bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of codon selection in regulation of translation efficiency deduced from synthetic libraries
Authors: Navon Sivan , Pilpel Yitzhak 
Published: February 2011

Abstract
Background
Translation efficiency is affected by a diversity of parameters, including secondary structure of the transcript and its codon usage. Here we examine the effects of codon usage on translation efficiency by re-analysis of previously constructed synthetic expression libraries in Escherichia coli.

Results
We define the region in a gene that takes the longest time to translate as the bottleneck. We found that localization of the bottleneck at the beginning of a transcript promoted a high level of expression, especially if the computed dwell time of the ribosome within this region was sufficiently long. The location and translation time of the bottleneck were not correlated with the cost of expression, approximated by the fitness of the host cell, yet utilization of specific codons was. Particularly, enhanced usage of the codons UCA and CAU was correlated with increased cost of production, potentially due to sequestration of their corresponding rare tRNAs.

Conclusions
The distribution of codons along the genes appears to affect translation efficiency, consistent with analysis of natural genes. This study demonstrates how synthetic biology complements bioinformatics by providing a set-up for well controlled experiments in biology.
Physical and Psychosocial Recovery in the Year After Primary Treatment of Breast Cancer
Authors: Ganz Patricia A. , Kwan Lorna , Stanton Annette L. , Bower Julienne E. , Belin Thomas R. 
Published: February 2011

Purpose The 2000 National Institutes of Health Consensus Conference on Adjuvant Therapy of Breast Cancer recommended chemotherapy for all women with invasive cancer greater than 1 centimeter. Studies of long-term breast cancer survivors have found poorer quality of life (QOL) in women who received adjuvant chemotherapy. The aim of this article is to characterize physical and psychosocial recovery as a function of chemotherapy receipt in the year after medical treatment completion. Patients and Methods Prospective longitudinal survey data (RAND SF-36 and Breast Cancer Prevention Trial [BCPT] Symptom Scales) collected from 558 women with breast cancer enrolled on the Moving Beyond Cancer (MBC) psychoeducational intervention trial were compared according to receipt of chemotherapy. MBC study enrollment occurred within 4 weeks after the end of primary treatment (eg, surgery, chemotherapy, radiation). Self-report questionnaire data collected at enrollment and at 2, 6, and 12 months thereafter were examined, controlling for intervention and with propensity score adjustment for imbalance of covariates. Outcome analyses were carried out by fitting linear mixed models by using SAS PROC MIXED. Results Longitudinal SF-36 scale scores did not differ by chemotherapy treatment exposure, and both groups improved significantly (P < .01) in the year after primary treatment ended. However, adjuvant chemotherapy treatment was associated with significantly more severe physical symptoms, including musculoskeletal pain (P = .01), vaginal problems (P < .01), weight problems (P = .01), and nausea (P = .03). Conclusion Physical and psychosocial functioning improved significantly after breast cancer treatment, independent of receipt of adjuvant chemotherapy. Women who received chemotherapy experienced more severe and persistent physical symptoms that should be more effectively managed as part of survivorship care.
Phase I/II Study of Pemetrexed With or Without ABT-751 in Advanced or Metastatic Non–Small-Cell Lung Cancer
Authors: Rudin Charles M. , Mauer Ann , Smakal Martin , Juergens Rosalyn , Spelda Stanislav , Wertheim Michael , Coates Andrew , McKeegan Evelyn , Ansell Peter , Zhou Xiangdong , Qian Jane , Pradhan Rajendra , Dowell Barry , Krivoshik Andrew , Gordon Gary 
Published: February 2011

Purpose ABT-751 is an antimitotic and vascular disrupting agent with potent preclinical anticancer activity. We conducted a phase I and randomized double-blind phase II study of pemetrexed with ABT-751 or placebo in patients with recurrent advanced or metastatic non–small-cell lung cancer (NSCLC). Methods One hundred seventy-one patients received intravenous pemetrexed 500 mg/m2 day 1 and oral ABT-751 or placebo days 1 to 14 of 21-day cycles. The primary end point was progression-free survival (PFS). Secondary end point included overall survival (OS); pharmacokinetic and pharmacodynamic parameters were also analyzed. Results The recommended phase II dose of ABT-751 with pemetrexed is 200 mg. Fatigue, constipation, anemia, nausea, and diarrhea were the most common toxicities in both study arms. No pharmacokinetic interactions were observed. Median PFS in the ABT-751 arm was 2.3 months versus 1.9 for placebo (P = .819, log-rank) for the intention-to-treat population. However, differences in PFS (P = .112, log-rank) and OS (P = .034, log-rank; median 3.3 v 8.1 months) favoring ABT-751 were seen in the squamous NSCLC subgroup. Baseline circulating tumor cell concentrations were predictive of improved OS (P = .013). Changes from baseline of greater than 20% in plasma levels of placenta growth factor (P = .056), squamous cell carcinoma antigen (P = .03), and cytokeratin 19 fragment antigen 21-1 (P = .01) were markers best associated with improved OS. Conclusion Addition of ABT-751 to pemetrexed is well-tolerated, but does not improve outcome in unselected patients with recurrent NSCLC. ABT-751 may have therapeutic potential in squamous NSCLC. Exploratory cellular and molecular analyses in this study identified biomarkers that may correlate with survival.
Features Predicting Sentinel Lymph Node Positivity in Merkel Cell Carcinoma
Authors: Schwartz Jennifer L. , Griffith Kent A. , Lowe Lori , Wong Sandra L. , McLean Scott A. , Fullen Douglas R. , Lao Christopher D. , Hayman James A. , Bradford Carol R. , Rees Riley S. , Johnson Timothy M. , Bichakjian Christopher K. 
Published: February 2011

Purpose Merkel cell carcinoma (MCC) is a relatively rare, potentially aggressive cutaneous malignancy. We examined the clinical and histologic features of primary MCC that may correlate with the probability of a positive sentinel lymph node (SLN). Methods Ninety-five patients with MCC who underwent SLN biopsy at the University of Michigan were identified. SLN biopsy was performed on 97 primary tumors, and an SLN was identified in 93 instances. These were reviewed for clinical and histologic features and associated SLN positivity. Univariate associations between these characteristics and a positive SLN were tested for by using either the χ2 or the Fisher's exact test. A backward elimination algorithm was used to help create a best multiple variable model to explain a positive SLN. Results SLN positivity was significantly associated with the clinical size of the lesion, greatest horizontal histologic dimension, tumor thickness, mitotic rate, and histologic growth pattern. Two competing multivariate models were generated to predict a positive SLN. The histologic growth pattern was present in both models and combined with either tumor thickness or mitotic rate. Conclusion Increasing clinical size, increasing tumor thickness, increasing mitotic rate, and infiltrative tumor growth pattern were significantly associated with a greater likelihood of a positive SLN. By using the growth pattern and tumor thickness model, no subgroup of patients was predicted to have a lower than 15% to 20% likelihood of a positive SLN. This suggests that all patients presenting with MCC without clinical evidence of regional lymph node disease should be considered for SLN biopsy.
Performance Evaluation of Recycled PMA Binders Containing Warm Mix Asphalt Additives
Authors: Kim Hakseo , Lee Soon-Jae , Amirkhanian Serji N. , Park Tae-Soon 
Published: February 2011

Abstract
The performance properties of recycled polymer modified asphalt (PMA) binders containing warm mix asphalt (WMA) additives at high, intermediate, and low temperatures were evaluated. First, each combination of two PMA binders (performance grade (PG) 76-22 from two different sources) and two WMA additives (i.e., Aspha-min® and Sasobit®) were blended to produce warm PMA binders. They were then artificially short-term and long-term aged through the rolling thin film oven and pressure aging vessel procedures. Second, long-term aged warm PMA binders were recycled using two virgin binders (PG 76-22 and PG 70-22), and the recycled binders were artificially aged again. Lastly, Superpave binder tests were performed through the rotational viscometer, the dynamic shear rheometer (DSR), and the bending beam rheometer (BBR). In general, the results of this study suggested that (1) the WMA additives and the aged PMA binders were found to have a significant influence on the performance properties of recycled binders (measured by the DSR and the BBR); (2) the use of PG 70-22 as a virgin binder was effective in offsetting the increase of binder stiffness due to the additives and the aged binders; and (3) the recycled warm PMA binders can result in satisfactory binder performance that meets current Superpave binder requirements.
Efficient Tool Replacement Procedure Based on Yield Evaluation
Authors: Lin Chen-ju , Pearn W. L. 
Published: February 2011

Abstract
Tool wear is an inevitable problem in many machining processes. The problem constitutes an inseparable component of variation and can be considered as a systematic assignable cause of process variability. Tool replacement should be initiated when the yield drops below a certain level. Determining the best time for tool replacement is essential to balance between production quality and tool utilization. The yield index, Spk, has been effectively applied to assess the yield of processes. However, its ordinary measure is inaccurate when data is contaminated by inseparable nonrandom variation. Yield evaluation becomes imprecise when a process is subjected to the tool wear problem. Thus, this paper presents an efficient procedure that determines the best time to replace tools under an extremely low fraction of defectives. The variation from assignable causes is removed by using the linear regression technique. A modified estimator of the Spk index with its distribution is proposed to evaluate the processes with the tool wear problem.
Flood, Disaster, and Turmoil: Social Issues in Cleft and Craniofacial Care and Crisis Relief
Authors: Strauss Ronald P. , Van Aalst John A. , Fox Lynn , Stein Margot , Moses Michael , Cassell Cynthia H. 
Published: February 2011

Objective To examine social issues in the conduct of cleft and craniofacial care through relief programs in disrupted crisis contexts. Method Social, health policy, and ethical analyses. Results At best, craniofacial team care is multidisciplinary, coordinated, and sustained, requiring a long-term relationship between team members, patients, and families. Disasters and societal turmoil interrupt such relationships, causing craniofacial care to become a secondary concern. Providing craniofacial team care in a crisis setting requires rebuilding disrupted coordination and communication. Crisis relief care involves a complex set of expectations and responsibilities and raises issues such as (1) quality assurance, infection control, appropriate standards of care, and follow-up care/continuity; (2) equity of access to services and clinical ethics in the context of war and/or deprivation; (3) training of visitors in the local nation or site; (4) disciplinary composition of teams, interprofessional communication/rivalry, and credentials of clinicians; (5) ownership of the site and local visitor relations; (6) fundraising and marketing strategies; and (7) ethical issues in the doctor-patient relationship. Conclusions Specific ethical standards for international cleft and craniofacial care delivery also apply to domestic and global crisis relief contexts. Guidance on issues related to professional experience, informed consent, and continuity of care will help care providers address social and ethical issues raised in crisis relief programs. This paper proposes that the Position Paper of the American Cleft Palate-Craniofacial Association (ACPA) on International Treatment Programs should be used as a template to develop and disseminate a set of standards that apply to crisis relief.
Simultaneous Increase in Gas and Liquid Relative Permeabilities and Reduction of High-Velocity Coefficient From Wettability Alteration
Authors: Wu Stanley , Firoozabadi Abbas 
Published: February 2011

Summary
The alteration of the wettability from liquid-wetting to intermediate gas-wetting results in improved liquid mobility, which has been demonstrated by a number of authors in recent years. In this work, we show that the gas-phase mobility may either increase or decrease in the state of intermediate gas-wetting. The increase or decrease in the gas-phase mobility is a function of the minimum liquid saturation. We also confirm that, as a result of the wettability alteration, there may be a substantial decrease in the two-phase high-velocity coefficient compared to the unaltered wettability state. The increase in the gas- and liquid-phase relative permeabilities and a decrease in the high-velocity coefficient of the two-phase flow from the wettability alteration contribute to improved gas well productivity.
Study of Diffusivity of Hydrocarbon Solvent in Heavy-Oil Saturated Sands Using X-Ray Computer Assisted Tomography
Authors: Luo Hongtao , Kantzas Apostolos 
Published: February 2011

Summary
Hydrocarbon solvent-assisted processes are thought to be effective EOR technologies for heavy oil and bitumen production. In order to describe those processes quantitatively, the diffusivity of hydrocarbon solvent in oil sands is a crucial required parameter.
Computer-assisted tomography (CAT), as a nonintrusive method, is a useful tool to obtain the physical properties of cores (density, porosity, heterogeneities) and the fluids within the cores (saturation or concentration profiles). However, the concentration profiles obtained from diffusion experiments of solvent in oil sands were fluctuating and could not be used to evaluate the diffusivity. In order to solve the problem, during the data processing of CAT scanning, porosity heterogeneity of porous media and volume changes on mixing are considered to improve the accuracy of concentration profiles dramatically. Subsequently, the diffusivity of hydrocarbon solvent in heavy-oil saturated sands is determined based on an updated mathematical model, which considers porosity heterogeneity of porous media in the major diffusion direction and volume changes on mixing. Thus, the diffusivity as a function of concentration and porosity is evaluated precisely and the impact of porosity heterogeneity of porous media on diffusivity determination of hydrocarbon solvent in heavy-oil saturated sands is investigated.
Identification of Metabolic Modifiers That Underlie Phenotypic Variations in Energy-Balance Regulation
Authors: Chang Chia Lin , Cai James J. , Cheng Po Jen , Chueh Ho Yen , Hsu Sheau Yu Teddy 
Published: February 2011

OBJECTIVE
Although recent studies have shown that human genomes contain hundreds of loci that exhibit signatures of positive selection, variants that are associated with adaptation in energy-balance regulation remain elusive. We reasoned that the difficulty in identifying such variants could be due to heterogeneity in selection pressure and that an integrative approach that incorporated experiment-based evidence and population genetics-based statistical judgments would be needed to reveal important metabolic modifiers in humans.

RESEARCH DESIGN AND METHODS
To identify common metabolic modifiers that underlie phenotypic variation in diabetes-associated or obesity-associated traits in humans, or both, we screened 207 candidate loci for regulatory single nucleotide polymorphisms (SNPs) that exhibited evidence of gene–environmental interactions.

RESULTS
Three SNPs (rs3895874, rs3848460, and rs937301) at the 5′ gene region of human GIP were identified as prime metabolic-modifier candidates at the enteroinsular axis. Functional studies have shown that GIP promoter reporters carrying derived alleles of these three SNPs (haplotype GIP−1920A) have significantly lower transcriptional activities than those with ancestral alleles at corresponding positions (haplotype GIP−1920G). Consistently, studies of pregnant women who have undergone a screening test for gestational diabetes have shown that patients with a homozygous GIP−1920A/A genotype have significantly lower serum concentrations of glucose-dependent insulinotropic polypeptide (GIP) than those carrying an ancestral GIP−1920G haplotype. After controlling for a GIPR variation, we showed that serum glucose concentrations of patients carrying GIP−1920A/A homozygotes are significantly higher than that of those carrying an ancestral GIP−1920G haplotype (odds ratio 3.53).

CONCLUSIONS
Our proof-of-concept study indicates that common regulatory GIP variants impart a difference in GIP and glucose metabolism. The study also provides a rare example that identified the common variant-common phenotypic variation pattern based on evidence of moderate gene–environmental interactions.
Function of coprophagous beetles (Coleoptera: Scarabaeidae, Geotrupidae, Hydrophilidae) in cattle pastures inferred from pitfall trapping data
Authors: Šlachta Martin , Frelich Jan , Tonka Tomáš 
Published: February 2011

Function of coprophagous beetles (Coleoptera: Scarabaeidae, Geotrupidae, Hydrophilidae) in cattle pastures inferred from pitfall trapping dataAn analysis of data on the dry weight biomass of coprophagous beetles in standardized dung (4.5 l) was conducted in order to characterize the spatial and the seasonal distribution of the beetles' biomass in cattle pastures and to elucidate their function in dung decomposition. Nested Anova with factors of farm, site (nested in farm), seasonal period and year was used to evaluate the effect of these factors on the biomass of four functional species groups: the dung dwellers ofScarabaeidae(subfamilyAphodiinae), the dung dwellers ofHydrophilidae, the small tunnellers ofScarabaeidae(subfamilyCoprinae) and the large tunnellers ofGeotrupidae. The spatial variation of biomass (between the sites and the farms) was insignificant (P>0.05) in the two dung-dweller groups and in the large-tunnellers group. On the other hand, a significant (P<0.05) seasonal variation of biomass was found in all but the large tunneller group. In dung dwellers, the spring biomass was formed mainly by two species,Aphodius prodromusandA. sphacelatus. In summer, most of the biomass was accounted for bySphaeridium lunatum, S. scarabaeoidesandA. rufipes. In the two tunneller groups,Onthophagus fracticornis, Geotrupes stercorariusandG. spinigerformed a majority of the biomass in dung.
Results of robotic milking on selected farms in the Czech Republic
Authors: Voříšková Jarmila , Maršálek Miroslav , Reichová Sandra , Zedníková Jana , Machálek Antonín 
Published: February 2011

Results of robotic milking on selected farms in the Czech RepublicThe introduction of robotic milking into farms in the Czech Republic began in 2003. This paper gives the results on 7 farms with robotic milking machines, with regard to breed (Bohemia Spotted cattle, Holstein), company size (number of robots 1 to 8) and type of ownership (private, cooperative). All farms used Lely Astronaut A3 robots. The companies showed statistical differences in average daily milk performance (P≤0.001) from 21.04 kg of milk/head/day to 40.43 kg of milk/head/day. Small private companies with one robot reached significantly (P≤0.001) higher milk performance of 28.79 kg of milk/head/day. On average, the daily milk performances of the Holstein cattle were 7.17 kg of milk higher than those of the Bohemia Spotted cattle (29.97 kg and 22.80 kg, respectively). The average number of milkings per head and day in individual companies ranged from 1.97 to 2.67. The average number of rejections per head and day (1.11) was low in companies with one robot and is influenced by the number of cows per one robot. The highest number of cows that had to be accompanied to the robot could be seen in large cooperatives - 20.1%. Bohemia Spotted cattle showed the lowest number of breeding-cows needing to be accompanied to the robot (8.8%).
Contribution to the diversity of soil mites (Acari, Gamasida) in southern Croatia (Dalmatia), with some ecological and zoogeographical notes
Authors: Kaczmarek Sławomir , Marquardt Tomasz 
Published: February 2011

Contribution to the diversity of soil mites (Acari, Gamasida) in southern Croatia (Dalmatia), with some ecological and zoogeographical notes
The species diversity of soil gamasid mites (Acari) in southern Croatia (Dalmatia) was studied in August 2002. In the Krka National Park, Brač Island, and near the town of Makarska, 320 samples were collected from various microhabitats: soil, grass and moss ground cover, wet moss, needle litter, moss covering tree trunks, and decaying wood). Altogether, 2097 mites of 56 gamasid species were recorded. Dominant species were: Polyaspis patavinus (Brač Island), Zercon fageticola (Makarska), and Cheiroseius serratus (Krka National Park). Analyses of ecological preferences and zoogeographic distribution were made for Polyaspis patavinus, Cheiroseius serratus, Zercon fageticola, Z. berlesei, Z. athiasi, Asca nova and A. aphidioides.
Le port de pêche des Sables-d'Olonne au cours de la période 1982-1990
Authors: Bouhier Abel 
Published: February 2011

ABSTRACT
The fishing port of Les Sables-d'Olonne was regarded by Philippe Fournet as a particularly dynamic port during the 1973-1981 period. The detailed study of the 1982-1990 period concerning the amount and the nature of the catch, the composition and the possibilities of the fishing fleet, the conditions of commissioning, the aspects of the commercialization and the characteristics of professional structures, permit to assert that during the 1982-1990 period the port kept all its activity, but rather serious difficulties began to appear in some areas.
Contribution à l'étude des cavités naturelles dans les argiles
Authors: Couderc Jean-Marie 
Published: February 2011

RÉSUMÉ
Sur les argiles-à-silex (et parfois les dépôts alluviaux argilo-sableux) se produisent, souvent au passage d'engins agricoles des effondrements brutaux laissant apparaître des cavités de 4 à 10 m de diamètre et de 2 à 6 m de profondeur, de forme cylindrique ou en cloche. Situées, en général, non loin du rebord des versants, ces cavités sont liées au lent entraînement par l'eau des particules argileuses en direction, soit des conduits du karst, soit des fissures de distention nées dans les calcaires sous-jacents après le creusement quaternaire des vallées.
Dynamique sédimentaire dans les baies de Lancieux et de l'Arguenon (Côte-d'Armor)
Authors: Vaucourt C , Bonnot-Courtois C 
Published: February 2011

RÉSUMÉ
L'estuaire de l'Arguenon et la baie de Lancieux sont situés dans le Golfe de Saint-Malo, au sud du Golfe normand-breton dans une région où les agents dynamiques sont particulièrement efficaces. Cependant, la position d'abri qu'offre le cap Fréhel à ces baies les protège de la circulation dominante d'ouest, d'où une sédimentation essentiellement constituée de vase et de sables fins. Dans l'estuaire de l'Arguenon, la sédimentation fine est renforcée par la présence d'installations conchylicoles à son embouchure, ce qui, en freinant la propagation des agents hydrodynamiques, accentue la tendance à l'envasement déjà sensible dans la partie amont de l'estuaire ; à ce premier impact, purement mécanique, s'ajoute un impact biologique dû aux rejets des mollusques.
Vivre au quotidien dans un espace périurbain : l'exemple de celui de Saintes
Authors: Morin Frédéric 
Published: February 2011

RÉSUMÉ
La périurbanisation favorise l'amélioration des équipements de la région de Saintes. La pratique sportive se développe et les fêtes attirent de plus en plus de monde avec l'aide d'associations et d'élus plus dynamiques. En revanche, le paysage politique change peu, la région restant favorable à la gauche.