalin-fixed, paraffin-wax-embedded sections using the streptavidin-biotin method. 91 samples were examined and their histological grade was defined. According to the intensity of Hsp16.2 immunoreactivity, low (+), moderate (++), high (+++) or none (-) scores were given.
Immunoblotting was carried out on 30 samples of brain tumors using SDS-polyacrylamide gel electrophoresis and Western-blotting.

Results
Low grade (grades 1–2) brain tumors displayed low cytoplasmic Hsp16.2 immunoreactivity, grade 3 tumors showed moderate cytoplasmic staining, while high grade (grade 4) tumors exhibited intensive cytoplasmic Hsp16.2 staining. Immunoblotting supported the above mentioned results. Normal brain tissue acted as a negative control for the experiment, since the cytoplasm did not stain for Hsp16.2. There was a positive correlation between the level of Hsp16.2 expression and the level of anaplasia in different malignant tissue samples.

Conclusion
Hsp16.2 expression was directly correlated with the histological grade of brain tumors, therefore Hsp16.2 may have relevance as becoming a possible tumor marker.
Using machine learning algorithms to guide rehabilitation planning for home care clients
Authors: Zhu Mu , Zhang Zhanyang , Hirdes John P , Stolee Paul 
Published: December 2007

Abstract

Background
Targeting older clients for rehabilitation is a clinical challenge and a research priority. We investigate the potential of machine learning algorithms – Support Vector Machine (SVM) and K-Nearest Neighbors (KNN) – to guide rehabilitation planning for home care clients.

Methods
This study is a secondary analysis of data on 24,724 longer-term clients from eight home care programs in Ontario. Data were collected with the RAI-HC assessment system, in which the Activities of Daily Living Clinical Assessment Protocol (ADLCAP) is used to identify clients with rehabilitation potential. For study purposes, a client is defined as having rehabilitation potential if there was: i) improvement in ADL functioning, or ii) discharge home. SVM and KNN results are compared with those obtained using the ADLCAP. For comparison, the machine learning algorithms use the same functional and health status indicators as the ADLCAP.

Results
The KNN and SVM algorithms achieved similar substantially improved performance over the ADLCAP, although false positive and false negative rates were still fairly high (FP > .18, FN > .34 versus FP > .29, FN. > .58 for ADLCAP). Results are used to suggest potential revisions to the ADLCAP.

Conclusion
Machine learning algorithms achieved superior predictions than the current protocol. Machine learning results are less readily interpretable, but can also be used to guide development of improved clinical protocols.
Process skill rather than motor skill seems to be a predictor of costs for rehabilitation after a stroke in working age; a longitudinal study with a 1 year follow up post discharge
Authors: Björkdahl Ann , Sunnerhagen Katharina Stibrant 
Published: December 2007

AbstractBackgroundIn recent years a number of costs of stroke studies have been conducted based on incidence or prevalence and estimating costs at a given time. As there still is a need for a deeper understanding of factors influencing these costs the aim of this study was to calculate the direct and indirect costs in a younger (<65) sample of stroke patients and to explore factors affecting the costs.MethodsFifty-eight patients included in a study of home rehabilitation and followed for 1 year after discharge from the rehabilitation unit, were interviewed about their use of health care services, assistance, medications and assistive devices. Costs (defined as the cost for society) were calculated. A linear regression of cost and variables of functioning, ability, community integration and health-related quality of life was done.ResultsInpatient care contributed substantially to the direct cost with a mean length of stay of 92 days. Rehabilitation during the first year constituted of an average of 28 days in day clinics, 38 physiotherapy sessions and 20 occupational therapy sessions. The total direct mean cost was 80 020 € and the indirect cost 35 129 €. The direct costs were influenced by the process skill (the ability to plan and perform a given task and to adapt when needed) and presence of aphasia. Indirect costs for informal care giving increased for patients with a lower health-related quality of life as well as a low score on home integration.ConclusionCosts are high in this group of young (< 65 years) stroke patients compared to other studies, partly due to the length of the stay and partly to loss of productivity.
Obesity and pre-hypertension in family medicine: Implications for quality improvement
Authors: Rohrer James E , Anderson Gregory J , Furst Joseph W 
Published: December 2007

Abstract
Background.
Prevention of pre-hypertension is an important goal for primary care patients. Obesity is a risk factor for hypertension, but has not been addressed for pre-hypertension in primary care populations. The objective of this study was to assess the degree to which obesity independently is associated with risk for pre-hypertension in family medicine patients.

Methods.
This study was a retrospective analysis of information abstracted from medical records of 707 adult patients. Multivariable logistic regression was used to test the relationship between body mass index (BMI) and pre-hypertension, after adjustment for comorbidity and demographic characteristics. Pre-hypertension was defined as systolic pressure between 120 and 139 mm Hg or diastolic pressure between 80 and 89 mm Hg.

Results.
In our sample, 42.9% of patients were pre-hypertensive. Logistic regression analysis revealed that, in comparison to patients with normal body mass, patients with BMI > 35 had higher adjusted odds of being pre-hypertensive (OR = 4.5, CI 2.55–8.11, p < .01). BMI between 30 and 35 also was significant (OR = 2.7, CI 1.61–4.63, p < 0.01) as was overweight (OR = 1.8, CI 1.14–2.92, p = 0.01).

Conclusion.
In our sample of family medicine patients, elevated BMI is a risk factor for pre-hypertension, especially BMI > 35. This relationship appears to be independent of age, gender, marital status and comorbidity. Weight loss intervention for obese patients, including patient education or referral to weight loss programs, might be effective for prevention of pre-hypertension and thus should be considered as a potential quality indicator.
Extensive population genetic structure in the giraffe
Authors: Brown David M , Brenneman Rick A , Koepfli Klaus-Peter , Pollinger John P , Milá Borja , Georgiadis Nicholas J , Louis Edward E , Grether Gregory F , Jacobs David K , Wayne Robert K 
Published: December 2007

AbstractBackgroundA central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation.ResultsBy analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations.ConclusionSuch extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separatein situandex situmanagement, not only of pelage morphs, but also of local populations.
Short-term effects of amelogenin gene splice products A+4 and A-4 implanted in the exposed rat molar pulp
Authors: Jegat Nadège , Septier Dominique , Veis Arthur , Poliard Anne , Goldberg Michel 
Published: December 2007

Abstract
In order to study the short-time effects of two bioactive low-molecular amelogenins A+4 and A-4, half-moon cavities were prepared in the mesial aspect of the first maxillary molars, and after pulp exposure, agarose beads alone (controls) or beads soaked in A+4 or A-4 (experimental) were implanted into the pulp. After 1, 3 or 7 days, the rats were killed and the teeth studied by immunohistochemistry. Cell proliferation was studied by PCNA labeling, positive at 3 days, but decreasing at day 7 for A+4, whilst constantly high between 3 and 7 days for A-4. The differentiation toward the osteo/odontoblast lineage shown by RP59 labeling was more apparent for A-4 compared with A+4. Osteopontin-positive cells were alike at days 3 and 7 for A-4. In contrast, for A+4, the weak labeling detected at day 3 became stronger at day 7. Dentin sialoprotein (DSP), an in vivo odontoblast marker, was not detectable until day 7 where a few cells became DSP positive after A-4 stimulation, but not for A+4. These results suggest that A +/- 4 promote the proliferation of some pulp cells. Some of them further differentiate into osteoblast-like progenitors, the effects being more precocious for A-4 (day 3) compared with A+4 (day 7). The present data suggest that A +/- 4 promote early recruitment of osteogenic progenitors, and evidence functional differences between A+4 and A-4.