bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Stable Isotopes in Life—Testing Isotopic Resonance Hypothesis
Authors: Zubarev Roman A. 
Published: June 2011

Abstract
Stable isotopes of most important biological elements, such as C, H, N and O, affect living organisms. In rapidly growing species, deuterium and to a lesser extent other heavy isotopes reduce the growth rate. At least for deuterium it is known that its depletion also negatively impacts the speed of biological processes. As a rule, living organisms “resist” changes in their isotopic environment, preferring natural isotopic abundances. This preference could be due to evolutionary optimization; an additional effect could be due to the presence of the “isotopic resonance”. The isotopic resonance phenomenon has been linked to the choice of earliest amino acids, and thus affected the evolution of genetic code. To test the isotopic resonance hypothesis, literature data were analyzed against quantitative and qualitative predictions of the hypothesis. Four studies provided five independent datasets, each in very good quantitative agreement with the predictions. Thus, the isotopic resonance hypothesis is no longer simply plausible; it can now be deemed likely. Additional testing is needed, however, before full acceptance of this hypothesis.
On the Organizational Dynamics of the Genetic Code
Authors: Zhang Zhang , Yu Jun 
Published: June 2011

Abstract
The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides—adenine, thymine, guanine and cytosine—according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.
Identification of Protein-Coding Regions in DNA Sequences Using A Time-Frequency Filtering Approach
Authors: Sahu Sitanshu Sekhar , Panda Ganapati 
Published: June 2011

Abstract
Accurate identification of protein-coding regions (exons) in DNA sequences has been a challenging task in bioinformatics. Particularly the coding regions have a 3-base periodicity, which forms the basis of all exon identification methods. Many signal processing tools and techniques have been applied successfully for the identification task but still improvement in this direction is needed. In this paper, we have introduced a new promising model-independent time-frequency filtering technique based on S-transform for accurate identification of the coding regions. The S-transform is a powerful linear time-frequency representation useful for filtering in time-frequency domain. The potential of the proposed technique has been assessed through simulation study and the results obtained have been compared with the existing methods using standard datasets. The comparative study demonstrates that the proposed method outperforms its counterparts in identifying the coding regions.
TAAPP: Tiling Array Analysis Pipeline for Prokaryotes
Authors: Kumar Ranjit , Burgess Shane C. , Lawrence Mark L. , Nanduri Bindu 
Published: June 2011

Abstract
High-density tiling arrays provide closer view of transcription than regular microarrays and can also be used for annotating functional elements in genomes. The identified transcripts usually have a complex overlapping architecture when compared to the existing genome annotation. Therefore, there is a need for customized tiling array data analysis tools. Since most of the initial tiling arrays were conducted in eukaryotes, data analysis methods are well suited for eukaryotic genomes. For using whole-genome tiling arrays to identify previously unknown transcriptional elements like small RNA and antisense RNA in prokaryotes, existing data analysis tools need to be tailored for prokaryotic genome architecture. Furthermore, automation of such custom data analysis workflow is necessary for biologists to apply this powerful platform for knowledge discovery. Here we describe TAAPP, a web-based package that consists of two modules for prokaryotic tiling array data analysis. The transcript generation module works on normalized data to generate transcriptionally active regions (TARs). The feature extraction and annotation module then maps TARs to existing genome annotation. This module further categorizes the transcription profile into potential novel non-coding RNA, antisense RNA, gene expression and operon structures. The implemented workflow is microarray platform independent and is presented as a web-based service. The web interface is freely available for acedemic use at http://lims.lsbi.mafes.msstate.edu/TAAPP-HTML/.
Undermining the case for evidential atheism
Authors: MOSER PAUL K. 
Published: June 2011

AbstractEvidential atheism, as espoused by various philosophical atheists, recommends belief that God does not exist on the basis of not just the evidence of which we are aware, but also our overall available evidence. This article identifies a widely neglected problem from potential surprise evidence that undermines an attempt to give a cogent justification of such evidential atheism. In addition, it contends that evidential agnosticism fares better than evidential atheism relative to this neglected problem, and that traditional monotheism has evidential resources, unavailable to evidential atheism, which promise to save it from the fate of evidential atheism.
Final compression beamline systems for heavy ion fusion drivers
Authors: Lau Y.Y. , Yu Simon S. , Barnard John J. , Seidl Peter A. 
Published: June 2011

AbstractWe have identified a general final compression section for HIF drivers, the section between accelerator and the target. The beams are given a head to tail velocity tilt at the beginning of the section for longitudinal compression, while going through bends that direct it to the target at specific angle. The aim is to get the beams compressed while maintaining a small centroid off-set after the bends. We used a specific example, 1 MJ driver with 500 MeV Rubidium + 1 ion beams. We studied the effect of minimizing dispersion using different bend strategies, and came up with a beamline point design with adiabatic bends. We also identified some factors that lead to emittance growth as well as the minimum pulse length and spot size on the target.
Self-reproduction for articulated behaviors with dual humanoid robots using on-line decision tree classification
Authors: Zurn Jane Brooks , Motai Yuichi , Vento Scott 
Published: June 2011

SUMMARYWe have proposed a new repetition framework for vision-based behavior imitation by a sequence of multiple humanoid robots, introducing an on-line method for delimiting a time-varying context. This novel approach investigates the ability of a robot “student” to observe and imitate a behavior from a “teacher” robot; the student later changes roles to become the “teacher” for a naïve robot. For the many robots that already use video acquisition systems for their real-world tasks, this method eliminates the need for additional communication capabilities and complicated interfaces. This can reduce human intervention requirements and thus enhance the robots' practical usefulness outside the laboratory. Articulated motions are modeled in a three-layer method and registered as learned behaviors using color-based landmarks. Behaviors were identified on-line after each iteration by inducing a decision tree from the visually acquired data. Error accumulated over time, creating a context drift for behavior identification. In addition, identification and transmission of behaviors can occur between robots with differing, dynamically changing configurations. ITI, an on-line decision tree inducer in the C4.5 family, performed well for data that were similar in time and configuration to the training data but the greedily chosen attributes were not optimized for resistance to accumulating error or configuration changes. Our novel algorithm, OLDEX identified context changes on-line, as well as the amount of drift that could be tolerated before compensation was required. OLDEX can thus identify time and configuration contexts for the behavior data. This improved on previous methods, which either separated contexts off-line, or could not separate the slowly time-varying context into distinct regions at all. The results demonstrated the feasibility, usefulness, and potential of our unique idea for behavioral repetition and a propagating learning scheme.
Long-term experience with 181 patients who received transperineal I-125 implants for prostate cancer: Efficacy and urinary toxicity
Authors: Gez Eliahu , Genesin Joshua , Shahar Daniel , Semenisty Valeriya , Mashiac Tanya , Deroma Rachel Bar , Kakiashvili David , Kuten Abraham , Meretyck Simon 
Published: June 2011

AbstractBackground: In low-risk prostate cancer, the target volume for radiotherapy is the prostate gland only and prostate brachytherapy with an I-125 implant provides the most conformal radiotherapy.Methods: Patients underwent a pre-implant prostate volume study from which a treatment plan was developed 2 weeks prior to implant. A dosimetric study was performed 1 month following the implant. The prescription dose was 145 Gy with the 95% isodose line covering the entire target volume. The maximal dose to the urethra was less than 210 Gy. Follow-up included serum PSA and IPSS evaluation every 3 months during the first year and then every 6 months beginning in the second year.Results: During December 2000–March 2009, 181 patients with early prostate cancer underwent I-125 implant. The median post-implant PSA value of the entire cohort was 0.7 ng/ml. No patient developed clinical failure. In the follow-up, nine patients had biochemical failure according to the RTOG-ASTRO Phoenix definition (Nadir + 2.0 ng/ml). Of these, one patient refused hormonal therapy desiring to preserve sexual potency, and eight patients received hormonal therapy with a decreased serum PSA to 0.0 ng/ml. The treatment side effects were primarily urinary disturbances.Conclusion: An I-125 implant is an effective and well-tolerated treatment and should be recommended for patients with low-risk prostate cancer.
Final report on the Seventh International Comparison of Absolute Gravimeters (ICAG 2005)*
Authors: Jiang Z , Francis O , Vitushkin L , Palinkas V , Germak A , Becker M , D'Agostino G , Amalvict M , Bayer R , Bilker-Koivula M , Desogus S , Faller J , Falk R , Hinderer J , Gagnon C , Jakob T , Kalish E , Kostelecky J , Lee Chiungwu , Liard J , Lokshyn Y , Luck B , Mäkinen J , Mizushima S , Le Moigne N , Origlia C , Pujol E R , Richard P , Robertsson L , Ruess D , Schmerge D , Stus Y , Svitlov S , Thies S , Ullrich C , Van Camp M , Vitushkin A , Ji W , Wilmes H 
Published: June 2011

The Bureau International des Poids et Mesures (BIPM), Sèvres, France, hosted the 7th International Comparison of Absolute Gravimeters (ICAG) and the associated Relative Gravity Campaign (RGC) from August to September 2005.
ICAG 2005 was prepared and performed as a metrological pilot study, which aimed:
(1) To determine the gravity comparison reference values;
(2) To determine the offsets of the absolute gravimeters; and
(3) As a pilot study to accumulate experience for the CIPM Key Comparisons.
This document presents a complete and extensive review of the technical protocol and data processing procedures. The 1st ICAG–RGC comparison was held at the BIPM in 1980–1981 and since then meetings have been organized every 4 years.
In this paper, we present an overview of how the meeting was organized, the conditions of BIPM gravimetric sites, technical specifications, data processing strategy and an analysis of the final results. This 7th ICAG final report supersedes all previously published reports.
Readings were obtained from participating instruments, 19 absolute gravimeters and 15 relative gravimeters. Precise levelling measurements were carried out and all measurements were performed on the BIPM micro-gravity network which was specifically designed for the comparison.
eResponseNet: a package prioritizing candidate disease genes through cellular pathways
Authors: Huang Jialiang , Liu Yi , Zhang Wei , Yu Hong , Han Jing-Dong J. 
Published: June 2011

Abstract
Motivation: Although genome-wide association studies (GWAS) have found many common genetic variants associated with human diseases, it remains a challenge to elucidate the functional links between associated variants and complex traits.
Results: We developed a package called eResponseNet by implementing and extending the existing ResponseNet algorithm for prioritizing candidate disease genes through cellular pathways. Using type II diabetes (T2D) as a study case, we demonstrate that eResponseNet outperforms currently available approaches in prioritizing candidate disease genes. More importantly, the package is instrumental in revealing cellular pathways underlying disease-associated genetic variations.
Availability: The eResponseNet package is freely downloadable at http://hanlab.genetics.ac.cn/eResponseNet.
Contact: jdhan@picb.ac.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
Food and feeding habits of cod (Gadus morhua) on the Faroe Bank
Authors: Magnussen Eyðfinn 
Published: June 2011

AbstractMagnussen, E. 2011. Food and feeding habits of cod (Gadus morhua) on the Faroe Bank. – ICES Journal of Marine Science, 68: 1909–1917. Data from ten bottom surveys on the Faroe Bank during the years 1994–1998 are used to describe the feeding habits of cod on the Faroe Bank. Cod are clearly omnivorous in their diet. Overall, fish were found in 82% of the stomachs, accounting for 59% of the food by weight, but just 35% of the food items by number. Of the fish, lesser sandeel was the most common, making up 78% of the fish biomass consumed. Cannibalism was practically non-existent. In some years, the squid Loligo forbesi formed an important component of the diet, was the main food and identified in up to 64% of the stomachs, and constituting 60% by weight of the diet; in other years, it was a negligible part. Crustaceans were found in 48% of the stomachs, accounting for 16% by weight but as much as 44% by numbers. The diet of cod shifts ontogenetically, with stomach fullness greater and nutrient quality of prey higher for cod <70 cm.
Robert Fabyan and the Nuremberg Chronicle
Authors: Payne M.T.W. 
Published: June 2011

Abstract
This article identifies one of Robert Fabyan's source books, his copy of the Nuremberg Chronicle, which contains extensive notes and annotations in his hand. The volume is among the collections at Guildhall Library, London. The marginal notes are of particular interest, not only for the light they shed on Fabyan's working practice, but also because the similarities with the hands of the extant manuscripts of the latter part of the Great Chronicle of London, and The Newe Cronycles of England and Fraunce (Fabyan's Chronicle), demonstrate Fabyan's involvement in each work. This attribution has been doubted for some time. Fabyan also added interesting ownership and purchase information to the Nuremberg Chronicle.
Maintenance nitrogen requirements of adult female ostriches (Struthio camelus)
Authors: Bennett D. C. , Kaneko A. , Karasawa Y. 
Published: June 2011

SummarySuccessful ostrich farming requires knowledge of the nutritional needs of the birds. While much information is available on the nutritional value of various feed ingredients fed to ostriches, there is little known about their specific nutrient requirements. In this study, we measured the maintenance nitrogen requirements (MNR) of ostriches by nitrogen balance. We predict, based on the previous analysis of nitrogen requirements of various species of birds, that ostriches would have a MNR of 13.6–19.1 g N/day and a total endogenous nitrogen loss (TENL) of 2.8–5.1 g N/day. Three adult female ostriches were fed five pelleted diets containing 0.6–2.3% N [4–14.6% crude protein (CP)], 17.5 kJ/g gross energy (11.4 kJ/g ME) and 30% neutral detergent fibre. Each dietary trial consisted of a 10‐day adaptation period, followed by a 5‐day total excreta collection period. Body mass (109 ± 3 kg) and metabolizable energy intake (20.5 ± 0.7 MJ/day) were unaffected by dietary nitrogen levels. After correcting for excreta nitrogen losses during drying, MNR was calculated to be 481 mg N/kg0.75/day or 16.2 g N/day (100 g CP/day), and TENL as 310 mg N/kg0.75/day or 10.5 g N/day. Failure to correct for the 10.9 ± 4.1% average N losses during drying would underpredict the ‘true’ MNR by 35% and TENL by 46%. Our estimate for MNR of ostriches predicts a dietary requirement of 6.7% protein. Our estimate of TENL was nearly twice that predicted, possibly reflecting the high fibre content of their diet.
Quality of Life and Sexual Health After Sex Reassignment Surgery in Transsexual Men
Authors: Wierckx Katrien , Van Caenegem Eva , Elaut Els , Dedecker David , Van de Peer Fleur , Toye Kaatje , Weyers Steven , Hoebeke Piet , Monstrey Stan , De Cuypere Griet , T’Sjoen Guy 
Published: June 2011

ABSTRACT

Introduction
Although sexual health after genital surgery is an important outcome factor for many transsexual persons, little attention has been attributed to this subject.

Aims
To provide data on quality of life and sexual health after sex reassignment surgery (SRS) in transsexual men.

Methods
A single-center, cross-sectional study in 49 transsexual men (mean age 37 years) after long-term testosterone therapy and on average 8 years after SRS. Ninety-four percent of the participants had phalloplasty.

Main Outcome Measures
Self-reported physical and mental health using the Dutch version of the Short Form-36 Health Survey; sexual functioning before and after SRS using a newly constructed specific questionnaire.

Results
Compared with a Dutch reference population of community-dwelling men, transsexual men scored well on self-perceived physical and mental health. The majority reported having been sexually active before hormone treatment, with more than a quarter having been vaginally penetrated frequently before starting hormone therapy. There was a tendency toward less vaginal involvement during hormone therapy and before SRS. Most participants reported an increase in frequency of masturbation, sexual arousal, and ability to achieve orgasm after testosterone treatment and SRS. Almost all participants were able to achieve orgasm during masturbation and sexual intercourse, and the majority reported a change in orgasmic feelings toward a more powerful and shorter orgasm. Surgical satisfaction was high, despite a relatively high complication rate.

Conclusion
Results of the current study indicate transsexual men generally have a good quality of life and experience satisfactory sexual function after SRS.
Sexual Function in Female Patients with Obstructive Sleep Apnea
Authors: Petersen Marian , Kristensen Ellids , Berg Søren , Giraldi Annamaria , Midgren Bengt 
Published: June 2011

ABSTRACT

Introduction
Obstructive sleep apnea is defined as repetitive (≥5/hour) partial or complete cessation of breathing during sleep. Whereas obstructive sleep apnea is often considered to be associated with sexual problems in men, studies concerning effects of obstructive sleep apnea on female sexual function and distress are sparse.

Aim
To investigate sexual dysfunction and sexual distress in female patients with obstructive sleep apnea and to determine which factors are of importance for their sexual function.

Methods
We investigated 80 female patients (ages 28–64) admitted to a sleep laboratory and who after investigation received a diagnosis of obstructive sleep apnea. All subjects answered questions drawn from three self-administered questionnaires on sexuality. The results were compared with a population sample (N = 240).

Main Outcome Measure
Data from nocturnal respiratory recordings. Female Sexual Function Index, Female Sexual Distress Scale and four questions from Life Satisfaction-11 (Lisat-11).

Results
Female Sexual Function Index indicated that obstructive sleep apnea patients were at a higher risk for having sexual difficulties. Female Sexual Distress Scale showed significantly more sexual distress in the obstructive sleep apnea group. Manifest Female Sexual Dysfunction (combined data from Female Sexual Function Index and Female Sexual Distress Scale) showed that female patients with obstructive sleep apnea also had more sexual dysfunction. Severity of sleep apnea was, however, not related to any of these indices but consumption of psychopharmaca was. In Lisat-11, we found that obstructive sleep apnea females scored lower than women in the population sample regarding life as a whole but not regarding domains of closeness.

Conclusions
This study indicates that sexuality of women with untreated obstructive sleep apnea is negatively affected compared with a female population sample. This was not related to severity of obstructive sleep apnea, whereas psychopharmaca may act as an important confounder.
Effect of Periodontitis on Erectile Function and Its Possible Mechanism
Authors: Zuo Zili , Jiang Jun , Jiang Rui , Chen Feng , Liu Junxiang , Yang Haifan , Cheng Yong 
Published: June 2011

ABSTRACT

Introduction
Periodontitis is one of the important risk factors resulting in cardiovascular diseases. Erectile dysfunction (ED) is strongly correlated with cardiovascular diseases. The expression of endothelial nitric oxide synthase (eNOS) in penile tissue has an important role in the mechanism of erection.

Aim
To investigate the effect of periodontitis on erectile function and the possible mechanism.

Methods
After induction of periodontitis in rat, the ratio of maximum intracavernosal pressure/mean arterial pressure (ICPmax/MAP) × 100, the expression of eNOS in penile tissue, the level of serum C-reactive protein (CRP) and tumor necrosis factor-α (TNF-α), and the ultrastructural changes of the cavernous tissue were examined and compared between periodontitis rats (group A) and control rats (group B).

Main Outcome Measure
Periodontitis significantly decrease not only the ICPmax/MAP × 100 and the expression of eNOS but also the activity of NOS and the level of cyclic guanosine monophosphate (cGMP) in cavernous tissue of rat.

Results
After electrostimulation by 3 and 5 voltage, the ratio of ICPmax/MAP × 100 in group A was significantly less than that in group B (19.54 ± 6.16 vs. 30.45 ± 3.12; 30.91 ± 5.61 vs. 50.52 ± 9.52, respectively; P &lt; 0.05).The level of serum CRP and TNF-α in group A is significantly higher in group B (P &lt; 0.05).The quantitative real-time reverse transcription polymerase chain reaction study demonstrated no statistically significant difference in the expression of mRNA of eNOS in cavernous tissue between the two groups (P &gt; 0.05).But there was significant decrease in eNOS protein of the cavernous tissue in group A than in group B (P &lt; 0.05). Total NOS activity and cGMP level in cavernosal tissue were significantly lower in group A than in group B (P &lt; 0.05). There was no significant alternation occurred in the ultrastructures of penile cavernous tissue.

Conclusions
The function of penile erection is impaired by periodontitis. The decreased in the expression of eNOS and NOS activity in penile cavernous tissue caused by mild systemic inflammatory status in periodontitis may be one of the important risk factors of ED.