bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental Memory from a Circadian Oscillator: The Arabidopsis thaliana Clock Differentially Integrates Perception of Photic vs. Thermal Entrainment
Authors: Boikoglou Eleni , Ma Zisong , von Korff Maria , Davis Amanda M , Nagy Ferenc , Davis Seth J 
Published: August 2011

Abstract
The constraint of a rotating earth has led to the evolution of a circadian clock that drives anticipation of future environmental changes. During this daily rotation, the circadian clock of Arabidopsis thaliana (Arabidopsis) intersects with the diurnal environment to orchestrate virtually all transcriptional processes of the plant cell, presumably by detecting, interpreting, and anticipating the environmental alternations of light and temperature. To comparatively assess differential inputs toward phenotypic and physiological responses on a circadian parameter, we surveyed clock periodicity in a recombinant inbred population modified to allow for robust periodicity measurements after entrainment to respective photic vs. thermal cues, termed zeitgebers. Lines previously thermally entrained generally displayed reduced period length compared to those previously photically entrained. This differential zeitgeber response was also detected in a set of diverse Arabidopsis accessions. Thus, the zeitgebers of the preceding environment direct future behavior of the circadian oscillator. Allelic variation at quantitative trait loci generated significant differences in zeitgeber responses in the segregating population. These were important for periodicity variation dependent on the nature of the subsequent entrainment source. Collectively, our results provide a genetic paradigm for the basis of environmental memory of a preceding environment, which leads to the integrated coordination of circadian periodicity.
Study Designs for Identification of Rare Disease Variants in Complex Diseases: The Utility of Family-Based Designs
Authors: Ionita-Laza Iuliana , Ottman Ruth 
Published: August 2011

Abstract
The recent progress in sequencing technologies makes possible large-scale medical sequencing efforts to assess the importance of rare variants in complex diseases. The results of such efforts depend heavily on the use of efficient study designs and analytical methods. We introduce here a unified framework for association testing of rare variants in family-based designs or designs based on unselected affected individuals. This framework allows us to quantify the enrichment in rare disease variants in families containing multiple affected individuals and to investigate the optimal design of studies aiming to identify rare disease variants in complex traits. We show that for many complex diseases with small values for the overall sibling recurrence risk ratio, such as Alzheimer’s disease and most cancers, sequencing affected individuals with a positive family history of the disease can be extremely advantageous for identifying rare disease variants. In contrast, for complex diseases with large values of the sibling recurrence risk ratio, sequencing unselected affected individuals may be preferable.
Translation Initiation: A Regulatory Role for Poly(A) Tracts in Front of the AUG Codon in Saccharomyces cerevisiae
Authors: Xia Xuhua , MacKay Vivian , Yao Xiaoquan , Wu Jianhua , Miura Fumihito , Ito Takashi , Morris David R 
Published: August 2011

Abstract
The 5′-UTR serves as the loading dock for ribosomes during translation initiation and is the key site for translation regulation. Many genes in the yeast Saccharomyces cerevisiae contain poly(A) tracts in their 5′-UTRs. We studied these pre-AUG poly(A) tracts in a set of 3274 recently identified 5′-UTRs in the yeast to characterize their effect on in vivo protein abundance, ribosomal density, and protein synthesis rate in the yeast. The protein abundance and the protein synthesis rate increase with the length of the poly(A), but exhibit a dramatic decrease when the poly(A) length is ≥12. The ribosomal density also reaches the lowest level when the poly(A) length is ≥12. This supports the hypothesis that a pre-AUG poly(A) tract can bind to translation initiation factors to enhance translation initiation, but a long (≥12) pre-AUG poly(A) tract will bind to Pab1p, whose binding size is 12 consecutive A residues in yeast, resulting in repression of translation. The hypothesis explains why a long pre-AUG poly(A) leads to more efficient translation initiation than a short one when PABP is absent, and why pre-AUG poly(A) is short in the early genes but long in the late genes of vaccinia virus.
Estimating Contemporary Effective Population Size on the Basis of Linkage Disequilibrium in the Face of Migration
Authors: Waples Robin S , England Phillip R 
Published: August 2011

Abstract
Effective population size (Ne) is an important genetic parameter because of its relationship to loss of genetic variation, increases in inbreeding, accumulation of mutations, and effectiveness of selection. Like most other genetic approaches that estimate contemporary Ne, the method based on linkage disequilibrium (LD) assumes a closed population and (in the most common applications) randomly recombining loci. We used analytical and numerical methods to evaluate the absolute and relative consequences of two potential violations of the closed-population assumption: (1) mixture LD caused by occurrence of more than one gene pool, which would downwardly bias N^e, and (2) reductions in drift LD (and hence upward bias in N^e) caused by an increase in the number of parents responsible for local samples. The LD method is surprisingly robust to equilibrium migration. Effects of mixture LD are small for all values of migration rate (m), and effects of additional parents are also small unless m is high in genetic terms. LD estimates of Ne therefore accurately reflect local (subpopulation) Ne unless m &gt; ∼5–10%. With higher m, N^e converges on the global (metapopulation) Ne. Two general exceptions were observed. First, equilibrium migration that is rare and hence episodic can occasionally lead to substantial mixture LD, especially when sample size is small. Second, nonequilibrium, pulse migration of strongly divergent individuals can also create strong mixture LD and depress estimates of local Ne. In both cases, assignment tests, Bayesian clustering, and other methods often will allow identification of recent immigrants that strongly influence results. In simulations involving equilibrium migration, the standard LD method performed better than a method designed to jointly estimate Ne and m. The above results assume loci are not physically linked; for tightly linked loci, the LD signal from past migration events can persist for many generations, with consequences for Ne estimates that remain to be evaluated.
Organization of the Synaptonemal Complex During Meiosis in Caenorhabditis elegans
Authors: Schild-Prüfert Kristina , Saito Takamune T , Smolikov Sarit , Gu Yanjie , Hincapie Marina , Hill David E , Vidal Marc , McDonald Kent , Colaiácovo Monica P 
Published: August 2011

Abstract
Four different SYP proteins (SYP-1, SYP-2, SYP-3, and SYP-4) have been proposed to form the central region of the synaptonemal complex (SC) thereby bridging the axes of paired meiotic chromosomes in Caenorhabditis elegans. Their interdependent localization suggests that they may interact within the SC. Our studies reveal for the first time how these SYP proteins are organized in the central region of the SC. Yeast two-hybrid and co-immunoprecipitation studies show that SYP-1 is the only SYP protein that is capable of homotypic interactions, and is able to interact with both SYP-2 and SYP-3 directly, whereas SYP-2 and SYP-3 do not seem to interact with each other. Specifically, the coiled-coil domain of SYP-1 is required both for its homotypic interactions and its interaction with the C-terminal domain of SYP-2. Meanwhile, SYP-3 interacts with the C-terminal end of SYP-1 via its N-terminal domain. Immunoelectron microscopy analysis provides insight into the orientation of these proteins within the SC. While the C-terminal domain of SYP-3 localizes in close proximity to the chromosome axes, the N-terminal domains of both SYP-1 and SYP-4, as well as the C-terminal domain of SYP-2, are located in the middle of the SC. Taking into account the different sizes of these proteins, their interaction abilities, and their orientation within the SC, we propose a model of how the SYP proteins link the homologous axes to provide the conserved structure and width of the SC in C. elegans.
A Boundary Element BetweenTsixandXistBinds the Chromatin Insulator Ctcf and Contributes to Initiation of X-Chromosome Inactivation
Authors: Spencer Rebecca J , del Rosario Brian C , Pinter Stefan F , Lessing Derek , Sadreyev Ruslan I , Lee Jeannie T 
Published: August 2011

AbstractIn mammals, X-chromosome inactivation (XCI) equalizes X-linked gene expression between XY males and XX females and is controlled by a specialized region known as the X-inactivation center (Xic). The Xic harbors two chromatin interaction domains, one centered around the noncoding Xist gene and the other around the antisense Tsix counterpart. Previous work demonstrated the existence of a chromatin transitional zone between the two domains. Here, we investigate the region and discover a conserved element, RS14, that presents a strong binding site for Ctcf protein. RS14 possesses an insulatory function suggestive of a boundary element and is crucial for cell differentiation and growth. Knocking out RS14 results in compromised Xist induction and aberrant XCI in female cells. These data demonstrate that a junction element between Tsix and Xist contributes to the initiation of XCI.
The TEA Transcription Factor Tec1 Links TOR and MAPK Pathways to Coordinate Yeast Development
Authors: Brückner Stefan , Kern Sandra , Birke Raphael , Saugar Irene , Ulrich Helle D , Mösch Hans-Ulrich 
Published: August 2011

Abstract
In Saccharomyces cerevisiae, the TEA transcription factor Tec1 controls several developmental programs in response to nutrients and pheromones. Tec1 is targeted by the pheromone-responsive Fus3/Kss1 mitogen-activated protein kinase (MAPK) cascade, which destabilizes the transcription factor to ensure efficient mating of sexual partner cells. The regulation of Tec1 by signaling pathways that control cell division and development in response to nutrients, however, is not known. Here, we show that Tec1 protein stability is under control of the nutrient-sensitive target of rapamycin complex 1 (TORC1) signaling pathway via the Tip41-Tap42-Sit4 branch. We further show that degradation of Tec1 upon inhibition of TORC1 by rapamycin does not involve polyubiquitylation and appears to be proteasome independent. However, rapamycin-induced Tec1 degradation depends on the HECT ubiquitin ligase Rsp5, which physically interacts with Tec1 via conserved PxY motives. We further demonstrate that rapamycin and mating pheromone control Tec1 protein stability through distinct mechanisms by targeting different domains of the transcription factor. Finally, we show that Tec1 is a positive regulator of yeast chronological lifespan (CLS), a known TORC1-regulated process. Our findings indicate that in yeast, Tec1 links TORC1 and MAPK signaling pathways to coordinate control of cellular development in response to different stimuli.
Új típusú, retrograd dissectio pancreatoduodenectomia során – korai tapasztalataink
Authors: Kelemen Dezső , Papp Róbert , Horváth Örs Péter 
Published: August 2011

Absztrakt
Szerzők felhívják rá a figyelmet, hogy a pancreascarcinoma miatt végzett műtétek késői eredményei javíthatók az R0 resectiók arányának növelésével. Ennek eléréséhez adhat segítséget egy a pancreasfej eltávolítása során alkalmazható új módszer, amikor a processus uncinatusnál kezdve, caudocranialis irányba (retrograd) történik a dissectio. Ezáltal már az elején látótérbe kerül az arteria mesenterica superior, ami mentén haladva tökéletesebben lehet eltávolítani a peripancreaticus szöveteket, emellett kisebb a vérzés és a nagyérsérülés veszélye is. Szerzők 6 esetük kapcsán is megtapasztalták az említett technikai előnyöket, és valamennyi resectio R0-nak bizonyult a szövettani feldolgozáskor. Irodalmi és saját eredmények alapján ajánlják kipróbálásra a hagyományostól eltérő, retrograd dissectiót carcinoma miatt végzett pancreatoduodenectomia során.
Community Stress, Psychosocial Hazards, and EPA Decision-Making in Communities Impacted by Chronic Technological Disasters
Authors: Couch Stephen R. , Coles Charlton J. 
Published: August 2011

Psychosocial stress has emerged as an important consideration in managing environmental health risks. Stress has adverse impacts on health and may interact with environmental hazards to increase health risk. This article's primary objective was to explore psychosocial stress related to environmental contamination. We hypothesized that knowledge about stress should be used in conjunction with chemical risk assessment to inform environmental risk management decisions. Knowledge of psychosocial stress at contaminated sites began by exploring the relationships among social capital, collective efficacy, and contamination at the community level. We discussed stress at the family and individual levels, focusing on stress proliferation, available resources, and coping styles and mechanisms. We then made recommendations on how to improve the use of information on psychosocial stress in environmental decision-making, particularly in communities facing chronic technological disasters.
Effectiveness of a Household Environmental Health Intervention Delivered by Rural Public Health Nurses
Authors: Butterfield Patricia G. , Hill Wade , Postma Julie , Butterfield Phillip W. , Odom-Maryon Tamara 
Published: August 2011

Objectives. Parents need meaningful and actionable information if they are to reduce household environmental health risks to their children. To address this issue, we tested the effectiveness of a multi-risk social/cognitive intervention on rural low-income parents' (1) environmental health self-efficacy and (2) stage of environmental health precautionary adoption. Methods. Biomarker (lead, cotinine) and household samples (carbon monoxide, radon, mold/mildew, and drinking water contaminants) were collected from 235 families (399 adults, 441 children) in Montana and Washington states. Families were randomly assigned to intervention or control groups; intervention families received 4 visits from public health nurses who provided tailored information and guidance to parents; controls received usual and customary public health services. Results. At 3 months, the intervention group had significantly higher scores on (1) all 6 risk-specific self-efficacy subscales (P < .01), (2) general environmental health self-efficacy (P < .001), (3) 5 of 6 risk-specific precaution adoption subscales (P < .05), and (4) general environmental health precaution adoption (P < .001). Conclusions. The intervention yielded significant improvements in both outcomes. This evidence supported the need for a policy discussion addressing the added value that broadbased public health nurse interventions might bring to children's environmental health.
Drinking Water Infrastructure and Environmental Disparities: Evidence and Methodological Considerations
Authors: VanDerslice James 
Published: August 2011

Potable drinking water is essential to public health; however, few studies have investigated income or racial disparities in water infrastructure or drinking water quality. There were many case reports documenting a lack of piped water or serious water quality problems in low income and minority communities, including tribal lands, Alaskan Native villages, colonias along the United States–Mexico border, and small communities in agricultural areas. Only 3 studies compared the demographic characteristics of communities by the quality of their drinking water, and the results were mixed in these studies. Further assessments were hampered by difficulties linking specific water systems to the sociodemographic characteristics of communities, as well as little information about how well water systems operated and the effectiveness of governmental oversight.
Ethical Issues in Using Children's Blood Lead Levels as a Remedial Action Objective
Authors: Moodie Sue M. , Evans Emily Lorraine 
Published: August 2011

The Environmental Protection Agency measures the success or failure of Superfund site remediation efforts against remedial action objectives (RAOs). RAOs are frequently based on environmental contaminant concentrations, but with lead exposure, blood lead levels from the population at risk are often used. Although childhood lead screening is an important public health tool, an RAO based on child blood lead levels raises ethical concerns: public health efforts that are more reactive than preventive, a blood lead standard (10 μg/dL) that may not be fully protective, the use of a measure whose validity and reliability may be easily compromised, and exacerbation of environmental injustice and systematic disadvantages. The example of Bunker Hill mine, Kellogg, Idaho, allowed an examination of these ethical concerns.
How the In-Situ Combustion Process Works in a Fractured System: 2D Core- and Block-Scale Simulation
Authors: Fadaei H.. , Debenest G.. , Kamp A.M.. M. , Quintard M.. , Renard G.. 
Published: August 2011

Summary
Simulation of an in-situ combustion (ISC) process was performed for a fractured system at core and matrix-block scales. The aim of this work was: (1) To predict the ISC extinction/propagation condition(s), (2) understand the mechanism of oil recovery, and (3) provide some guidelines for ISC upscaling for a fractured system. The study was based on a fine-grid, single-porosity, multiphase, and multicomponent simulation using a thermal reservoir simulator.
First, the simulator was validated for 1D combustion using the corresponding analytical solutions. 2D combustion was validated using experimental results available in the literature. It was found that the grid size should not be larger than the combustion-zone thickness in order for the results to be independent of grid size. ISC in the fractured system was strongly dependent on the oxygen diffusion coefficient, while the matrix permeability played an important role in oil production. The effect of each production mechanism was studied separately whenever it was possible. Oil production is governed mainly by oil drainage because of gravity force, which is enhanced by viscosity reduction; possible pressure-gradient generation in the ISC process seems to have a minor effect. The nature (oil-production rate, saturations distribution, shape of the combustion front) of ISC at core scale was different from that in a single block with surrounding fracture. The important characteristics of different zones (i.e., combustion, coke, and oil zones) at block scale were studied, and some preliminary guidelines for upscaling are presented.
Application of the Bergman-Sutton Method for Determining Blend Viscosity
Authors: Sutton Robert P. , Bergman David F. 
Published: August 2011

Summary
As the petroleum industry accesses more low-gravity-oil resources, modification of viscosity by blending lighter hydrocarbons has become a necessity in order to attain bulk properties that will flow though a pipeline. In the more conventional oil reservoirs, the need to estimate the viscosity of oil blends occurs when reservoir fluids are contaminated with oil-based muds or when production streams from different reservoirs or fields are commingled in a single pipeline. Several methods have appeared in the literature for estimating blend viscosity. All of these methods require a measured viscosity for each component of the blend. The number of viscosity measurements is compounded when the viscosity of the blended mixture is required at several temperatures. Of the viscosity correlations published, the Bergman and Sutton method has the widest range of temperature and oil API gravity and has been consistently demonstrated to provide accurate results over these conditions. This method requires the component specific gravity, the Watson characterization factor (Watson K factor), and temperature to estimate viscosity. By using the proper mixing rules, an estimate of blend viscosity can be made with comparable or improved accuracy over the "best" published methods without the need for individual-component viscosity measurements. A database of 2,059 blend-viscosity measurements from more than 800 mixtures was created to compare the accuracy of the various methods. Viscosity measurements of the individual components in the blends studied exceeded 7,600 data points. A diverse group of mixtures, ranging from light alkane or aromatic pure components to bitumen, diesel, biodiesel, condensate, crude, and assay fractions, was included in this database. Blends comprised the typical binary mixtures but ranged up to a maximum of eight components in the mixture.
The Impact of Rotating Control Devices on the Incidence of Blowouts: A Case Study for Onshore Texas, USA
Authors: Jablonowski C.J.. J. , Podio A.L.. L. 
Published: August 2011

Summary
Rotating control devices (RCDs) are used to provide a closed circulating system. Conventional wisdom suggests that drilling with RCDs improves kick detection and thus that fewer blowouts should occur when this equipment and related practices are deployed. Some insurers require RCDs, based in part on this perception. However, there is no published analysis that demonstrates a definitive link between the use of RCDs and the incidence of blowouts. In this paper, the authors use regression analysis to test for such a link. The authors find consistent statistical evidence, across a variety of regression models and variable specifications, that the use of RCDs decreases the incidence of blowouts. Future investigations could incorporate additional RCD-usage data and perform a definitive benefit/cost analysis, test hypotheses about other potential benefits of RCDs (e.g., preventing drilling problems, increasing general drilling efficiency), and examine performance in other regions (US, international).