bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring genetic interactions via a nonlinear model and an optimization algorithm
Authors: Chen Chung-Ming , Lee Chih , Chuang Cheng-Long , Wang Chia-Chang , Shieh Grace S 
Published: February 2010

Abstract

Background
Biochemical pathways are gradually becoming recognized as central to complex human diseases and recently genetic/transcriptional interactions have been shown to be able to predict partial pathways. With the abundant information made available by microarray gene expression data (MGED), nonlinear modeling of these interactions is now feasible. Two of the latest advances in nonlinear modeling used sigmoid models to depict transcriptional interaction of a transcription factor (TF) for a target gene, but do not model cooperative or competitive interactions of several TFs for a target.

Results
An S-shape model and an optimization algorithm (GASA) were developed to infer genetic interactions/transcriptional regulation of several genes simultaneously using MGED. GASA consists of a genetic algorithm (GA) and a simulated annealing (SA) algorithm, which is enhanced by a steepest gradient descent algorithm to avoid being trapped in local minimum. Using simulated data with various degrees of noise, we studied how GASA with two model selection criteria and two search spaces performed. Furthermore, GASA was shown to outperform network component analysis, the time series network inference algorithm (TSNI), GA with regular GA (GAGA) and GA with regular SA. Two applications are demonstrated. First, GASA is applied to infer a subnetwork of human T-cell apoptosis. Several of the predicted interactions are supported by the literature. Second, GASA was applied to infer the transcriptional factors of 34 cell cycle regulated targets in S. cerevisiae, and GASA performed better than one of the latest advances in nonlinear modeling, GAGA and TSNI. Moreover, GASA is able to predict multiple transcription factors for certain targets, and these results coincide with experiments confirmed data in YEASTRACT.

Conclusions
GASA is shown to infer both genetic interactions and transcriptional regulatory interactions well. In particular, GASA seems able to characterize the nonlinear mechanism of transcriptional regulatory interactions (TIs) in yeast, and may be applied to infer TIs in other organisms. The predicted genetic interactions of a subnetwork of human T-cell apoptosis coincide with existing partial pathways, suggesting the potential of GASA on inferring biochemical pathways.
Oxygen- and capacity-limitation of thermal tolerance: a matrix for integrating climate-related stressor effects in marine ecosystems
Authors: Pörtner H.-O. 
Published: February 2010

SUMMARYThe concept of oxygen- and capacity-dependent thermal tolerance in aquatic ectotherms has successfully explained climate-induced effects of rising temperatures on species abundance in the field. Oxygen supply to tissues and the resulting aerobic performance characters thus form a primary link between organismal fitness and its role and functioning at the ecosystem level. The thermal window of performance in water breathers matches their window of aerobic scope. Loss of performance reflects the earliest level of thermal stress, caused by hypoxaemia and the progressive mismatch of oxygen supply and demand at the borders of the thermal envelope. Oxygen deficiency elicits the transition to passive tolerance and associated systemic and cellular stress signals like hormonal responses or oxidative stress as well as the use of protection mechanisms like heat shock proteins at thermal extremes. Thermal acclimatization between seasons or adaptation to a climate regime involves shifting thermal windows and adjusting window widths. The need to specialize on a limited temperature range results from temperature-dependent trade-offs at several hierarchical levels, from molecular structure to whole-organism functioning, and may also support maximized energy efficiency. Various environmental factors like CO2 (ocean acidification) and hypoxia interact with these principal relationships. Existing knowledge suggests that these factors elicit metabolic depression supporting passive tolerance to thermal extremes. However, they also exacerbate hypoxaemia, causing a narrowing of thermal performance windows and prematurely leading the organism to the limits of its thermal acclimation capacity. The conceptual analysis suggests that the relationships between energy turnover, the capacities of activity and other functions and the width of thermal windows may lead to an integrative understanding of specialization on climate and, as a thermal matrix, of sensitivity to climate change and the factors involved. Such functional relationships might also relate to climate-induced changes in species interactions and, thus, community responses at the ecosystem level.
What are the physiological and immunological responses of coral to climate warming and disease?
Authors: Mydlarz Laura D. , McGinty Elizabeth S. , Harvell C. Drew 
Published: February 2010

SUMMARYCoral mortality due to climate-associated stress is likely to increase as the oceans get warmer and more acidic. Coral bleaching and an increase in infectious disease are linked to above average sea surface temperatures. Despite the uncertain future for corals, recent studies have revealed physiological mechanisms that improve coral resilience to the effects of climate change. Some taxa of bleached corals can increase heterotrophic food intake and exchange symbionts for more thermally tolerant clades; this plasticity can increase the probability of surviving lethal thermal stress. Corals can fight invading pathogens with a suite of innate immune responses that slow and even arrest pathogen growth and reduce further tissue damage. Several of these responses, such as the melanin cascade, circulating amoebocytes and antioxidants, are induced in coral hosts during pathogen invasion or disease. Some components of immunity show thermal resilience and are enhanced during temperature stress and even in bleached corals. These examples suggest some plasticity and resilience to cope with environmental change and even the potential for evolution of resistance to disease. However, there is huge variability in responses among coral species, and the rate of climate change is projected to be so rapid that only extremely hardy taxa are likely to survive the projected changes in climate stressors.
Diversity, decoys and the dilution effect: how ecological communities affect disease risk
Authors: Johnson P. T. J. , Thieltges D. W. 
Published: February 2010

SUMMARY
Growing interest in ecology has recently focused on the hypothesis that community diversity can mediate infection levels and disease (‘dilution effect’). In turn, biodiversity loss — a widespread consequence of environmental change — can indirectly promote increases in disease, including those of medical and veterinary importance. While this work has focused primarily on correlational studies involving vector-borne microparasite diseases (e.g. Lyme disease, West Nile virus), we argue that parasites with complex life cycles (e.g. helminths, protists, myxosporeans and many fungi) offer an excellent additional model in which to experimentally address mechanistic questions underlying the dilution effect. Here, we unite recent ecological research on the dilution effect in microparasites with decades of parasitological research on the decoy effect in macroparasites to explore key questions surrounding the relationship between community structure and disease. We find consistent evidence that community diversity significantly alters parasite transmission and pathology under laboratory as well as natural conditions. Empirical examples and simple transmission models highlight the diversity of mechanisms through which such changes occur, typically involving predators, parasite decoys, low competency hosts or other parasites. However, the degree of transmission reduction varies among diluting species, parasite stage, and across spatial scales, challenging efforts to make quantitative, taxon-specific predictions about disease. Taken together, this synthesis highlights the broad link between community structure and disease while underscoring the importance of mitigating ongoing changes in biological communities owing to species introductions and extirpations.
Avian distributions under climate change: towards improved projections
Authors: La Sorte F. A. , Jetz W. 
Published: February 2010

SUMMARYBirds are responding to recent climate change in a variety of ways including shifting their geographic ranges to cooler climates. There is evidence that northern-temperate birds have shifted their breeding and non-breeding ranges to higher latitudes, and tropical birds have shifted their breeding ranges to higher altitudes. There is further evidence these shifts have affected migration strategies and the composition and structure of communities. Projections based on correlative distributional models suggest many birds will experience substantial pressures under climate change, resulting in range contraction and shifts. Inherent limitations of correlative models, however, make it difficult to develop reliable projections and detailed inference. Incorporating a mechanistic perspective into species distribution models enriches the quality of model inferences but also severely narrows the taxonomic and geographic relevance. Mechanistic distributional models have seen increased applications, but so far primarily in ectotherms. We argue that further development of similar models in birds would complement existing empirical knowledge and theoretical projections. The considerable data already available on birds offer an exciting basis. In particular, information compiled on flight performance and thermal associations across life history stages could be linked to distributional limits and dispersal abilities, which could be used to develop more robust and detailed projections. Yet, only a broadening of taxonomic scale, specifically to appropriately represented tropical diversity, will allow for truly general inference and require the continued use of correlative approaches that may take on increasingly mechanistic components. The trade-off between detail and scale is likely to characterize the future of global change biodiversity research, and birds may be an excellent group to improve, integrate and geographically extend current approaches.
Global warming and the Arctic: a new world beyond the reach of the Grinnellian niche?
Authors: MacDonald G. M. 
Published: February 2010

SUMMARYThe levels of CO2 in the atmosphere have already far exceeded values attained at any other time over at least the past 650,000 years. Temperature increases due to rising greenhouse gases will be amplified in Arctic and subarctic regions, and winter warming will be enhanced relative to summer warming. Climate in large areas of high latitudes may have no analogue in current climates or those of the recent geological past. Experimental field manipulations and laboratory studies indicate that plants will exhibit complex responses in photosynthesis, growth rates, phenology and reproductive functioning due to this combination of increasing temperatures, changing seasonality and increasing levels of CO2. The resulting changes in the abundance, distribution, growth rates and production of fruit and phenology of plant species will in turn impact animal populations. In predicting what the future biota of the ‘New Arctic’ will be like and developing appropriate conservation strategies, Grinnellian niche-based approaches are likely to be insufficient, and experimental ecological studies of organism response to specific anticipated changes in climate are crucial.
The Impact of a Pharmacist's Participation on Hospitalists' Rounds
Authors: Patel Reena , Butler Kimberly , Garrett Deidra , Badger Naadede , Cheoun Diane , Hallman Laura 
Published: February 2010

Background Expanding the role of pharmacists in the hospital setting has the potential to positively impact the quality of patient care and provide cost savings. Previous studies have shown that integrating pharmacists into rounding teams can enhance patient care through interventions at the point of assessment and prescribing. This study examines these potential benefits at a community hospital that does not have formal hospitalist rounds and in which the pharmacists must make recommendations via written communication. Objective The primary objective was to identify the number of interventions and to determine how to optimally utilize a pharmacist for a group of 19 hospitalists. Secondary objectives included estimating pharmacist time invested and cost savings. Methods Initially, methods in this study included reviewing patient medication profiles and informally rounding with the hospitalists. Interventions were performed at the time of rounding. After 2 weeks of rounding, methods were altered to improve the efficiency of the pharmacist's time. Patient profiles were reviewed and interventions were performed by written communication. Results A total of 386 patients were reviewed, with 117 interventions discovered. Fifty-eight verbal interventions were made during rounds with a 93% acceptance rate. Fifty-nine written interventions were made in the second part of the study with a 76% acceptance rate. The pharmacist spent an average of 10 minutes reviewing each patient profile, which resulted in a savings of $16 per hour of time invested. An actual cost savings of $3,900 was produced by 64 of the interventions, and the potential cost savings of the remaining 53 interventions exceeded $100,000. Conclusion Opportunities for pharmacist interventions exist within a hospitalists' team and the potential benefits to patient care, along with the actual and potential cost savings, should justify creating collaborations between pharmacists and hospitalists.
New Meconium Biomarkers of Prenatal Methamphetamine Exposure Increase Identification of Affected Neonates
Authors: Gray Teresa R , Kelly Tamsin , LaGasse Linda L , Smith Lynne M , Derauf Chris , Grant Penny , Shah Rizwan , Arria Amelia , Haning William , Della Grotta Sheri , Strauss Arthur , Lester Barry M , Huestis Marilyn A 
Published: February 2010

AbstractBackground: Prenatal methamphetamine (MAMP) exposure is poorly reflected in neonatal meconium. Often, maternal self-reported MAMP use is not corroborated by positive results in amphetamines immunoassays of meconium, and even if initial test results are positive, they frequently are not confirmed for MAMP or amphetamine (AMP) by chromatographic analysis. The presence of the MAMP metabolites p-hydroxymethamphetamine (pOHMAMP), p-hydroxyamphetamine (pOHAMP), and norephedrine (NOREPH) in meconium may improve the identification of MAMP- and AMP-exposed neonates.Methods: Immunoassay-positive and -negative meconium samples were subjected to liquid chromatography– tandem mass spectrometric reanalysis for these recently identified metabolites.Results: pOHAMP and NOREPH were detected only when MAMP and/or AMP were present and thus do not appear to be promising biomarkers of prenatal MAMP exposure. pOHMAMP, in contrast, identified 6 additional neonates whose mothers reported MAMP exposure, yet had a meconium sample screened as negative; pOHMAMP was more likely to be present if maternal MAMP use continued into the third trimester. Although the pOHMAMP results for meconium samples corroborated the maternal self-reports, the confirmation rate for positive meconium screening results did not improve with the inclusion of these new biomarkers.Conclusions: pOHMAMP identified additional MAMP- exposed neonates; therefore, MAMP, AMP, and pOHMAMP should be included in meconium chromatographic analyses. Maximizing the identification of MAMP-exposed children requires improvement in immunoassay screening tests to reduce false-negative and false-positive results. Additional research will help clarify which AMP-related compounds, if any, contribute to unconfirmed positive results in screening tests. Furthermore, nonamphetamine compounds endogenous to the complex meconium matrix also may cross-react, making chromatographic confirmation of screening results essential.
Association of matrix metalloproteinase 9 genotypes and cardiovascular disease risk factors with serum matrix metalloproteinase 9 concentrations in Taiwanese individuals
Authors: Wu Semon , Hsu Lung-An , Teng Ming-Sheng , Lin Jeng Feng , Chang Hsien-Hsun , Chang Pi-Yueh , Hu Chiao-Feng , Ko Yu-Lin 
Published: February 2010

Abstract

Background: Circulating concentrations of matrix metalloproteinase 9 (MMP-9) are associated with cardiovascular disease mortality in patients with coronary artery disease. We investigated the determinants of MMP-9 concentrations by analyzing MMP-9 genotypes and risk factors for cardiovascular disease.

Methods: A total of 596 individuals were recruited for this study. Six single nucleotide polymorphisms (SNP) with coverage of the MMP-9 gene region were analyzed; and two genotypes, rs3918242-TT and rs2274756-AA, which were in nearly complete linkage disequilibrium, were associated with higher MMP-9 values (p=0.007 and p=0.008, respectively). In age- and gender-adjusted regression models, MMP-9 concentrations were positively associated with the homeostasis model assessment of insulin resistance (HOMA-IR) index and triglyceride concentrations, fasting serum insulin, fasting plasma glucose, C-reactive protein, fibrinogen, and serum amyloid A. By multivariate analysis, rs2274756 genotypes, age, smoking status, fibrinogen and fasting plasma glucose concentrations were all independently associated with MMP-9 (p=0.007, p=0.033, p=0.003, p=0.013, and p=0.012, respectively).

Conclusions: The rs2274756-AA and rs3918242-TT genotypes, younger age, current smoking status and increased fasting plasma glucose, and fibrinogen concentrations were independently associated with high serum MMP-9 concentrations in Taiwanese individuals.
Clin Chem Lab Med 2010;48:543–9.
FOXL2 mutations in Taiwanese patients with blepharophimosis, ptosis, epicanthus inversus syndrome
Authors: Lin Wei-De , Chou I-Ching , Lee Ni-Chung , Wang Chung-Hsing , Hwu Wuh-Liang , Lin Shuan-Pei , Chao Mei-Chyn , Tsai Yushin , Tsai Fuu-Jen 
Published: February 2010

Abstract

Background: Blepharophimosis, ptosis, epicanthus inversus syndrome (BPES) is an autosomal dominant developmental disorder that includes an eyelid malformation associated with (type I) or without (type II) premature ovarian failure (POF). Mutations in the forkhead transcription factor 2 (FOXL2) gene, a member of winged/forkhead transcription factor family, are responsible for both types of BPES. The purpose of this study was to identify mutations in FOXL2 in Taiwanese patients with BPES.

Methods: The karyotype and genomic DNA was prepared from the leukocytes of peripheral venous blood samples. The coding and flanking region sequences of FOXL2 were analyzed by directed or cloning sequencing.

Results: The karyotypes of these patients did not show significant variation, especially on the 3q23 region. Two mutations in FOXL2 were identified in two familial cases. One was c.855-871dup (17-bp insertion) associated with POF. The other was c.384G>A (TGG>TGA), a novel mutation that resulted in non-sense changes of the encoded protein, i.e., p.W128X.

Conclusions: Our results expand the spectrum of FOXL2 mutations and confirm the mutation hotspot in FOXL2 in Taiwanese BPES patients.
Clin Chem Lab Med 2010;48:485–8.
C-reactive protein variants are not associated with susceptibility to stroke and stroke recurrence
Authors: Song Weihua , Yu Hui , Chen Jingzhou , Sun Kai , Hui Rutai 
Published: February 2010

Abstract

Background: C-reactive protein (CRP) has been shown to contribute to the risk of cardiovascular disease. Several single nucleotide polymorphisms (SNPs) at the CRP locus have been found to be associated with CRP concentrations. We hypothesized that genetic variants associated with high CRP may confer a greater risk of stroke and recurrence. The hypothesis was tested in a case-control study and during follow-up of the case population.

Methods: Two genetic variants associated with serum CRP in the CRP gene were genotyped in a Chinese case-control study comprised of 1572 stroke patients and 1485 controls. The case population was followed for a median of 4.5 years (range, 0.1–6.0 years).

Results: During a median 4.5-year follow-up for 1526 stroke patients, 299 recurrent strokes were identified. No association was found between the SNPs or haplotypes of the CRP gene and stroke and its recurrence.

Conclusions: Although these variants and corresponding haplotypes in the CRP gene are associated with serum CRP concentrations, our study does not support that variants and corresponding haplotypes studied here have a major influence on risk of stroke and stroke recurrence. Therefore, we speculate that CRP is not a causal factor for stroke.
Clin Chem Lab Med 2010;48:551–4.
Macro- and micro-mechanical properties of red oak wood (Quercus rubra L.) treated with hemicellulases
Authors: Konnerth Johannes , Eiser Martina , Jäger Andreas , Bader Thomas Karl , Hofstetter Karin , Follrich Jürgen , Ters Thomas , Hansmann Christian , Wimmer Rupert 
Published: February 2010

AbstractRed oak wood (Quercus rubraL.) samples were submitted to an enzymatic treatment with a commercial mixture of hemicellulases aiming at the selective depolymerization and removal of the hemicelluloses. Mechanical properties of treated samples were characterized and compared with untreated samples at two hierarchical levels. At the macrolevel, tensile properties revealed to be less sensitive to degradation of the cell wall matrix compared to compression and hardness properties. Results obtained through indentation at the microlevel indicated that hardness and the so-called reduced modulus of treated wood were significantly lowered. Accordingly, hardness and reduced elastic modulus have proven to be most sensitive to modification of the cell wall matrix by reducing the content of hemicelluloses. It is proposed that transversal and shear stresses, which are mainly carried by the cell wall matrix, are additional parameters having strong effects on elastic modulus obtained by nanoindentation. Micromechanical modeling was employed to confirm the observed changes. There is consistency between the measured and the modeled properties, obtained at both the microlevel and the macrolevel of wood.
Activities and social interactions in captive Antillean manatees in Mexico
Authors: Hénaut Yann , Becerra Lopez Sylvia P. , Machkour-M'Rabet Salima , Morales-Vela Benjamín , Winterton Peter , Delfour Fabienne 
Published: February 2010

Abstract
Behavioural research in endangered manatees is essential for successful conservation management. We examined the activities and social interactions of a captive group of Antillean manatees located in the Dolphin Discovery Park in Mexico. The group studied was composed of two adults, one subadult and one calf. We determined activity patterns and space use of the manatees in a natural water pool over a daytime period and a night-time period. The behavioural strategies of the manatees included (1) during the day, mainly foraging, feeding, and remaining inactive, and (2) evening activities were divided among social interaction, environment exploration, and resting activities. All the behaviour patterns of the captive manatees seemed to be influenced by the feeding schedule during the day. The number of contacts between manatees increased strongly at night, each individual having a preferred partner for social interaction. The cow-calf dyad showed the highest intensity of contacts, whereas subadults showed the lowest. The relationships observed among individuals reveal a higher social activity than previously described in Antillean manatees.