bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxidative stress response of Forster's terns (Sterna forsteri) and Caspian terns (Hydroprogne caspia) to mercury and selenium bioaccumulation in liver, kidney, and brain
Authors: Hoffman David J , Eagles-Smith Collin A , Ackerman Joshua T , Adelsbach Terrence L , Stebbins Katherine R
Published: December 2010

Bioindicators of oxidative stress were examined in prebreeding and breeding adult and chick Forster's terns (Sterna forsteri) and in prebreeding adult Caspian terns (Hydroprogne caspia) in San Francisco Bay, California. Highest total mercury (THg) concentrations (mean ± standard error; µg/g dry wt) in liver (17.7 ± 1.7), kidney (20.5 ± 1.9), and brain (3.0 ± 0.3) occurred in breeding adult Forster's terns. The THg concentrations in liver were significantly correlated with hepatic depletion of reduced glutathione (GSH), increased oxidized glutathione (GSSG):GSH ratio, and decreased hepatic gamma-glutamyl transferase (GGT) activity in adults of both tern species. Prefledging Forster's tern chicks with one-fourth the hepatic THg concentration of breeding adults exhibited effects similar to adults. Total mercury–related renal GSSG increased in adults and chicks. In brains of prebreeding adults, THg was correlated with a small increase in glucose-6–phosphate dehydrogenase (G-6-PDH) activity, suggestive of a compensatory response. Brain THg concentrations were highest in breeding adult Forster's terns and brain tissue exhibited increased lipid peroxidation as thiobarbituric acid-reactive substances, loss of protein bound thiols (PBSH), and decreased activity of antioxidant enzymes, GSSG reductase (GSSGrd), and G-6-PDH. In brains of Forster's tern chicks there was a decrease in total reduced thiols and PBSH. Multiple indicator responses also pointed to greater oxidative stress in breeding Forster's terns relative to prebreeding terns, attributable to the physiological stress of reproduction. Some biondicators also were related to age and species, including thiol concentrations. Enzymes GGT, G-6-PDH, and GSSGred activities were related to species. Our results indicate that THg concentrations induced oxidative stress in terns, and suggest that histopathological, immunological, and behavioral effects may occur in terns as reported in other species. Environ. Toxicol. Chem. 2011; 30:920–929. © 2010 SETAC
Mining gold dust under the genome wide significance level: a two‐stage approach to analysis of GWAS
Authors: Shi Gang , Boerwinkle Eric , Morrison Alanna C. , Gu C. Charles , Chakravarti Aravinda , Rao D.C.
Published: December 2010

We propose a two‐stage approach to analyze genome‐wide association data in order to identify a set of promising single‐nucleotide polymorphisms (SNPs). In stage one, we select a list of top signals from single SNP analyses by controlling false discovery rate. In stage two, we use the least absolute shrinkage and selection operator (LASSO) regression to reduce false positives. The proposed approach was evaluated using simulated quantitative traits based on genome‐wide SNP data on 8,861 Caucasian individuals from the Atherosclerosis Risk in Communities (ARIC) Study. Our first stage, targeted at controlling false negatives, yields better power than using Bonferroni‐corrected significance level. The LASSO regression reduces the number of significant SNPs in stage two: it reduces false‐positive SNPs and it reduces true‐positive SNPs also at simulated causal loci due to linkage disequilibrium. Interestingly, the LASSO regression preserves the power from stage one, i.e., the number of causal loci detected from the LASSO regression in stage two is almost the same as in stage one, while reducing false positives further. Real data on systolic blood pressure in the ARIC study was analyzed using our two‐stage approach which identified two significant SNPs, one of which was reported to be genome‐significant in a meta‐analysis containing a much larger sample size. On the other hand, a single SNP association scan did not yield any significant results.Genet. Epidemiol. 32:111‐118, 2011.© 2010 Wiley‐Liss, Inc.
Inferring genetic causal effects on survival data with associated endo‐phenotypes
Authors: Lipman Peter J. , Liu Kuang‐Yu , Muehlschlegel Jochen Daniel , Body Simon , Lange Christoph
Published: December 2010

Age‐at‐onset phenotypes are important traits in genetic association analyses. Often, intermediate phenotypes that are related to the age‐at‐onset phenotype are also associated with the marker loci that are associated with the age‐at‐onset phenotype. In order to understand the genetic etiology of the observed associations, statistical methodology is needed to distinguish between a direct genetic effect on the age‐at‐onset phenotype and an indirect effect induced by the genetic association with the endo‐phenotype that is correlated with the age‐at‐onset phenotype. In this communication, we introduce a new statistical approach to detect causal genetic effects on survival data in the presence of genetic associations with secondary phenotypes that might influence survival as well and thereby induce seemingly causal relationships. Derived using causal inference methodology, the proposed method is based on standard statistical methodology and can be implemented straight‐forwardly, using standard software. Using simulation studies, the theoretical properties of the approach are verified and the power is assessed under realistic scenarios. The practical relevance of the approach is illustrated by an application to survival after cardiac surgery, where genetic components of myocardial infarctions are determined to not influence post‐surgery hospital duration except through the MI‐pathway. Genet. Epidemiol. 32:119‐124, 2011.  © 2010 Wiley‐Liss, Inc.
Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method
Authors: Bruckner Stefan , Boresch Stefan
Published: December 2010

We investigate the relative efficiency of thermodynamic integration, three variants of the exponential formula, also referred to as thermodynamic perturbation, and Bennett's acceptance ratio method to compute relative and absolute solvation free energy differences. Our primary goal is the development of efficient protocols that are robust in practice. We focus on minimizing the number of unphysical intermediate states (λ‐states) required for the computation of accurate and precise free energy differences. Several indicators are presented which help decide when additional λ‐states are necessary. In all tests Bennett's acceptance ratio method required the least number of λ‐states, closely followed by the “double‐wide” variant of the exponential formula. Use of the exponential formula in only strict “forward” or “backward” mode was not found to be competitive. Similarly, the performance of thermodynamic integration in terms of efficiency was rather poor. We show that this is caused by the use of the trapezoidal rule as method of numerical quadrature. A systematic study focusing on the optimization of thermodynamic integration is presented in a companion paper. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
O(NlogN) Continuous electrostatics method for fast calculation of solvation energies of biomolecules
Authors: Fedichev P. O. , Getmantsev E. G. , Menshikov L. I.
Published: December 2010

We report the development of a new, fast, surface‐based method for numerical calculations of the solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size, both in time and memory requirements, produces explicit values for the reaction field potential and stable values of the polar energy within only a few percent error margin practically for any molecular configurations. The method works well both for large and small molecules and thus gives stable energy differences for quantities such as the polar energy contributions to molecular complex formation energies. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): Structure and phylogenetic significance
Authors: Grechko Vernata V. , Kosushkin Sergei A. , Borodulina Olga R. , Butaeva Fatima G. , Darevsky Ilya S.
Published: December 2010

Short interspersed elements (SINEs) are important nuclear molecular markers of the evolution of many eukaryotes. However, the SINEs of squamate reptile genomes have been little studied. We first identified two families of SINEs, termed Squam1 and Squam2, in the DNA of meadow lizard Darevskia praticola (Lacertidae) by performing DNA hybridization and PCR. Later, the same families of retrotransposons were found using the same methods in members of another 25 lizard families (from Iguania, Scincomorpha, Gekkota, Varanoidea, and Diploglossa infraorders) and two snake families, but their abundances in these taxa varied greatly. Both SINEs were Squamata‐specific and were absent from mammals, birds, crocodiles, turtles, amphibians, and fish. Squam1 possessed some characteristics common to tRNA‐related SINEs from fish and mammals, while Squam2 belonged to the tRNAAla group of SINEs and had a more unusual and divergent structure. Squam2‐related sequences were found in several unannotated GenBank sequences of squamate reptiles. Squam1 abundance in the Polychrotidae, Agamidae, Leiolepididae, Chamaeleonidae, Scincidae, Lacertidae, Gekkonidae, Varanidae, Helodermatidae, and two snake families were 102–104 times higher than those in other taxa (Corytophanidae, Iguanidae, Anguidae, Cordylidae, Gerrhosauridae, Pygopodidae, and Eublepharidae). A less dramatic degree of copy number variation was observed for Squam2 in different taxa. Several Squam1 copies from Lacertidae, Chamaeleonidae, Gekkonidae, Varanidae, and Colubridae were sequenced and found to have evident orthologous features, as well as taxa‐specific autapomorphies. Squam1 from Lacertidae and Chamaeleonidae could be divided into several subgroups based on sequence differences. Possible applications of these SINEs as Squamata phylogeny markers are discussed. J. Exp. Zool. (Mol. Dev. Evol.) 316:212–226, 2011. © 2010 Wiley‐Liss, Inc.
Localization of burn mark under an abnormal topography on MOSFET chip surface using liquid crystal and emission microscopy tools
Authors: Lau C. K. , Sim K. S. , Tso C. P.
Published: December 2010

This article focuses on the localization of burn mark in MOSFET and the scanning electron microscope (SEM) inspection on the defect location. When a suspect abnormal topography is shown on the die surface, further methods to pin‐point the defect location is necessary. Fault localization analysis becomes important because an abnormal spot on the chip surface may and may not have a defect underneath it. The chip surface topography can change due to the catastrophic damage occurred at layers under the chip surface, but it could also be due to inconsistency during metal deposition in the wafer fabrication process. Two localization techniques, liquid crystal thermography and emission microscopy, were performed to confirm that the abnormal topography spot is the actual defect location. The tiny burn mark was surfaced by performing a surface decoration at the defect location using hot hydrochloric acid. SEM imaging, which has the high magnification and three‐dimensional capabilities, was used to capture the images of the burn mark. SCANNING 33: 13–20, 2011. © 2010 Wiley Periodicals, Inc.
Computational systems biology of aging
Authors: Kriete Andres , Lechner Mark , Clearfield Drew , Bohmann Dirk
Published: December 2010

Computational systems biology is expected to make major contributions to unravel the complex molecular mechanisms underlying the progression of aging in cells, tissues, and organisms. The development of computational approaches is, however, challenged by a wide spectrum of aging mechanisms participating on different levels of biological organization. The tight connectivity between the molecular constituents, functions, and cell states requires frameworks and strategies that extend beyond current practice to model, simulate, and predict the progression of aging and the emerging aging phenotypes. We provide a general overview of the specific computational tasks and opportunities in aging research, and discuss some illustrative systems level concepts in more detail. One example provided here is the assembly of a conceptual whole cell model that considers the temporal dynamics of the aging process grounded on molecular mechanisms. Another application is the assembly of interactomes, such as protein networks that allow us to analyze changes in network topology and interaction of proteins that have been implicated in aging with other cellular constituents and processes. We introduce the necessary key steps to build these applications and discuss their merits and future extensions for aging research. WIREs Syst Biol Med 2011 3 414–428 DOI: 10.1002/wsbm.126

This article is categorized under:

Physiology > Mammalian Physiology in Health and Disease
Where gene discovery turns into systems biology: genome‐scale RNAi screens in Drosophila
Authors: Neumüller Ralph A. , Perrimon Norbert
Published: December 2010

Systems biology aims to describe the complex interplays between cellular building blocks which, in their concurrence, give rise to the emergent properties observed in cellular behaviors and responses. This approach tries to determine the molecular players and the architectural principles of their interactions within the genetic networks that control certain biological processes. Large‐scale loss‐of‐function screens, applicable in various different model systems, have begun to systematically interrogate entire genomes to identify the genes that contribute to a certain cellular response. In particular, RNA interference (RNAi)‐based high‐throughput screens have been instrumental in determining the composition of regulatory systems and paired with integrative data analyses have begun to delineate the genetic networks that control cell biological and developmental processes. Through the creation of tools for both, in vitro and in vivo genome‐wide RNAi screens, Drosophila melanogaster has emerged as one of the key model organisms in systems biology research and over the last years has massively contributed to and hence shaped this discipline. WIREs Syst Biol Med 2011 3 471–478 DOI: 10.1002/wsbm.127

This article is categorized under:

Laboratory Methods and Technologies > RNA Methods
Genome‐wide approaches in the study of microRNA biology
Authors: Wilbert Melissa L. , Yeo Gene W.
Published: December 2010

MicroRNAs (miRNAs), a class of ∼21–23 nucleotide long non‐coding RNAs (ncRNAs), have critical roles in diverse biological processes that encompass development, proliferation, apoptosis, stress response, and fat metabolism. miRNAs recognize their target mRNA transcripts by partial sequence complementarity and collectively have been estimated to regulate the majority of human genes. Consequently, misregulation of miRNAs or disruption of their target sites in genes has been implicated in a variety of human diseases ranging from cancer metastasis to neurological disorders. With the development and availability of genomic technologies and computational approaches, the field of miRNA biology has advanced tremendously over the last decade. Here we review the genome‐wide approaches that have allowed for the discovery of new miRNAs, the characterization of their targets, and a systems‐level view of their impact. WIREs Syst Biol Med 2011 3 491–512 DOI: 10.1002/wsbm.128

This article is categorized under:

Laboratory Methods and Technologies > Genetic/Genomic Methods
Cardiac function and disease: emerging role of small ubiquitin‐related modifier
Authors: Wang Jun
Published: December 2010

Small ubiquitin‐related modifiers, or SUMOs, have emerged as versatile regulators of many biological functions that do so by covalent attachment to a variety of substrates via enzymatic reactions. SUMO conjugation has also been shown to be involved in a number of human pathogenic processes. More recent advances in the SUMO field have indicated a potential role for SUMO conjugation pathway in cardiogenesis. This advanced review will describe the basic features of the SUMO conjugation pathway and will summarize the most recent studies implicating the influence of the sumoylation pathway in cardiac function under both physiological and pathological conditions. WIREs Syst Biol Med 2011 3 446–457 DOI: 10.1002/wsbm.130

This article is categorized under:

Developmental Biology > Developmental Processes in Health and Disease
Network biology: a direct approach to study biological function
Authors: Emmert‐Streib Frank , Glazko Galina V.
Published: December 2010

In this paper we discuss the dualism of gene networks and their role in systems biology. We argue that gene networks (1) can serve as a conceptual framework, forming a fundamental level of a phenomenological description, and (2) are a means to represent and analyze data. The latter point does not only allow a systems analysis but is even amenable for a direct approach to study biological function. Here we focus on the clarity of our main arguments and conceptual meaning of gene networks, rather than the causal inference of gene networks from data.WIREs Syst Biol Med2011 3 379–391 DOI: 10.1002/wsbm.134

This article is categorized under:

Biological Mechanisms > Regulatory Biology
Adaptation of cells to new environments
Authors: Brooks Aaron N. , Turkarslan Serdar , Beer Karlyn D. , Yin Lo Fang , Baliga Nitin S.
Published: December 2010

The evolutionary success of an organism is a testament to its inherent capacity to keep pace with environmental conditions that change over short and long periods. Mechanisms underlying adaptive processes are being investigated with renewed interest and excitement. This revival is partly fueled by powerful technologies that can probe molecular phenomena at a systems scale. Such studies provide spectacular insight into the mechanisms of adaptation, including rewiring of regulatory networks via natural selection of horizontal gene transfers, gene duplication, deletion, readjustment of kinetic parameters, and myriad other genetic reorganizational events. Here, we discuss advances in prokaryotic systems biology from the perspective of evolutionary principles that have shaped regulatory networks for dynamic adaptation to environmental change.WIREs Syst Biol Med2011 3 544–561 DOI: 10.1002/wsbm.136

This article is categorized under:

Biological Mechanisms > Cell Fates

Laboratory Methods and Technologies > Genetic/Genomic Methods

Physiology > Organismal Responses to Environment

Biological Mechanisms > Regulatory Biology
Are extremity musculoskeletal injuries in children related to obesity and social status? A prospective observational study in a district general hospital
Authors: Pullagura Mohan , Gopisetti Sharmila , Bateman Belinda , van Kampen Maria
Published: December 2010

Background

Obesity is one of the several independent risk factors for the risk of fractures. Major epidemiological studies also suggested the social status of the patients to be a confounding factor. We aimed to look at the influence of obesity on fractures and to determine if the social status of the patients is a confounding factor.

Methods

This is an observational study of 560 children with musculoskeletal injuries who presented over a period of 8 months and the data were collected prospectively. Obesity status and social deprivation index were estimated.

Results

The prevalence of overweight and obese children was 29.9%. Twenty-four percent of the boys and 31% of the girls were obese ( P = 0.2). In the group of most deprived areas, the prevalence of obesity increased to 40% in those needing admission for intervention.

Conclusions

Although there is a slight increase in obesity, there is no suggestion of increased rate of fractures in deprived areas. Upper limb injuries were more predominant, with distal radius fracture being the most common injury. Boys sustain fractures twice as often as girls. There is a tendency to increasing obesity with increasing age.
The contrasting effects of negative word of mouth in the post‐consumption stage
Authors: Chan Haksin , Cui Selina
Published: December 2010

We explore the effects of negative word of mouth (NWOM) from worse‐off or similar others in the post‐consumption stage. In four experiments, we show that the ramifications of NWOM are more complex than portrayed in the literature. Specifically, we demonstrate that attribute‐based NWOM has a negative (i.e., aggravating) effect on dissatisfied consumers, whereas experience‐based NWOM has a positive (i.e., alleviating) effect. Thought‐listing data reveal distinct processes underlying the contrasting effects. On one hand, these results are consistent with the predictions of attitude polarization and downward comparison research. On the other hand, they are explainable in terms of the disconfirmation model.
Pyrosequencing/Sanger Plant Genome Assembly (Limitations, Problems And Solutions) - On The Way To Cucumber (Cucumis sativus L. cv. Borszczagowski) Draft Genome Sequence Publishing
Authors: Woycicki Rafal , Przybecki Zbigniew
Published: December 2010

Genome sequencing give us an opportunity to broaden the range and improve the quality of omics studies. New sequencing technologies make it possible to achieve the sequencing reads fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects.We focus here on the wide range of approaches undertaken to assemble the draft cucumber (Cucumis sativus L. cv. Borszczagowski) genome done by using 12x coverage of pyrosequencing Titanium chemistry shotgun paired and unpaired reads combined with Sanger reads.
Some Pragmatic Tips for Dealing With Clinical Uncertainty
Authors: Bernstein Ratner Nan
Published: January 2011

Purpose

This article proposes some recommendations to enable clinicians to balance certainty and uncertainty when evaluating the currency and effectiveness of their treatment approaches.

Method

I offer the following advice: (a) Question the authority of the information previously learned in one’s career; (b) be cognizant of what we do not yet know about best clinical practice; (c) understand that knowledge of “best practices” is both temporary and relative; (d) enable access to new information by the use of electronic alerts; (e) be flexible in reading new clinical reports, keeping an open mind as to their value; (f) get the clinically relevant details of new approaches by reading the full reports; and (g) employ, and then evaluate the outcomes of, new approaches used in treating individuals on our caseload.

Results

Examples are provided to show that proactive participation in research-alert programs can enable clinicians to access emerging, clinically relevant information, some of which is controversial. Staying abreast of such information is more efficient than performing guided searches for information as challenging cases arise.

Conclusions

Applications of these recommendations should enable practicing clinicians to entertain new, clinically useful concepts while not taxing the limited time that clinicians typically have to engage in continuing education.
Balancing Certainty and Uncertainty in Clinical Practice
Authors: Kamhi Alan G.
Published: January 2011

Purpose

In this article, I question how practitioners can balance the certainty and confidence that they can help their patients with the uncertainty that makes them continually question their beliefs and assumptions.

Method

I compare the mechanisms of science and models of clinical practice that may help practitioners achieve the right balance between total acceptance of the status quo and an open willingness to explore and accept new ideas.

Conclusion

Clinical practice, unlike science, has no independent self-correction mechanism that leads to consensus about best clinical practices. Evidence-based models provide principles and guidelines for clinical practice, but ultimately, clinical decisions may be influenced most by a practitioner’s epistemology (belief systems) and propensity for rational thinking.
Critical Thinking: Knowledge and Skills for Evidence-Based Practice
Authors: Finn Patrick
Published: January 2011

Purpose

I respond to Kamhi’s (2011) conclusion in his article “Balancing Certainty and Uncertainty in Clinical Practice” that rational or critical thinking is an essential complement to evidence-based practice (EBP).

Method

I expand on Kamhi’s conclusion and briefly describe what clinicians might need to know to think critically within an EBP profession. Specifically, I suggest how critical thinking is relevant to EBP, broadly summarize the relevant skills, indicate the importance of thinking dispositions, and outline the various ways our thinking can go wrong.

Conclusion

I finish the commentary by suggesting that critical thinking skills should be considered a required outcome of our professional training programs.
Providing Written Language Services in the Schools: The Time Is Now
Authors: Fallon Karen A. , Katz Lauren A.
Published: January 2011

Purpose

The current study was conducted to investigate the provision of written language services by school-based speech-language pathologists (SLPs). Specifically, the study examined SLPs' knowledge, attitudes, and collaborative practices in the area of written language services as well as the variables that impact provision of these services.

Method

Public school–based SLPs from across the country were solicited for participation in an online, Web-based survey. Data from 645 full-time SLPs from 49 states were evaluated using descriptive statistics and logistic regression.

Results

Many school-based SLPs reported not providing
any
services in the area of written language to students with written language weaknesses. Knowledge, attitudes, and collaborative practices were mixed. A logistic regression revealed three variables likely to predict high levels of service provision in the area of written language.

Conclusion

Data from the current study revealed that many struggling readers and writers on school-based SLPs' caseloads are not receiving services from their SLPs. Implications for SLPs' preservice preparation, continuing education, and doctoral preparation are discussed.
A Comparison of Oral and Written English Styles in African American Students at Different Stages of Writing Development
Authors: Ivy Lennette J. , Masterson Julie J.
Published: January 2011

Purpose

The purpose of this investigation was to compare the rates of using African American English (AAE) grammatical features in spoken and written language at different points in literacy development. Based on Kroll’s model (1981), a high degree of similarity in use between the modalities was expected at Grade 3, and lower similarity was expected at Grade 8.

Method

Spoken and written language samples were analyzed for the occurrence of 6 AAE morphosyntactic features. Fifteen third graders and 15 eighth graders were asked to respond to interview questions and to retell stories in both modalities. Percentage use of the AAE grammatical features and a dialectal density measure were used to measure rates of AAE occurrence.

Results

Findings indicated comparable use of dialect in spoken and written modalities for 3rdgraders, but a difference in use between the modalities for 8thgraders. The 8thgraders used more dialectal features in speaking than writing.

Conclusion

These results suggest that there is likely a period in writing development when speakers of AAE learn to dialect switch in their writing.
Knowledge of Mathematical Equivalence in Children With Specific Language Impairment: Insights From Gesture and Speech
Authors: Mainela-Arnold Elina , Alibali Martha W. , Ryan Kristin , Evans Julia L.
Published: January 2011

Purpose

This study investigated understanding of mathematical equivalence in children with and without specific language impairment (SLI).

Method

A total of 34 children (ages 8;1 [years;months] to 11;7), including 9 with expressive SLI (E-SLI), 8 with expressive and receptive SLI (ER-SLI), and 17 age-matched typically developing (TD) children completed addition and mathematical equivalence problems. The problem-solving strategies revealed in solutions and in gestural and verbal explanations were coded.

Results

The children with SLI were less accurate than their TD peers in solving addition and equivalence problems. None of the children in the ER-SLI group solved the equivalence problems correctly; however, the number of children who solved any of the equivalence problems correctly did not differ in the E-SLI and CA groups. Children in the ER-SLI group tended to express incorrect strategies for solving the equivalence problems in both gesture and speech, whereas children in the E-SLI group often expressed
correct
strategies in gestures, but
incorrect
strategies in speech.

Conclusion

Children with SLI showed delays in their knowledge of mathematical equivalence. Children with ER-SLI displayed greater delays than children with E-SLI. Children with E-SLI sometimes expressed more advanced knowledge in gestures, suggesting that their knowledge is represented in a nonverbal format.
Phase Transition Enthalpy Measurements of Organic and Organometallic Compounds. Sublimation, Vaporization and Fusion Enthalpies From 1880 to 2010
Authors: Acree William , Chickos James S.
Published: December 2010

A compendium of phase change enthalpies published within the period 1880–2010 is reported. Phase change enthalpies including fusion,vaporization, and sublimation are included for organic, organometallic,and a few inorganic compounds. This compendium is a combination of three previous series focusing on phase change enthalpies updated to 2009. Sufficient data are presently available for some compounds to permit thermodynamic cycles to be constructed, an important manner of evaluating the reliability of the measurements. Temperature adjustments of phase change enthalpies from the temperature of measurement to the standard reference temperature, T=298.15 K, are briefly discussed and a protocol for doing so is illustrated.
The Thermodynamic Properties of the f-Elements and Their Compounds. I. The Lanthanide and Actinide Metals
Authors: Konings Rudy J. M. , Beneš Ondrej
Published: December 2010

A critical review of the thermodynamic properties of the lanthanide and actinide elements is presented. The available literature data for the solid, liquid, and gaseous state have been collected and recommended values are presented. In case experimental data are missing, estimates have been made based on the trends in the two series.
Tunable visual color filter using microfluidic grating
Authors: Li Z. G. , Yang Y. , Zhang X. M. , Liu A. Q. , Zhang J. B. , Cheng L. , Li Z. H.
Published: December 2010

This paper reports a tunable visual color filter based on a microfluidic transmission grating. The grating lines are formed by the microflows in an array of evenly spaced straight microchannels. In experimental study, the transmission of white light measures a shift of visual color from red to blue in the zeroth order diffraction in response to a change of the refractive index from 1.3290 to 1.3782 in the microflows. The merit of large tunability of transmission peak (Δλ=408 nm) makes this grating potential for various applications in biological and chemical measurements, such as space- and time-resolving micropattern spectrophotometers and separation of the fluorescence from the excitation.
Release monitoring of single cells on a microfluidic device coupled with fluorescence microscopy and electrochemistry
Authors: Shi Bao-Xian , Wang Yu , Lam Tin-Lun , Huang Wei-Hua , Zhang Kai , Leung Yun-Chung , Chan Helen L. W.
Published: December 2010

A method for monitoring the biological exocytotic phenomena on a microfluidic system was proposed. A microfluidic device coupled with functionalities of fluorescence imaging and amperometric detection has been developed to enable the real-time monitoring of the exocytotic events. Exocytotic release of single SH-SY5Y neuroblastoma cells was studied. By staining the cells located on integrated microelectrodes with naphthalene-2,3-dicarboxaldehyde, punctuate fluorescence consistent with localization of neurotransmitters stored in vesicles was obtained. The stimulated exocytotic release was successfully observed at the surface of SH-SY5Y cells without refitting the commercial inverted fluorescence microscope. Spatially and temporally resolved exocytotic events from single cells on a microfluidic device were visualized in real time using fluorescence microscopy and were amperometrically recorded by the electrochemical system simultaneously. This coupled technique is simple and is hoped to provide new insights into the mechanisms responsible for the kinetics of exocytosis.
Miniaturization of dielectric liquid microlens in package
Authors: Yang Chih-Cheng , Tsai C. Gary , Yeh J. Andrew
Published: December 2010

This study presents packaged microscale liquid lenses actuated with liquid droplets of 300–700 μm in diameter using the dielectric force manipulation. The liquid microlens demonstrated function focal length tunability in a plastic package. The focal length of the liquid lens with a lens droplet of 500 μm in diameter is shortened from 4.4 to 2.2 mm when voltages applied change from 0 to 79 Vrms. Dynamic responses that are analyzed using 2000 frames/s high speed motion cameras show that the advancing and receding times are measured to be 90 and 60 ms, respectively. The size effect of dielectric liquid microlens is characterized for a lens droplet of 300–700 μm in diameter in an aspect of focal length.
Cell rotation using optoelectronic tweezers
Authors: Liang Yuan-Li , Huang Yuan-Peng , Lu Yen-Sheng , Hou Max T. , Yeh J. Andrew
Published: December 2010

A cell rotation method by using optoelectronic tweezers (OET) is reported. The binary image of a typical OET device, whose light and dark sides act as two sets of parallel plates with different ac voltages, was used to create a rotating electric field. Its feasibility for application to electrorotation of cells was demonstrated by rotating Ramos and yeast cells in their pitch axes. The electrorotation by using OET devices is dependent on the medium and cells’ electrical properties, the cells’ positions, and the OET device’s geometrical dimension, as well as the frequency of the electric field.
Optofluidic tunable microlens by manipulating the liquid meniscus using a flared microfluidic structure
Authors: Mao Xiaole , Stratton Zackary I. , Nawaz Ahmad Ahsan , Lin Sz-Chin Steven , Huang Tony Jun
Published: December 2010

We have designed, demonstrated, and characterized a simple, novel in-plane tunable optofluidic microlens. The microlens is realized by utilizing the interface properties between two different fluids: CaCl2 solution and air. A constant contact angle of ∼90° is the pivotal factor resulting in the outward bowing and convex shape of the CaCl2 solution-air interface. The contact angle at the CaCl2 solution-air interface is maintained by a flared structure in the polydimethylsiloxane channel. The resulting bowing interface, coupled with the refractive index difference between the two fluids, results in effective in-plane focusing. The versatility of such a design is confirmed by characterizing the intensity of a traced beam experimentally and comparing the observed focal points with those obtained via ray-tracing simulations. With the radius of curvature conveniently controlled via fluid injection, the resulting microlens has a readily tunable focal length. This ease of operation, outstandingly low fluid usage, large range tunable focal length, and in-plane focusing ability make this lens suitable for many potential lab-on-a-chip applications such as particle manipulation, flow cytometry, and in-plane optical trapping.
Characterization of a microflow cytometer with an integrated three-dimensional optofluidic lens system
Authors: Rosenauer M. , Vellekoop M. J.
Published: December 2010

Flow cytometry is a standard analytical method in cell biology and clinical diagnostics and is widely distributed for the experimental investigation of microparticle characteristics. In this work, the design, realization, and measurement results of a novel planar optofluidic flow cytometric device with an integrated three-dimensional (3D) adjustable optofluidic lens system for forward-scattering/extinction-based biochemical analysis fabricated by silicon micromachining are presented. To our knowledge, this is the first planar cytometric system with the ability to focus light three-dimensionally on cells/particles by the application of fluidic lenses. The single layer microfluidic platform enables versatile 3D hydrodynamic sample focusing to an arbitrary position in the channel and incorporates integrated fiber grooves for the insertion of glass fibers. To confirm the fluid dynamics and raytracing simulations and to characterize the sensor, different cell lines and sets of microparticles were investigated by detecting the extinction (axial light loss) signal, demonstrating the high sensitivity and sample discrimination capability of this analysis system. The unique features of this planar microdevice enable new biotechnological analysis techniques due to the highly increased sensitivity.
Optical manipulation and binding of microrods with multiple traps enabled in an inclined dual-fiber system
Authors: Liu Yuxiang , Yu Miao
Published: December 2010

We present experimental demonstrations of optical manipulation and optical binding of microscopic glass rods using the multiple traps created by a dual-fiber optical trapping system. Trapping, alignment, rotation, and stacking of glass rods were realized. To the best of our knowledge, this is the first time that cylindrical particles are optically trapped and bound by an optical fiber-based system. The optical manipulation of rods is also investigated through numerical simulations, which are used to quantitatively explain the experimental results. The ability of manipulating multiple particles of different shapes, as well as the integrable nature of the fiber-based setup, bestows the system the potential to be used in microfluidic systems for versatile particle manipulations.
Transfer-matrix-based method for an analytical description of velocity-map-imaging spectrometers
Authors: Harb M. M. , Cohen S. , Papalazarou E. , Lépine F. , Bordas C.
Published: December 2010

We propose a simple and general analytical model describing the operation of a velocity-map-imaging spectrometer. We show that such a spectrometer, possibly equipped with a magnifying lens, can be efficiently modeled by combining analytical expressions for the axial potential distributions along with a transfer matrix method. The model leads transparently to the prediction of the instrument's operating conditions as well as to its resolution. A photoelectron velocity-map-imaging spectrometer with a magnifying lens, built and operated along the lines suggested by the model has been successfully employed for recording images at threshold photoionization of atomic lithium. The model's reliability is demonstrated by the fairly good agreement between experimental results and calculations. Finally, the limitations of the analytical method along with possible generalizations, extensions, and potential applications are also discussed. The model may serve as a guide for users interested in building and operating such spectrometers as well as a tutorial tool.
Optofluidic tweezer on a chip
Authors: Ono K. , Kaneda S. , Shiraishi T. , Fujii T.
Published: December 2010

A novel method to realize an optical tweezer involving optofluidic operation in a microchannel is proposed. To manipulate the optical tweezer, light from an optical fiber is passed through both PDMS (polydimethylsiloxane)-air surface lenses and an optofluidic region, which is located in a control channel. Two liquids with different refractive indices (RIs) are introduced into the control channel to form two different flow patterns (i.e., laminar and segmented flows), depending on the liquid compositions, the channel geometry, and the flow rates. By altering the shapes of the interface of the two liquids in the optofluidic region, we can continuously or intermittently control the optical paths of the light. To demonstrate the functionality of the proposed method, optical tweezer operations on a chip are performed. Changing the flow pattern of two liquids with different RIs in the optofluidic region results in successful trapping of a 25 μm diameter microsphere and its displacement by 15 μm.
Understanding free-energy perturbation calculations through a model of harmonic oscillators: Theory and implications to improve the sampling efficiency by molecular simulation
Authors: Wu Di
Published: December 2010

Free-energy perturbation calculation is frequently used to calculate free-energy differences because it is easy to implement and the computation is fast. However, the calculation is subject to large inaccuracies in some circumstances due to the insufficient sampling of the relevant tails of the energy-difference distributions. Here we expand this knowledge of insufficient sampling into a two-dimensional (2D) energy space using a model of harmonic oscillators. We show analytically the relation between the energies of the sampling system and those of the desired target energy spaces, which provide the basis to understand the difficulties in free-energy perturbation calculations. We clarify the reasons of the inaccurate calculation in the different harmonic cases that stem from the spatial separations of the reference and the target energy pairs located in the two-dimensional energy space. The potential-energy space introduced into this 2D energy-space model provides additional clues to improve the sampling efficiency. Based on this understanding, we propose two ways to calculate the free-energy differences using the two schemes of the distribution method. We show that the distribution method implemented in the appropriate energy space—the energy-difference space and the potential-energy space, respectively—can improve the calculation of free energies in different circumstances. This analysis implies that the sampling can be improved if it is directed toward the appropriate region in the potential-energy space, which is easily implemented in various types of free-energy calculations. To test this, we calculate the free-energy surface of alanine dipeptide in gas phase and in aqueous phase, respectively. We demonstrate that the free-energy surface calculation is improved when the biased sampling of the potential energy is integrated into the sampling scheme.
Review Article: Recent advancements in optofluidic flow cytometer
Authors: Cho Sung Hwan , Godin Jessica M. , Chen Chun-Hao , Qiao Wen , Lee Hosuk , Lo Yu-Hwa
Published: December 2010

There is an increasing need to develop optofluidic flow cytometers. Optofluidics, where optics and microfluidics work together to create novel functionalities on a small chip, holds great promise for lab-on-a-chip flow cytometry. The development of a low-cost, compact, handheld flow cytometer and microfluorescence-activated cell sorter system could have a significant impact on the field of point-of-care diagnostics, improving health care in, for example, underserved areas of Africa and Asia, that struggle with epidemics such as HIV/AIDS. In this paper, we review recent advancements in microfluidics, on-chip optics, novel detection architectures, and integrated sorting mechanisms.
Topological structures enhance the presence of dynamical regimes in synthetic networks
Authors: Koseska A. , Kurths J.
Published: December 2010

Genetic and protein networks, through their underlying dynamical behavior, characterize structural and functional cellular processes, and are thus regarded as “driving forces” of all living systems. Understanding the rhythm generation mechanisms that emerge from such complex networks has benefited in recent years by synthetic approaches, through which simpler network modules (e.g., switches and oscillators) have been built. In this manner, a significant attention to date has been focused on the dynamical behavior of these isolated synthetic circuits, and the occurrence of unifying rhythms in systems of globally coupled genetic units. In contrast to this, we address here the question: Could topologically distinct structures enhance the presence of various dynamical regimes in synthetic networks? We show that an intercellular mechanism, engineered to operate on a local scale, will inevitably lead to multirhythmicity, and to the appearance of several coexisting (complex) dynamical regimes, if certain preconditions regarding the dynamical structure of the synthetic circuits are met. Moreover, we discuss the importance of regime enhancement in synthetic structures in terms of memory storage and computation capabilities.
Optofluidic in situ maskless lithography of charge selective nanoporous hydrogel for DNA preconcentration
Authors: Kim Hyoki , Kim Junhoi , Kim Eun-Geun , Heinz Austen James , Kwon Sunghoon , Chun Honggu
Published: December 2010

An optofluidic maskless photopolymerization process was developed for in situ negatively charged nanoporous hydrogel [poly-AMPS (2-acrylamido-2-methyl-1-propanesulfonic acid)] fabrication. The optofluidic maskless lithography system, which combines a high power UV source and digital mirror device, enables fast polymerization of arbitrary shaped hydrogels in a microfluidic device. The poly-AMPS hydrogel structures were positioned near the intersections of two microchannels, and were used as a cation-selective filter for biological sample preconcentration. Preconcentration dynamics as well as the fabricated polymer shape were analyzed in three-dimensions using fluorescein sample and a confocal microscope. Finally, single-stranded DNA preconcentration was demonstrated for polymerase chain reaction-free signal enhancement.
Transmittance tuning by particle chain polarization in electrowetting-driven droplets
Authors: Fan Shih-Kang , Chiu Cheng-Pu , Huang Po-Wen
Published: December 2010

A tiny droplet containing nano/microparticles commonly handled in digital microfluidic lab-on-a-chip is regarded as a micro-optical component with tunable transmittance at programmable positions for the application of micro-opto-fluidic-systems. Cross-scale electric manipulations of droplets on a millimeter scale as well as suspended particles on a micrometer scale are demonstrated by electrowetting-on-dielectric (EWOD) and particle chain polarization, respectively. By applying electric fields at proper frequency ranges, EWOD and polarization can be selectively achieved in designed and fabricated parallel plate devices. At low frequencies, the applied signal generates EWOD to pump suspension droplets. The evenly dispersed particles reflect and/or absorb the incident light to exhibit a reflective or dark droplet. When sufficiently high frequencies are used on to the nonsegmented parallel electrodes, a uniform electric field is established across the liquid to polarize the dispersed neutral particles. The induced dipole moments attract the particles each other to form particle chains and increase the transmittance of the suspension, demonstrating a transmissive or bright droplet. In addition, the reflectance of the droplet is measured at various frequencies with different amplitudes.