bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sarcopenia is not due to lack of regenerative drive in senescent skeletal muscle
Authors: Edström Erik , Ulfhake Brun 
Published: March 2005

SummarySarcopenia, loss of skeletal muscle mass, is a hallmark of aging commonly attributed to a decreased capacity to maintain muscle tissue in senescence, yet the mechanism behind the muscle wasting remains unresolved. To address these issues we have explored a rodent model of sarcopenia and age‐related sensorimotor impairment, allowing us to discriminate between successfully and unsuccessfully aged cohort members. Immunohistochemistry and staining of cell nuclei revealed that senescent muscle has an increased density of cell nuclei, occurrence of aberrant fibers and fibers expressing embryonic myosin. Using real‐time PCR we extend the findings of increased myogenic regulatory factor mRNA to show that very high levels are found in unsuccessfully aged cohort members. This pattern is also reflected in the number of embryonic myosin‐positive fibers, which increase with the degree of sarcopenia. In addition, we confirm that there is no local down‐regulation of IGF‐I and IGF‐IR mRNA in aged muscle tissue; on the contrary, the most sarcopenic individuals showed significantly higher local expression of IGF‐I mRNA. Combined, our results show that the initial drive to regenerate myofibers is most marked in cases with the most advanced loss of muscle mass, a pattern that may have its origin in differences in the rate of tissue deterioration and/or that regenerating myofibers in these cases fail to mature into functional fibers. Importantly, the genetic background is a determinant of the pace of progression of sarcopenia.
Assessment of systemic inflammation markers to differentiate a stable from a deteriorating clinical course in patients with febrile neutropenia
Authors: Persson Lennart , Söderquist Bo , Engervall Per , Vikerfors Tomas , Hansson Lars‐Olof , Tidefelt Ulf 
Published: March 2005

Abstract:In this study, we evaluated the predictive values of procalcitonin (PCT), C‐reactive protein (CRP), interleukin‐6 (IL‐6) and serum amyloid A (SAA) for determining the clinical course in febrile neutropenic patients. Daily plasma analyses during the fever course were performed in 101 episodes with fever and chemotherapy‐induced neutropenia (neutrophil count <0.5 × 109/L). Procalcitonin (PCT) and IL‐6 values were significantly higher in febrile episodes in patients who developed complications. Procalcitonin with a cut‐off value of ≤0.4 ng/mL or IL‐6 ≤50 pg/mL 3 d after fever onset indicated daily high negative predictive values (NPVs) (91–100%) for episodes with complications. No marker could predict deterioration; however, daily low plasma concentrations of PCT or IL‐6 during the first 8 d of fever were found to be a good predictor of no subsequent complications in neutropenic patients and therefore to be a helpful tool for limiting anti‐microbial therapy.
T‐DNA Integration Category and Mechanism in Rice Genome
Authors: WANG Jiang , LI Lin , SHI Zhen‐Ying , WAN Xin‐Shan , AN Lin‐Sheng , ZHANG Jing‐Liu 
Published: March 2005

Abstract: T‐DNA integration is a key step in the process of plant transformation, which is proven to be important for analyzing T‐DNA integration mechanism. The structures of T‐DNA right borders inserted into the rice (Oryza sativa L.) genome and their flanking sequences were analyzed. It was found that the integrated ends of the T‐DNA right border occurred mainly on five nucleotides “TGACA” in inverse repeat (IR) sequence of 25 bp, especially on the third base “A”. However, the integrated ends would sometimes lie inward of the IR sequence, which caused the IR sequence to be lost completely. Sometimes the right integrated ends appeared on the vector sequences rightward of the T‐DNA right border, which made the T‐DNA, carrying vector sequences, integrated into the rice genome. These results seemingly suggest that the IR sequence of the right border plays an important role in the process of T‐DNA integration into the rice genome, but is not an essential element. The appearance of vector sequences neighboring the T‐DNA right border suggested that before being transferred into the plant cell from Agrobacterium, the entire T‐DNA possibly began from the left border in synthesis and then read through at the right border. Several nucleotides in the T‐DNA right border homologous with plant DNA and filler DNAs were frequently discovered in the integrated position of T‐DNA. Some small regions in the right border could match with the plant sequence, or form better matches, accompanied by the occurrence of filler DNA, through mutual twisting, and then the T‐DNA was integrated into plant chromosome through a partially homologous recombination mechanism. The appearance of filler DNA would facilitate T‐DNA integration. The fragments flanking the T‐DNA right border in transformed rice plants could derive from different parts of the inner T‐DNA region; that is, disruption and recombination could occur at arbitrary positions in the entire T‐DNA, in which the homologous area was comparatively easier to be disrupted. The structure of flanking sequences of T‐DNA integrated in the rice chromosome presented various complexities. These complexities were probably a result of different patterns of recombination in the integrating process. Some types of possible integrating mechanism are detailed.(Managing editor: Li‐Hui ZHAO)
Isolation of a Mutant of Fer1 Gene, Acting Synergistically with the ARF8 Gene to Control Development of the Anther and Filament in Arabidopsis
Authors: TIAN Chang‐En , ZHOU Yu‐Ping , LIU Shun‐Zhi , YAMAMOTO Kotaro 
Published: March 2005

Abstract: Auxin response factors (ARFs) play a central role in plants as transcriptional factors in response to auxin. The Arabidopsis ARF8 gene is a light‐inducible gene and ARF8 protein might control auxin homeostasis in a negative feed‐back fashion through regulation of GH3 gene expression. In a double mutant designated infertile line including arf8‐1 (a T‐DNA insertion mutant of ARF8), we isolated fertility1‐1 (fer1‐1), a mutant of Fer1, which acts synergistically with ARF8 to control the development of the anther and filament in Arabidopsis. Genetics analysis has demonstrated that fer 1‐1 is a T‐DNA insertion line, indicating that Fer1 might be cloned by inverse polymerase chain reaction (PCR) or the TAIL‐PCR approach. Phenotypic identification and molecular analysis of fer 1‐1 and the infertile line will be helpful to characterize the function of Fer1, to further study the function of ARF8, and to reveal the molecular mechanism underlying the interaction of Fer1 and ARF8 in controlling development of the anther and filament.(Managing editor: Li‐Hui ZHAO)
Carbon Dioxide Exchange Between the Atmosphere and an Alpine Shrubland Meadow During the Growing Season on the Qinghai‐Tibetan Plateau
Authors: ZHAO Liang , LI Ying‐Nian , GU Song , ZHAO Xing‐Quan , XU Shi‐Xiao , YU Gui‐Rui 
Published: March 2005

Abstract: In the present study, we used the eddy covariance method to measure CO2 exchange between the atmosphere and an alpine shrubland meadow ecosystem (37°36’N, 101°18’E; 3 250 m a.s.l.) on the Qinghai‐Tibetan Plateau, China, during the growing season in 2003, from 20 April to 30 September. This meadow is dominated by formations of Potentilla fruticosa L. The soil is Mol‐Cryic Cambisols. During the study period, the meadow was not grazed. The maximum rates of CO2 uptake and release derived from the diurnal course of CO2 flux were ‐9.38 and 5.02 μmol·m‐2·s‐1, respectively. The largest daily CO2 uptake was 1.7 g C·m‐2·d‐1 on 14 July, which is less than half that of an alpine Kobresia meadow ecosystem at similar latitudes. Daily CO2 uptake during the measurement period indicated that the alpine shrubland meadow ecosystem may behave as a sink of atmospheric CO2 during the growing season. The daytime CO2 uptake was correlated exponentially or linearly with the daily photo synthetic photon flux density each month. The daytime average water use efficiency of the ecosystem was 6.47 mg CO2/g H2O. The efficiency of the ecosystem increased with a decrease in vapor pressure deficit.(Managing editor: Ya‐Qin HAN)
The Triggering Procedure of the International Criminal Court, Procedural Treatment of the Principle of Complementarity, and the Role of Office of the Prosecutor
Authors: Olásolo Héctor 
Published: March 2005

AbstractThis article addresses the most fundamental procedural issues arising from Arts. 13, 14, 15, 18 and 53(1), (2) and (4) of the ICC Statute (hereinafter “the Rome Statute” or “RS”). It first analyses the reasons why the proceedings provided for in those articles constitute, referred to in this article as “Triggering Procedure”, within the complex procedural system provided for in the ICC Statute, an autonomous procedure whose object, parties and proceedings are perfectly distinguishable from the object, parties and proceedings of the Criminal and Civil Procedures. Once the relationship between the Triggering Procedure and the Criminal and Civil Procedures is introduced, the article analyses the procedural treatment of the principle of complementarity in the different procedures provided for in the ICC Statute. Finally, the last part of the article brie fly addresses the key role of the Of fice of the Prosecutor in the Triggering Procedure, and the duties imposed upon the competent Chamber of the Court to control, propio motu or at the request of a party to the proceedings, that the Of fice of the Prosecutor is acting within the powers granted to it by the RS and fully respecting the substantive and procedural standards set out by the RS.
TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
Authors: Garrow Andrew G , Agnew Alison , Westhead David R 
Published: March 2005

Abstract
Background
Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discriminating between bbtm proteins and other proteins, screening of entire genomes remains troublesome as these molecules only constitute a small fraction of the sequences screened. Therefore, novel methods are still required capable of detecting new families of bbtm protein in diverse genomes.

Results
We present TMB-Hunt, a program that uses a k-Nearest Neighbour (k-NN) algorithm to discriminate between bbtm and non-bbtm proteins on the basis of their amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, an accuracy of 92.5% was achieved, with 91% sensitivity and 93.8% positive predictive value (PPV), using a rigorous cross-validation procedure.
A major advantage of this approach is that because it does not rely on beta-strand detection, it does not require resolved structures and thus larger, more representative, training sets could be used. It is therefore believed that this approach will be invaluable in complementing other, physicochemical and homology based methods. This was demonstrated by the correct reassignment of a number of proteins which other predictors failed to classify. We have used the algorithm to screen several genomes and have discussed our findings.

Conclusion
TMB-Hunt achieves a prediction accuracy level better than other approaches published to date. Results were significantly enhanced by use of evolutionary information and a system for calibrating k-NN scoring. Because the program uses a distinct approach to that of other discriminators and thus suffers different liabilities, we believe it will make a significant contribution to the development of a consensus approach for bbtm protein detection.
A dual fluorescent multiprobe assay for prion protein genotyping in sheep
Authors: Van Poucke Mario , Vandesompele Jo , Mattheeuws Marc , Van Zeveren Alex , Peelman Luc J 
Published: March 2005

Abstract
Background
Scrapie and BSE belong to a group of fatal, transmissible, neurodegenerative diseases called TSE. In order to minimize the risk of natural scrapie and presumed natural BSE in sheep, breeding programmes towards TSE resistance are conducted in many countries based on resistance rendering PRNP polymorphisms at codons 136 (A/V), 154 (R/H) and 171 (R/H/Q). Therefore, a reliable, fast and cost-effective method for routine PRNP genotyping in sheep, applicable in standard equipped molecular genetic laboratories, will be a vital instrument to fulfill the need of genotyping hundreds or thousands of sheep.

Methods
A dual fluorescent multiprobe assay consisting of 2 closed tube PCR reactions containing respectively 4 and 3 dual-labelled fluorescent ASO probes for the detection in real-time of the 7 allelic variants of sheep PRNP mentioned above.

Results
The assay is succesfully performed using unpurified DNA as a template for PCR, without any post-PCR manipulations and with semi-automatic determination of the PRNP genotypes. The performance of the assay was confirmed via PCR-RFLP and sequencing in a cross-validation study with 50 sheep.

Conclusions
We report the development and validation of a robust, reliable and reproducible method for PRNP genotyping of a few to many sheep samples in a fast, simple and cost-effective way, applicable in standard equipped molecular genetic laboratories. The described primer/probe design strategy can also be applied for the detection of other polymorphisms or disease causing mutations.
Public access defibrillation: Suppression of 16.7 Hz interference generated by the power supply of the railway systems
Authors: Christov Ivaylo I , Iliev Georgi L 
Published: March 2005

Abstract

Background
A specific problem using the public access defibrillators (PADs) arises at the railway stations. Some countries as Germany, Austria, Switzerland, Norway and Sweden are using AC railroad net power-supply system with rated 16.7 Hz frequency modulated from 15.69 Hz to 17.36 Hz. The power supply frequency contaminates the electrocardiogram (ECG). It is difficult to be suppressed or eliminated due to the fact that it considerably overlaps the frequency spectra of the ECG. The interference impedes the automated decision of the PADs whether a patient should be (or should not be) shocked.
The aim of this study is the suppression of the 16.7 Hz interference generated by the power supply of the railway systems.

Methods
Software solution using adaptive filtering method was proposed for 16.7 Hz interference suppression. The optimal performance of the filter is achieved, embedding a reference channel in the PADs to record the interference. The method was tested with ECGs from AHA database.

Results
The method was tested with patients of normal sinus rhythms, symptoms of tachycardia and ventricular fibrillation. Simulated interference with frequency modulation from 15.69 Hz to 17.36 Hz changing at a rate of 2% per second was added to the ECGs, and then processed by the suggested adaptive filtering. The method totally suppresses the noise with no visible distortions of the original signals.

Conclusion
The proposed adaptive filter for noise suppression generated by the power supply of the railway systems has a simple structure requiring a low level of computational resources, but a good reference signal as well.
Localization of the immunodominant region on human thyroid peroxidase in autoimmune thyroid diseases: an update
Authors: Bresson Damien , Rebuffat Sandra A , Péraldi-Roux Sylvie 
Published: March 2005

Abstract
Recent studies in the field of autoimmune thyroid diseases have largely focused on the delineation of B-cell auto-epitopes recognized by the main autoantigens to improve our understanding of how these molecules are seen by the immune system. Among these autoantigens which are targeted by autoantibodies during the development of autoimmune thyroid diseases, thyroid peroxidase is a major player. Indeed, high amounts of anti-thyroid peroxidase autoantibodies are found in the sera of patients suffering from Graves' disease and Hashimoto's thyroiditis, respectively hyper and hypothyroidism. Since anti-thyroid peroxidase autoantibodies from patients'sera mainly recognize a discontinuous immunodominant region on thyroid peroxidase and due to the complexity of the three dimensional structure of human thyroid peroxidase, numerous investigations have been necessary to closely localize this immunodominant region. The aim of the present review is to summarize the current knowledge regarding the localization of the immunodominant region recognized by human thyroid peroxidase-specific autoantibodies generated during the development of autoimmune thyroid diseases.
Bacteriophages: The viruses for all seasons of molecular biology
Authors: Karam Jim D 
Published: March 2005

AbstractBacteriophage research continues to break new ground in our understanding of the basic molecular mechanisms of gene action and biological structure. The abundance of bacteriophages in nature and the diversity of their genomes are two reasons why phage research brims with excitement. The pages of Virology Journal will reflect the excitement of the "New Phage Biology."
Contribution of transcriptional regulation to natural variations in Arabidopsis
Authors: Chen Wenqiong J , Chang Sherman H , Hudson Matthew E , Kwan Wai-King , Li Jingqiu , Estes Bram , Knoll Daniel , Shi Liang , Zhu Tong 
Published: March 2005

Abstract
Background
Genetic control of gene transcription is a key component in genome evolution. To understand the transcriptional basis of natural variation, we have studied genome-wide variations in transcription and characterized the genetic variations in regulatory elements among Arabidopsis accessions.

Results
Among five accessions (Col-0, C24, Ler, WS-2, and NO-0) 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis. Two-way ANOVA analysis has identified 60 genes whose mRNA levels differed in different accession backgrounds in an organ-dependent manner. Most of these genes were involved in stress responses and late stages of plant development, such as seed development. Correlation analysis of expression patterns of these 7,508 genes between pairs of accessions identified a group of 65 highly plastic genes with distinct expression patterns in each accession.

Conclusion
Genes that show substantial genetic variation in mRNA level are those with functions in signal transduction, transcription and stress response, suggesting the existence of variations in the regulatory mechanisms for these genes among different accessions. This is in contrast to those genes with significant polymorphisms in the coding regions identified by genomic hybridization, which include genes encoding transposon-related proteins, kinases and disease-resistance proteins. While relatively fewer sequence variations were detected on average in the coding regions of these genes, a number of differences were identified from the upstream regions, several of which alter potential cis-regulatory elements. Our results suggest that nucleotide polymorphisms in regulatory elements of genes encoding controlling factors could be primary targets of natural selection and a driving force behind the evolution of Arabidopsis accessions.
Pilot Anopheles gambiaefull-length cDNA study: sequencing and initial characterization of 35,575 clones
Authors: Gomez Shawn M , Eiglmeier Karin , Segurens Beatrice , Dehoux Pierre , Couloux Arnaud , Scarpelli Claude , Wincker Patrick , Weissenbach Jean , Brey Paul T , Roth Charles W 
Published: March 2005

AbstractWe describe the preliminary analysis of over 35,000 clones from a full-length enriched cDNA library from the malaria mosquito vector Anopheles gambiae. The clones define nearly 3,700 genes, of which around 2,600 significantly improve current gene definitions. An additional 17% of the genes were not previously annotated, suggesting that an equal percentage may be missing from the current Anopheles genome annotation.
Evaluation of Some Adjuvants for Improving Glyphosate Efficacy
Authors: Singh S , Singh M 
Published: March 2005

Abstract
Glyphosate is the most common non-selective post-emergence herbicide used under diverse conditions. The efficacy of foliar applied herbicides is greatly influenced by adjuvants, but not all adjuvants have a synergistic effect. Greenhouse experiments were conducted using weed species of Echinochola crus-galli, Panicum maximum, Bidens pilosa, and Abutilon theophrasti to evaluate glyphosate efficacy by tank mixing with 0.5 % of Blaze®, Condition®, Improve®, and Induce®. Glyphosate at 0, 0.14, 0.28, and 0.56 kg ae/ha alone and with adjuvants was sprayed at the 4 leaf stage of weeds. Surface tension and contact angle were measured under lab conditions.
Adjuvants increased the activity of glyphosate by 15–29 % compared to glyphosate alone. Among the weed species, higher mortality was observed in P. maximum and B. pilosa followed by E. crus-galli and lowest in A. theophrasti. On mortality of grass and broadleaf weed species, significant differences were observed by tank mixing glyphosate with different adjuvants. Lowest Contact Angle (CA) and Surface Tension (ST) were recorded when glyphosate (Rodeo®, with no surfactant) was mixed with Improve and Blaze surfactants, which was significantly lower than glyphosate formulation pre-mixed with surfactant (Roundup UltraMax®). In the case of Condition, the relative decrease in CA was less than ST when added to glyphosate, compared to Improve and Blaze. Lower ST and CA of glyphosate tank mixed with Improve and Blaze correlated with improved weed mortality in the activity study.
Improving the Effectiveness of Aerial Pesticide Sprays
Authors: Smith DB , Kirk IW , Ross JB 
Published: March 2005

Abstract
Thirty-eight aircraft setups were submitted in order to have droplet size and drift analyses performed. Four of the eleven insecticides predicted Dv0.5s were in the 351–400 µm range. Seven of the herbicide setups had predicted Dv0.5s in the 205–250 µm range, while ten Dv0.5s were &gt; 351 µm. Five of the ten predicted Dv0.5s were between 386 and 413 μm. Twelve different herbicides were reported as having been applied with aircraft setups that had predicted Dv0.5s between 386 and 413 µm. A summary of the prior swath deposit data indicated that the percent recovery generally increased as the Dv0.5 increased. The magnitudes of the deposits on inert targets and cotton leaves appeared to be about equal for a given Dv0.5. The correlation coefficient between the “percent of the spray volume in droplets ≤100 µm and ≤200 µm in diameter” was 0.983. This result is consistent with prior results and indicates that either 100 or 200 µm can be effectively used as the upper limit when studying the “small droplet” component in sprays. We found several similarities or differences in the “small droplet” components based on data from different atomization tests. According to one set of atomization models, agricultural aircraft will be limited to about 225 km/h (i.e., 140 mph) in order to produce a 400 µm Dv0.5 spray when using currently available nozzles and water plus one or more pesticides. The extremes of the predicted drift deposits for 38 agricultural aircraft setups were over 30-fold apart.