bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray
Authors: von Schalburg Kristian R , Rise Matthew L , Cooper Glenn A , Brown Gordon D , Gibbs A Ross , Nelson Colleen C , Davidson William S , Koop Ben F 
Published: September 2005

Abstract

Background
We have developed and fabricated a salmonid microarray containing cDNAs representing 16,006 genes. The genes spotted on the array have been stringently selected from Atlantic salmon and rainbow trout expressed sequence tag (EST) databases. The EST databases presently contain over 300,000 sequences from over 175 salmonid cDNA libraries derived from a wide variety of tissues and different developmental stages. In order to evaluate the utility of the microarray, a number of hybridization techniques and screening methods have been developed and tested.

Results
We have analyzed and evaluated the utility of a microarray containing 16,006 (16K) salmonid cDNAs in a variety of potential experimental settings. We quantified the amount of transcriptome binding that occurred in cross-species, organ complexity and intraspecific variation hybridization studies. We also developed a methodology to rapidly identify and confirm the contents of a bacterial artificial chromosome (BAC) library containing Atlantic salmon genomic DNA.

Conclusion
We validate and demonstrate the usefulness of the 16K microarray over a wide range of teleosts, even for transcriptome targets from species distantly related to salmonids. We show the potential of the use of the microarray in a variety of experimental settings through hybridization studies that examine the binding of targets derived from different organs and tissues. Intraspecific variation in transcriptome expression is evaluated and discussed. Finally, BAC hybridizations are demonstrated as a rapid and accurate means to identify gene content.
Mycelium development in Streptomyces antibioticus ATCC11891 occurs in an orderly pattern which determines multiphase growth curves
Authors: Manteca Angel , Fernandez Marisol , Sanchez Jesus 
Published: September 2005

AbstractBackgroundThe current model for the developmental cycle ofStreptomycesconfluent cultures on agar surface is based on the assumption that the only differentiation takes place along the transverse axis (bottom-up): a vegetative (substrate) mycelium grows completely live and viable on the surface and inside the agar until it undergoes a death process and differentiates to a reproductive (aerial) mycelium which grows into the air. Hence, this vertical description assumes that the development in the pre-sporulating phases is more or less homogeneous in all zones of the plate surface.ResultsThe work presents a detailed analysis of the differentiation cycle inStreptomyces antibioticusATCC11891 considering a different spatial dimension: the longitudinal axes, represented by the plate surface. A previously unsuspected complexity during the substrate mycelial phase was detected. We have demonstrated that the young substrate hyphae suffer an early death round that has not been previously described. Subsequently, the remaining mycelium grows in successive waves which vary according to the density of the spore inoculum. In the presence of dense inocula (1.5 × 106spores per plate), the hyphae develop in regular circles, approximately 0.5 cm in diameter. By contrast, with highly diluted inocula (6 × 103spores per plate), aerial mycelium develops initially in the form of islands measuring 0.9 mm in diameter. Further mycelial development occurs between the circles or islands until the plate surface is totally covered. This pattern persists throughout the entire developmental cycle including the sporulation phases.ConclusionAn early death round during the substrate mycelial phase ofStreptomyces antibioticusATCC11891 takes place prior to successive growth periods in surface cultures. These developmental periods in turn, determine the shape of the complex multiphase growth curves observed. As shown here, these results also apply to otherStreptomycesstrains and species. Understanding these peculiarities of theStreptomycesdevelopmental cycle is essential in order to properly interpret the morphological/biochemical data obtained from solid cultures and will expand the number of potential phenotypes subject to study.
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods
Authors: Martin Juliette , Letellier Guillaume , Marin Antoine , Taly Jean-François , de Brevern Alexandre G , Gibrat Jean-François 
Published: September 2005

Abstract

Background
A number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure.

Methods
To address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures).

Results
A detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior.

Conclusion
Our method provides valuable assignments which favor the regularity of secondary structure segments.
A situational picture of HIV/AIDS and injection drug use in Vinnitsya, Ukraine
Authors: Barcal Katerina , Schumacher Joseph E , Dumchev Kostyantyn , Moroz Larisa Vasiliyevna 
Published: September 2005

Abstract
Background
New and explosive HIV epidemics are being witnessed in certain countries of Eastern Europe, including Ukraine, as well as a rapid and dramatic increase in the supply, use, and negative public health consequences of illicit drugs. A majority of registered HIV cases in Ukraine occur among injection drug users (IDUs), large numbers of whom report HIV risk behaviors such as needle sharing. The purpose of this study was to apply the World Health Organization's Rapid Assessment and Response on Injection Drug Use (IDU-RAR) guide to create a situational picture in the Vinnitsya Oblast, Ukraine, a region with very scarce information about the HIV/AIDS and injection drug use (IDU) epidemics.

Methods
The IDU-RAR uses a combination of qualitative data collection techniques commonly employed in social science and evaluation research to quickly depict the extent and nature of the given health problem and propose locally relevant recommendations for improvement. The investigators focused their assessment on the contextual factors, drug use, and intervention and policy components of the IDU-RAR. A combination of network and block sampling techniques was used. Data collection methods included direct observation, review of existing data, structured and unstructured interviews, and focus group discussions. Key informants and locations were visited until no new information was being generated.

Results
The number of registered HIV cases in Vinnitsya has increased from 3 (1987–1995) to 860 (1999–10/2004), 57 of whom have already died. Ten percent of annual admissions to the area's Regional Narcological Dispensary were for opiate disorders, and the number of registered IDUs rose by 20% from 1999 to 2000. The level of HIV/AIDS awareness is generally poor among the general population but high among high-risk populations. Both HIV/AIDS and injection drug use carry a strong stigma in the community, even among medical professionals. There was very little evidence of primary HIV/AIDS prevention efforts, and IDU prevention efforts focused on promotion of anti-drug messages in the schools.

Conclusion
Given that Ukraine has sparse resources to be devoted to this problem, action recommendations should be prioritized, realistic, and initially targeted to persons in greatest need. The following action recommendations are prioritized by the following categories: First priority: Voluntary Counseling and Testing; Second Priority: Prevention and Education; and Third Priority: Harm Reduction and Treatment. They are provided in this sequence based on what response can realistically be implemented first with limited additional resources and can make the greatest immediate impact. The persons at greatest risk, HIV positive persons and IDUs, should be attended to first.
Immunologic aspect of ovarian cancer and p53 as tumor antigen
Authors: Nijman HW , Lambeck A , van der Burg SH , van der Zee AGJ , Daemen T 
Published: September 2005

AbstractOvarian cancer represents the fifth leading cause of death from all cancers for women. During the last decades overall survival has improved due to the use of new chemotherapy schedules. Still, the majority of patients die of this disease. Research reveals that ovarian cancer patients exhibit significant immune responses against their tumor. In this review the knowledge obtained thus far on the interaction of ovarian cancer tumor cells and the immune system is discussed. Furthermore the role of p53 as tumor antigen and its potential role as target antigen in ovarian cancer is summarized. Based on the increased knowledge on the role of the immune system in ovarian cancer major improvements are to be expected of immunotherapy based treatment of this disease.
The HTLV-1 Tax protein binding domain of cyclin-dependent kinase 4 (CDK4) includes the regulatory PSTAIRE helix
Authors: Fraedrich Kirsten , Müller Birthe , Grassmann Ralph 
Published: September 2005

AbstractBackgroundThe Tax oncoprotein of human T-cell leukemia virus type 1 (HTLV-1) is leukemogenic in transgenic mice and induces permanent T-cell growthin vitro. It is found in active CDK holoenzyme complexes from adult T-cell leukemia-derived cultures and stimulates the G1- to-S phase transition by activating the cyclin-dependent kinase (CDK) CDK4. The Tax protein directly and specifically interacts with CDK4 and cyclin D2 and binding is required for enhanced CDK4 kinase activity. The protein-protein contact between Tax and the components of the cyclin D/CDK complexes increases the association of CDK4 and its positive regulatory subunit cyclin D and renders the complex resistant to p21CIPinhibition. Tax mutants affecting the N-terminus cannot bind cyclin D and CDK4.ResultsTo analyze, whether the N-terminus of Tax is capable of CDK4-binding,in vitrobinding -, pull down -, and mammalian two-hybrid analyses were performed. These experiments revealed that a segment of 40 amino acids is sufficient to interact with CDK4 and cyclin D2. To define a Tax-binding domain and analyze how Tax influences the kinase activity, a series of CDK4 deletion mutants was tested. Different assays revealed two regions which upon deletion consistently result in reduced binding activity. These were isolated and subjected to mammalian two-hybrid analysis to test their potential to interact with the Tax N-terminus. These experiments concurrently revealed binding at the N- and C-terminus of CDK4. The N-terminal segment contains the PSTAIRE helix, which is known to control the access of substrate to the active cleft of CDK4 and thus the kinase activity.ConclusionSince the N- and C-terminus of CDK4 are neighboring in the predicted three-dimensional protein structure, it is conceivable that they comprise a single binding domain, which interacts with the Tax N-terminus.
Immunolocalization of RANKL is Increased and OPG Decreased During Dietary Magnesium Deficiency in the Rat
Authors: Rude Robert K , Gruber Helen E , Wei Livia Y , Frausto Angelica 
Published: September 2005

Abstract

Background
Epidemiological studies have linked low dietary magnesium (Mg) to low bone mineral density and osteoporosis. Mg deficiency in animal models has demonstrated a reduction in bone mass and increase in skeletal fragility. One major mechanism appears to be an increase in osteoclast number and bone resorption. The final pathway of osteoclastogenesis involves three constituents of a cytokine system: receptor activator of nuclear factor kB ligand (RANKL); its receptor, receptor activator of nuclear factor kB (RANK); and its soluble decoy receptor, osteoprotegerin (OPG). The relative presence of RANKL and OPG dictates osteoclastogenesis. The objective of this study was to assess the presence of RANKL and OPG in rats on a low Mg diet.

Methods
RANKL and OPG were assessed by immunocytochemistry staining in the tibia for up to 6 months in control rats on regular Mg intake (0.5 g/kg) and experimental rats on reduction of dietary Mg (.04%, 25% and 50% of this Nutrient Requirement).

Results
At all dietary Mg intakes, alteration in the presence of immunocytochemical staining of RANKL and OPG was observed. In general, OPG was decreased and RANKL increased, reflecting an alteration in the RANKL/OPG ratio toward increased osteoclastogenesis.

Conclusion
We have, for the first time demonstrated that a reduction in dietary Mg in the rat alters the presence of RANKL and OPG and may explain the increase in osteoclast number and decrease in bone mass in this animal model. As some of these dietary intake reductions in terms of the RDA are present in a large segment of or population, Mg deficiency may be another risk factor for osteoporosis.
Vapor Pressure Measurements of LiI + C2H5OH Solutions
Authors: Safarov Javid T. 
Published: September 2005

Abstract
Vapor pressure p of LiI + C2H5OH solutions at T = (298.15 to 323.15) K were measured by the static method. The osmotic Φ and activity coefficients γ and activity of solvent a
s have been evaluated. The experiments were carried out in molality range m = (0.34523 to 8.61859) mol kg−1. The Antoine equation for the empiric description of experimental vapor pressure results and the Pitzer–Mayorga model with inclusion of Archer's ionic strength dependence of the third virial coefficient for the description of calculated osmotic coefficients were used. The parameters of Archer extended Pitzer model was used for evaluation of activity coefficients.
Characterization and drainage kinetics of colloidal gas aphrons
Authors: Bhatia Divesh , Goel Gaurav , Bhimania Sidhartha K. , Bhaskarwar Ashok N. 
Published: September 2005

AbstractThe variation of air holdup and stability of colloidal gas aphrons (CGAs) with stirring time, surfactant concentration [6, 8.1, 10, and 12 mM sodium lauryl sulfate (SLS)], and stirring speed (3500–7000 rpm) was investigated, and an empirical correlation between the air holdup and stirring time was obtained. A first‐order model for the drainage of CGAs was proposed and it correlated very well with the experimental data. A population balance model was proposed and correlated to the first‐order drainage model to obtain an expression for the size distribution of CGA bubbles. A narrower size distribution at large stirring times was observed, which was correlated to the stability of CGAs. The stabilization of CGA dispersion with attainment of equilibrium size distribution at longer stirring times, analogous to homogenization of emulsions, was observed and an empirical expression for this time was reported. Mixing of two oppositely charged CGAs, generated using SLS (anionic) and cetyl trimethyl ammonium bromide (CTAB) (cationic), showed no effect on their stability, air holdup, and drainage kinetics. © 2005 American Institute of Chemical Engineers AIChE J, 2005
Measurement of flow in microfluidic networks with micrometer‐sized flow restrictors
Authors: Bao Jian‐Bin , Jed Harrison D. 
Published: September 2005

AbstractThe fluid dynamics in micrometer‐sized flow restrictors was evaluated, to test the predictions of the Hagen–Poiseuille equation in small microchip devices. A photobleaching, time‐of‐flight linear flow rate measurement method was developed for the evaluation of flow in slot‐shaped channels with at least one dimension in the size range of 1–3 μm. For a linear flow rate range in the narrowest dimension of 0.3 to 16 mm/s (volumetric flow rates of 0.6 to 32 nL/s, maximum Reynolds number of 0.3), observed flow rates agreed with theoretical predictions within experimental error (2–3%). An empirical equation for the geometric form factor of a D‐shaped channel was developed, providing a useful working curve for use of the Hagen–Poiseuille equation in microfluidics design. The Hagen–Poiseuille solution can be used to design multiport devices with intersecting flow channel networks, achieving the intended flow rate ratios in channels with differing flow resistance with an accuracy of 1–2%. Despite the differences between achieved etched dimensions and the nominal design values a deviation of only 1–4% in the flow ratios was also achieved. This observation provides a useful guideline for predicting tolerance sensitivity in device manufacture. © 2005 American Institute of Chemical Engineers AIChE J, 2006
A model for bubble–bubble and bubble–wall interaction in bubble formation
Authors: Xiao Zongyuan , Tan Reginald B. H. 
Published: September 2005

AbstractA theoretical model for bubble formation at a submerged orifice has been developed, which takes into account the interaction between the column wall and the growing bubble at the orifice, as well as the interaction between subsequent bubbles formed and detached from the orifice. Experiments involving high‐speed photography and bubble frequency measurements were carried out with different chamber volumes, column and orifice diameters, and gas flow. In particular, it was found that decreasing the column diameter (that is, increasing the bubble–wall interaction) led to increased bubble–bubble interaction, as evidenced by a greater tendency for pairing and multiple bubbling. Simulated results using the theoretical model agreed very well with experimental data. © 2005 American Institute of Chemical Engineers AIChE J, 2006
Assay of urinary α‐fluoro‐β‐alanine by gas chromatography–mass spectrometry for the biological monitoring of occupational exposure to 5‐fluorouracil in oncology nurses and pharmacy technicians
Authors: Rubino Federico Maria , Verduci Cinzia , Buratti Marina , Fustinoni Silvia , Campo Laura , Omodeo‐Salè Emanuela , Giglio Margherita , Iavicoli Sergio , Brambilla Gabri , Colombi Antonio 
Published: September 2005

AbstractThe validation of an analytical method for the measurement of the unnatural amino acid α‐fluoro‐β‐alanine (AFBA), the main metabolite of the antineoplastic drug 5‐fluorouracil (5FU), in urine for the biological monitoring of the exposure of hospital workers to the drug when preparing the therapeutical doses and administering to cancer patients is described. The method employed a two‐step extractive derivatization of the analyte from urine to the N‐trifluoroacety‐n‐butyl ester derivative and detection by selected‐ion monitoring gas chromatography–mass spectrometry of structurally specific fragments. The limit of detection was 20 ng/mL with quantification accuracy better than ±20% and precision (CV%) better than ±20% in the range 0.020–10 µg/mL. Norleucine was used as the internal standard and the sample‐to‐sample analysis time was less than 15 min. The validated method has been applied to the biological monitoring of some hospital workers potentially exposed to 5FU and to matched control subjects. On a total number of 65 analyzed urine samples from control and exposed subjects, only three, obtained from exposed subjects, were found to be positive, with values of 20, 30 and 1150 ng/mL, respectively. Copyright © 2005 John Wiley & Sons, Ltd.
Entropy‐based motion extraction for motion capture animation
Authors: So Clifford K. F. , Baciu George 
Published: September 2005

AbstractIn this paper, we present a new segmentation solution for extracting motion patterns from motion capture data by searching for critical keyposes in the motion sequence. A rank is established for critical keyposes that identifies the significance of the directional change in motion data. The method is based on entropy metrics, specifically the mutual information measure. Displacement histograms between frames are evaluated and the mutual information metric is employed in order to calculate the inter‐frame dependency. The most significant keypose identifies the largest directional change in the motion data. This will have the lowest mutual information level from all the candidate keyposes. Less significant keyposes are then listed with higher mutual information levels. The results show that the method has higher sensitivity in the directional change than methods based on the magnitude of the velocity alone. This method is intended to provide a summary of a motion clip by ranked keyposes, which is highly useful in motion browsing and motion retrieve database system. Copyright © 2005 John Wiley & Sons, Ltd.
A feature‐based approach to facial expression cloning
Authors: Park Bongcheol , Chung Heejin , Nishita Tomoyuki , Shin Sung Yong 
Published: September 2005

AbstractIn this paper, we present a feature‐based approach to cloning facial expressions from an input face model to an output model, using predefined source key‐models and the corresponding target key‐models. Adopting a scattered data interpolation technique, our approach consists of two parts: analysis of face key‐models and synthesis of facial expressions. In the analysis part carried out once at the beginning, key‐models are segmented automatically into five regions, each containing one of five facial features, that is, eyes, cheeks, and the mouth, which give rise to five sets of source key‐shapes and the corresponding sets of target key‐shapes. Using the key‐shapes of each source feature, those of the corresponding target feature are parameterized. In the synthesis part, given a sequence of face models comprising an input animation, five output features are obtained separately by blending their own target key‐shapes. These separately produced features are combined to synthesize the output face model at each frame. Our feature‐based approach enables cloning of diverse expressions including asymmetric ones convincingly with a small number of face key‐models while exhibiting an on‐line, real‐time performance. Copyright © 2005 John Wiley & Sons, Ltd.