bluuebunny/crossref_metadata_2025 huggingface dataset:
The twists and turns of rotating turbulence
Authors: DALZIEL STUART B.
Published: January 2011

Turbulence is widely considered one of the most important and most difficult unsolved problems in classical physics. It is also the area of fluid mechanics where the greatest effort is exerted, the most papers published and, some would argue, the least progress made. Although direct numerical simulation is becoming an increasingly valuable tool, there remains a need for high-quality experiments to underpin our theoretical and numerical progress. Such statements apply equally to the ‘classical’ problem of homogeneous isotropic turbulence and to turbulence in its many other guises. Of particular interest is turbulence in a rotating system, where it is well known that the influence of rotation leads to the development of anisotropy and the elongation of scales parallel to the rotation axis. Moisy et al. (J. Fluid Mech., 2010, this issue, vol. 666, pp. 5–35) present new experiments in the free decay of grid-generated turbulence in a rotating system. They investigate the emergence of anisotropy from essentially isotropic initial conditions. While it is well known that rotation suppresses velocity gradients parallel to the rotation axis, Moisy et al. (2010) uncover some startling and previously overlooked implications.
Emotional triggering and low socio-economic status as determinants of depression following acute coronary syndrome
Authors: Steptoe A. , Molloy G. J. , Messerly-Bürgy N. , Wikman A. , Randall G. , Perkins-Porras L. , Kaski J. C.
Published: January 2011

Background

The determinants of depression following acute coronary syndrome (ACS) are poorly understood. Triggering of ACS by emotional stress and low socio-economic status (SES) are predictors of adverse outcomes. We therefore investigated whether emotional triggering and low SES predict depression and anxiety following ACS.

Method

This prospective observational clinical cohort study involved 298 patients with clinically verified ACS. Emotional stress was assessed for the 2 h before symptom onset and compared with the equivalent period 24 h earlier using case-crossover methods. SES was defined by household income and education. Depression was measured with the Beck Depression Inventory and the Hamilton Rating Scale for Depression and anxiety with the Hospital Anxiety and Depression Scale 3 weeks after ACS and again at 6 and 12 months. Age, gender, ethnicity, marital status, the Global Registry of Acute Coronary Events risk score, duration of hospital stay and history of depression were included as covariates.

Results

Emotional stress during the 2-h hazard period was associated with increased risk of ACS (odds ratio 1.88, 95% confidence interval 1.01–3.61). Both low income and emotional triggering predicted depression and anxiety at 3 weeks and 6/12 months independently of covariates. The two factors interacted, with the greatest depression and anxiety in lower income patients who experienced acute emotional stress. Education was not related to depression.

Conclusions

Patients who experience acute emotional stress during their ACS and are lower SES as defined by current affluence and access to resources are particularly vulnerable to subsequent depression and anxiety.
RECONNOITERING THE SONIC SPECTRUM OF SALVATORE SCIARRINO IN ‘ALL' AURE IN UNA LONTANANZA’
Authors: McConville Brendan P.
Published: January 2011

The above quote, extracted from his L'Opere per Flauto (1977–1990), provides not only a colorful introduction to the effusive imagination of Italian composer Salvatore Sciarrino, but also a preview of what an unfamiliar listener may expect to find in his music. His largely unchanging musical language has slowly yet deliberately – like the four-minute unbroken cello glissando found near the end of his Vanitas for voice, cello and piano (1981)– captured the attention of composers, performers, scholars, and new music enthusiasts for over 30 years. Moreover, examination of Sciarrino's music provokes consideration for fascinating compositional comparisons, particularly in 20th-century Italian music, as his oeuvre demonstrates similarities with, and advancements of, the music of his compatriots. In this article, we will ‘reconnoiter’ the music of Sciarrino on two different levels, by: 1) contextualizing the formulization of his compositional language from developmental and sociological perspectives, and 2) conceptualizing these investigations in All'Aure in Una Lontananza (1977), a work which would perhaps forecast goals of his life output.
The Simulation of Smiles (SIMS) model: Embodied simulation and the meaning of facial expression
Authors: Niedenthal Paula M. , Mermillod Martial , Maringer Marcus , Hess Ursula
Published: January 2011

Recent application of theories of embodied or grounded cognition to the recognition and interpretation of facial expression of emotion has led to an explosion of research in psychology and the neurosciences. However, despite the accelerating number of reported findings, it remains unclear how the many component processes of emotion and their neural mechanisms actually support embodied simulation. Equally unclear is what triggers the use of embodied simulation versus perceptual or conceptual strategies in determining meaning. The present article integrates behavioral research from social psychology with recent research in neurosciences in order to provide coherence to the extant and future research on this topic. The roles of several of the brain's reward systems, and the amygdala, somatosensory cortices, and motor centers are examined. These are then linked to behavioral and brain research on facial mimicry and eye gaze. Articulation of the mediators and moderators of facial mimicry and gaze are particularly useful in guiding interpretation of relevant findings from neurosciences. Finally, a model of the processing of the smile, the most complex of the facial expressions, is presented as a means to illustrate how to advance the application of theories of embodied cognition in the study of facial expression of emotion.
Cultural variations on the SIMS model
Authors: Covas-Smith Christine M. , Fine Justin , Glenberg Arthur M. , Keylor Eric , Li Yexin Jessica , Marsh Elizabeth , Osborne Elizabeth A. , Soliman Tamer , Yee Claire
Published: January 2011

Niedenthal et al. recognize that cultural differences are important when interpreting facial expressions. Nonetheless, many of their core observations derive more from individualistic cultures than from collectivist cultures. We discuss two examples from the latter: (1) lower rates of mutual eye contact, and (2) the ubiquity of specific “functional smiles.” These examples suggest constraints on the assumptions and applicability of the SIMS model.
Le bon dieu est dans le detail: Is smiling the recognition of happiness?
Authors: Fernández-Dols José-Miguel , Carrera Pilar
Published: January 2011

We question two conceptual assumptions made by Niedenthal et al.: the dichotomy between true and false smiles and the close tie between recognition and experience of emotion. An excessive dependence on everyday language suggests overly parsimonious accounts of a complex set of relations between smile, experience, and context.
Does motor mimicry contribute to emotion recognition?
Authors: Hamon-Hill Cindy , Barresi John
Published: January 2011

We focus on the role that motor mimicry plays in the SIMS model when interpreting whether a facial emotional expression is appropriate to an eliciting context. Based on our research, we find general support for the SIMS model in these situations, but with some qualifications on how disruption of motor mimicry as a process relates to speed and accuracy in judgments.
The proximate mechanisms and ultimate functions of smiles
Authors: Mehu Marc , N'Diaye Karim
Published: January 2011

Niedenthal et al's classification of smiles erroneously conflates psychological mechanisms and adaptive functions. This confusion weakens the rationale behind the types of smiles they chose to individuate, and it obfuscates the distinction between the communicative versus denotative nature of smiles and the role of perceived-gaze direction in emotion recognition.
What's behind the smile?
Authors: Ohala John J.
Published: January 2011

Many species' non-threat facial expression involves an open mouth and retracted lip corners – the smile. This served to make an accompanying vocalization sound like it originated from a smaller vocalizer. That such signals are deceptive and benefit primarily the signaler undermines the notion that the perception of the smile employs embodied simulation of the smiler's state.
Baby smile response circuits of the parental brain
Authors: Swain James E. , Ho S. Shaun
Published: January 2011

The parent-infant dyad, characterized by contingent social interactions that develop over the first three months postpartum, may depend heavily on parental brain responses to the infant, including the capacity to smile. A range of brain regions may subserve this social key function in parents and contribute to similar capacities in normal infants, capacities that may go awry in circumstances of reduced care.
The future of SIMS: Who embodies which smile and when?
Authors: Niedenthal Paula M. , Mermillod Martial , Maringer Marcus , Hess Ursula
Published: January 2011

The set of 30 stimulating commentaries on our target article helps to define the areas of our initial position that should be reiterated or else made clearer and, more importantly, the ways in which moderators of and extensions to the SIMS can be imagined. In our response, we divide the areas of discussion into (1) a clarification of our meaning of “functional,” (2) a consideration of our proposed categories of smiles, (3) a reminder about the role of top-down processes in the interpretation of smile meaning in SIMS, (4) an evaluation of the role of eye contact in the interpretation of facial expression of emotion, and (5) an assessment of the possible moderators of the core SIMS model. We end with an appreciation of the proposed extensions to the model, and note that the future of research on the problem of the smile appears to us to be assured.
Editorial
Authors: ASTON ELAINE
Published: January 2011

‘Radical bodies’, to borrow from Diana Looser's title, emerge as a central concern in this general issue of TRI, where five articles explore the policitizing possibilities of theatre in relation to multifaceted questions of gender, cultural hybridity, identity and social democracy, in a rich and diverse range of performances and geographical locations.
Renaming and Performative Reconstructions: The Uncanny Multiplication of Janez Janša
Authors: WILMER S. E.
Published: January 2011

This article considers the uncanny action by three Slovenian artists in 2007 to rename themselves Janez Janša, the name of the right-wing prime minister of Slovenia. It assesses specific performances by the artists, including the Slovene National Theatre, a postdramatic verbatim piece about a Roma family evicted from their homes by Janša's government in response to the mob action of Slovenian villagers. It also interrogates their performance event for the Transmediale Festival at the Holocaust Memorial in Berlin in 2008, first banned and then reinstated by the festival organizers, where they created a virtual signature of their new name on the memorial. Theoretically, the importance of naming and renaming as practised by the artists is examined in relation to concepts of subversive affirmation, the author-function in society and postdramatic theatre.
Temple, Community, and Sacred Narrative in the Dura-Europos Synagogue
Authors: Schenk Kära L.
Published: January 2011

The painted decoration in the Dura-Europos synagogue (Syria, 244–245 CE) is the most extensive surviving example of Jewish pictorial narrative in the ancient world. In its final stage, the decoration consisted of three bands of narrative panels that surrounded all four walls of the synagogue's assembly hall and led up to the Torah shrine at the center of the west wall (Figure 1). Imagery related to the Jerusalem Temple, including a symbolic image of the Temple on the Torah shrine, made up a significant part of the decoration of the Dura synagogue. There is, however, considerable scholarly disagreement as to how this imagery should be interpreted, particularly as part of a “programmatic” structure. Because the Temple image on the Torah shrine was positioned at the liturgical focal point of the synagogue and was created before the other surrounding narrative panels, the function of this image is a key component of the synagogue's decoration as a whole. Two contextualizing factors would have informed the function and meaning of the image: the reception of the image as part of the liturgical activity carried out by the congregation, and the place of the image as the conclusion to the middle level of surrounding narrative panels that depicted the journey of the Ark of the Covenant from Sinai to Zion. This narrative helped to situate the members of the congregation in relation to the Temple image, defining the community's active role as a part of the narrative itself.
War within, War without: Russian Refugee Rabbis during World War I
Authors: Koss Andrew N.
Published: January 2011

After the outbreak of World War I in 1914, Rabbi Ya‘akov Landa was one of some 250,000 Russian Jews who had fled, or been forcibly expelled, from their homes in Russia's western provinces to settle in the country's interior. After Landa's exile, he spent several months traveling amid refugee communities in Voronezh, Tambov, Penza, Saratov, and Samara provinces. At the conclusion of his journey, he composed a detailed report about the state of religious observance among the refugees, which he sent to Rabbi Shalom Dov-Ber Schneerson of Lubavitch. Landa's observations during these months shocked his core sensibilities as a rabbi and an observant Jew. He noted that refugees were disregarding such fundamental aspects of Jewish practice as Sabbath observance and were living without the basic institutions that had traditionally defined religious and communal life.
Between Zionism and Liberalism: Oscar Janowsky and Diaspora Nationalism in America
Authors: Loeffler James
Published: January 2011

Of all the varieties of modern Jewish politics, none has experienced a more curious fate than Diaspora Nationalism. This nonterritorial strain of Jewish nationalism, also known as Autonomism, was once widely regarded as “together with Zionism the most important political expression of the Jewish people in the modern era.” From its fin-de-siècle origins in the Russian and Austro-Hungarian empires, it spread rapidly across Eastern Europe, sprouting various movements for Jewish national-cultural autonomy. After World War II, however, Diaspora Nationalism vanished almost overnight. So too was its intellectual afterlife marked by silence, as postwar historians of Jewish political thought largely ignored its legacy. Recently, however, Diaspora Nationalism has emerged as a growing field of scholarship. The results are impressive: a striking new wave of studies on its intellectual leadership, political parties, cultural projects, and various interwar East European Autonomist experiments. This abundance of fresh research promises to reframe not only the history of Diaspora Nationalism, but also that of Zionism and Jewish nationalism more generally.
The Dead Sea Scrolls and the History of the Jewish Book
Authors: Schiffman Lawrence H.
Published: January 2011

The complicated process whereby the biblical books took shape and were copied and transmitted in biblical times can only be partly reconstructed based on biblical evidence, with the help of ancient Near Eastern parallels. Clearly, the biblical era constitutes the first stage in the history of the Jewish book, or more correctly,theJewish bookpar excellence. However, for the period immediately following, the Second Temple period, the level of documentation for creating, editing/redacting, and copying and disseminating Jewish books is now enormous due to the discovery, publication, and analysis of the Dead Sea Scrolls. While this information relates directly to the period in which the Scrolls were copied, from the last part of the third centurybcethrough the early first centuryce, it also allows us a model with which to supplement our understanding of the biblical period, and much of it is directly relevant to the rabbinic period in which most of the same scribal conventions were in use.
The Jewish Book and Beyond in Modern Times
Authors: Shandler Jeffrey
Published: January 2011

How might one begin to think about the Jewish book in the modern era? The period is defined by unprecedented proliferation—not only of many new books, but also of an array of new kinds of books, as well as a plethora of new print and other communications technologies, new professions and institutions associated one way or another with books, and new text practices. This burgeoning volume of material, as well as the expansive range of possibilities for books and how they figure in Jewish life, demand that those who would study the place of the book in modern Jewish life (up to and including contemporary phenomena) would do well to begin with reconnaissance, casting the net wide and considering which larger issues this wealth of materials and practices suggests for further study. This survey not only yields an impressive roster of potential subjects of inquiry; the information itself suggests possibilities for understanding Jewish books and book practices as a defining feature of modern Jewish life.
A Matter of Distinction: On Recent Work by Jan Assmann
Authors: Slavet Eliza
Published: January 2011

The study of memory and its collaborators (history, narrative, and trauma) has been at the center of both the German- and English-language academic worlds for at least the last fifteen years. While many of the “canonical” texts overlap, the anxieties and implications of recent scholarship have often been quite distinct, particularly in discussions of the memory and history of the Holocaust, and more generally, anti-Semitism, Jews, and Judaism. This phenomenon is played out in the debates about Jan Assmann's work, particularly since the publication ofMoses the Egyptian: The Memory of Egypt in Western Monotheism(1997).
Between Past and Present, Jew and Arab: An Exchange between Gil Anidjar and David N. Myers
Authors: Anidjar Gil , Myers David N.
Published: January 2011

Amira Hass,Haaretz's fearless journalist, recently told the following joke, an allegory of sorts, set during the Turco-Russian war. Moishele is about to depart for the front, and so his mother offers some sensible advice. “Please take care of yourself, my son. Pace yourself. Kill a Turk all right, but then make sure you rest afterwards. Eat something. Sleep a little. Then go back if you must, kill another Turk, and take another break. Drink lots of fluids, and make sure you maintain and replenish your strength.” “But Mamele,” retorts Moishele, “What if while I am eating and resting, there comes a Turk to kill me?” “Oy va voy, my son! Why would anyone do such a thing? What could he possibly have against you?”
Circulation of Aichi virus genotype B strains in children with acute gastroenteritis in India
Authors: VERMA H. , CHITAMBAR S. D. , GOPALKRISHNA V.
Published: January 2011

Acute gastroenteritis (AG) is considered as one of the major health problems affecting humans of all ages. A number of viruses have been recognized as important causes of this disease. Recently, Aichi virus has been shown to play an aetiological role in sporadic infections and outbreaks of AG. A study on surveillance of enteric viruses was conducted during 2004–2008 in three cities in Maharashtra state, western India. A total of 1240 stool specimens from children aged ⩽8 years hospitalized for AG were screened for the presence of Aichi virus by RT–PCR of the 3C–3D junction region followed by sequencing for the identification of genotype. Aichi virus was detected at a prevalence of 1·1% in the <5 years age group and characterized as genotype B. This is the first report on the circulation of Aichi virus genotype B in India.
Facemasks and intensified hand hygiene in a German household trial during the 2009/2010 influenza A(H1N1) pandemic: adherence and tolerability in children and adults
Authors: SUESS T. , REMSCHMIDT C. , SCHINK S. , LUCHTENBERG M. , HAAS W. , KRAUSE G. , BUCHHOLZ U.
Published: January 2011

Non-pharmaceutical interventions (NPI) such as facemasks and intensified hand hygiene may be effective in preventing influenza infections in households. It may be equally important that household members, especially children, can learn to use, maintain and tolerate these measures. We monitored adherence and tolerability of these NPI within a cluster-randomized trial in households with influenza index patients. We recruited 147 participants in 41 households, 39 (95%) out of 41 index patients were children (aged <14 years). In households assigned to wear facemasks, their use peaked on day 4 after symptom onset of the index patient at 73% and at 65% for children and adults, respectively. Mean daily frequency of hand disinfection in households assigned to intensified hand hygiene measures peaked at 7·7 (day 6) for children and at 10·1 (day 5) for adults. The majority of participants reported no problems with mask wearing. Data suggest that usage of NPI can be taught and that measures are well tolerated by adults and even sick children alike.
Phonotactics and the prestopped velar lateral of Hiw: resolving the ambiguity of a complex segment
Authors: François Alexandre
Published: January 2011

Complex segments consisting of two phases are potentially ambivalent as to which phase determines their phonemic status – e.g. whether // is a stop or a nasal. This theoretical problem is addressed here with respect to a typologically unusual phoneme in Hiw, an endangered Oceanic language of Vanuatu. This complex segment, //, combines a velar voiced stop and a velar lateral approximant. Similar phonemes, in the few languages which have them, have been variously described as (laterally released) stops, affricates or (prestopped) laterals. The nature of Hiw // can be established from its patterning in tautosyllabic consonant clusters. The licensing of word-initial CC clusters in Hiw complies with the Sonority Sequencing Principle, albeit with some adjustments. Consequently, the well-formedness of words like /mejiŋə/ ‘berserk’ relies on // being analysed as a prestopped velar lateral approximant – the only liquid in the system.
The EU and constitutional change: a research proposal
Authors: WTE  , TWB
Published: January 2011

The first punctual question arising is how, in its (single) constitutional being, a body such as the Union combines its constituent roots in the original founding authorities (the states) with those, autonomous, in its own institutions. These are the ECJ for interpretation; the political institutions for practice and convention. In other words, what is the actual relationship, under the urge of change, between the states as treaty masters and the European Council, the Council, the Parliament and the Court? Secondly, there is the question as to how these shared constituent roots reflect not on constitutional change but on the day-to-day legislative and executive functioning of the Union's body politic. The coming constitutional settlement on the euro's financial support mechanism will not only consist of a new treaty. It will also take the form of secondary legislation and case-law. A third, most fundamental, question is how this ever-unfinished constitutional situation, imperfect by definition, will ultimately allow the development of a sound relationship between the authorities and the people, a relationship which is at the heart of any constitutional settlement. The last question (for now) sends us back to the one put in a previous editorial (in issue 1 of this year). It is: how to account for this incomplete and urged situation in a single and coherent constitutional reading?
Supreme Court of the United Kingdom: To Be or Not To Be Jewish: The UK Supreme Court Answers the Question; Judgment of 16 December 2009, R v The Governing Body of JFS, 2009 UKSC 15
Authors: Mancini Susanna
Published: January 2011

On 16 December 2009, the UK Supreme Court held a state-funded Jewish school to be guilty of discrimination based on ethnic origin in the way it operated its admissions policies. The Jewish Free School (JFS), one of the top-performing schools in the country, refused a place to a thirteen year old boy, M., because it did not consider him Jewish. It is a fundamental tenet of traditional Judaism that to be Jewish one must be born of Jewish mother or to a woman who converted into Judaism prior to his/her birth. M.'s father was Jewish by birth, but his mother, who was originally an Italian Catholic, had converted to Judaism with the criteria set by a non-orthodox branch of Judaism. The School's admissions standards only recognized orthodox criteria for conversion as valid, hence deeming neither M. nor his mother to be Jewish.
Struggles for Institutional Space in France and the United Kingdom: Intersectionality and the Politics of Policy
Authors: Bassel Leah , Emejulu Akwugo
Published: January 2011

This article uses intersectionality as an analytical tool to explore struggles for institutional space in policy processes in two ostensibly contrasting contexts: “republican” France and the “multicultural” United Kingdom. Specifically, the article undertakes within-case analysis of three policy processes. In France, we discuss the debate overlaïcité, or secularism, the subsequent formulation of the March 2004 law banning the wearing of religious signs in state schools, and the creation of the High Authority for the Fight Against Discrimination (HALDE). In the UK, we examine the problem definitions, language, and subject positions constructed by the 2008 Single Equality Bill. The result of these analyses is that institutional actors employ similar (though not identical) practices in relation to intersections, which have similar outcomes for minority groups on either side of the English Channel. Through what we term a “logic of separation,” institutional actors severely curtail the “institutional space” available to minority ethnic groups to make complex and intersectional social justice claims. Even though France and the UK are often portrayed as opposites with regard to constructions of citizenship, we argue that these seemingly differing traditions of citizenship end up having a similar effect of misrecognizing minority women and men's experiences and demands.
Women's Movement Institutionalization: The Need for New Approaches
Authors: Andrew Merrindahl
Published: January 2011

The social movements that first flourished in the 1960s and 1970s were initially characterized by protest activity against the state and against dominant norms, and by their only loosely organized structures. Over time, however, these social movements, including feminism, have become partially institutionalized in government and nongovernment bodies, and in policies, practices, and social norms.
The ovarian dysgenesis syndrome
Authors: Buck Louis G. M. , Cooney M. A. , Peterson C. M.
Published: January 2011

New thinking has arisen about the origin of adult onset diseases stemming from a collective body of evidence commonly referred to as the developmental origins of health and disease. This conceptual paradigm posits that certain adult onset diseases arise during critical or sensitive windows of human development or even transgenerationally. The testicular dysgenesis hypothesis (TDS) postulates anin uteroorigin for adverse male reproductive outcomes, and is an excellent example of the early origins of the paradigm. Despite similarities in the development of the male and female reproductive tracks, noticeably absent is a collective body of evidence focusing on the plausibility of an early origin for gynecologic outcomes and later onset of adult diseases. Using the TDS paradigm, we synthesized the available literature relative to the ovarian dysgenesis syndrome (ODS), which we define as alterations in ovarian structure or function that may manifest as fecundity impairments, gynecologic disorders, gravid diseases or later onset adult diseases. We evaluated environmental exposures, particularly the role of endocrine disrupting chemicals, in relation to these outcomes, and found evidence (although fragmented) consistent with anin uteroorigin of gynecologic outcomes, which in turn is associated with later onset of adult diseases. The findings are interpreted within the ODS paradigm while delineating methodological challenges and future research opportunities designed to answer critical data gaps regarding the origin of fecundity, gravid health and chronic diseases affecting the female population.
Using spacecraft measurements ahead of Earth in the Parker spiral to improve terrestrial space weather forecasts
Authors: Turner D. L. , Li X.
Published: January 2011

Space weather forecasting is important for mitigating the risks that the effects of the near‐Earth space environment have on man‐made systems. Here we investigate an innovative technique for extending the temporal range of solar wind–based forecast models by using solar wind measurements made azimuthally ahead of Earth in the Parker spiral near 1 AU. Cross correlations between STEREO (near 1 AU) and ACE (at L1) solar wind quantities are examined for a 1 year period during the most recent solar minimum, and we show that data from STEREO‐B, which is azimuthally behind Earth in its orbit but ahead of Earth in the Parker spiral, can be used as an input to a relativistic electron forecast model to extend its capability to +6 days from its original range of +2 days. We show that this extended forecast performs better than simple persistence or average models for all 6 forecast days. We also compare +1 day solar wind speed forecasts using offset STEREO‐B data and the Wang‐Sheeley‐Arge model, and we find that the offset STEREO‐B data performs significantly better for estimating the future solar wind at Earth during the investigation period. We conclude that this technique could be particularly beneficial to space weather forecasting and argue for a permanent solar wind monitor at the fifth Lagrange point in the Sun‐Earth system.
Develop reusable and combinable designs for transcriptional logic gates
Authors: Zhan Jian , Ding Bo , Ma Rui , Ma Xiaoyu , Su Xiaofeng , Zhao Yun , Liu Ziqing , Wu Jiarui , Liu Haiyan
Published: January 2011

One limit on developing complex synthetic gene circuits is the lack of basic components such as transcriptional logic gates that can process combinatorial inputs. Here, we propose a strategy to construct such components based on reusable designs and convergent reengineering of well‐studied natural systems. We demonstrated the strategy using variants of the transcription factor (TF) LacI and operator Olac that form specifically interacting pairs. Guided by a mathematical model derived from existing quantitative knowledge, rational designs of transcriptional NAND, NOR and NOT gates have been realized. The NAND gates have been designed based on direct protein–protein interactions in coupling with DNA looping. We demonstrated that the designs are reusable: a multiplex of logic devices can be readily created using the same designs but different combinations of sequence variants. The designed logic gates are combinable to form compound circuits: a demonstration logic circuit containing all three types of designed logic gates has been synthesized, and the circuit truthfully reproduces the pre‐designed input–output logic relations.
Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection
Authors: Peña Matthew I , Davlieva Milya , Bennett Matthew R , Olson John S , Shamoo Yousif
Published: January 2011

Systems biology can offer a great deal of insight into evolution by quantitatively linking complex properties such as protein structure, folding, and function to the fitness of an organism. Although the link between diseases such as Alzheimer's and misfolding is well appreciated, directly showing the importance of protein folding to success in evolution has been more difficult. We show here that predicting success during adaptation can depend critically on enzyme kinetic and folding models. We used a ‘weak link’ method to favor mutations to an essential, but maladapted, adenylate kinase gene within a microbial population that resulted in the identification of five mutants that arose nearly simultaneously and competed for success. Physicochemical characterization of these mutants showed that, although steady‐state enzyme activity is important, success within the population is critically dependent on resistance to denaturation and aggregation. A fitness function based on in vitro measurements of enzyme activity, reversible and irreversible unfolding, and the physiological context reproduces in vivo evolutionary fates in the population linking organismal adaptation to its physical basis.
A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock
Authors: Brettschneider Christian , Rose Rebecca J , Hertel Stefanie , Axmann Ilka M , Heck Albert J R , Kollmann Markus
Published: January 2011

The circadian rhythm of the cyanobacterium Synechococcus elongatus is controlled by three proteins, KaiA, KaiB, and KaiC. In a test tube, these proteins form complexes of various stoichiometry and the average phosphorylation level of KaiC exhibits robust circadian oscillations in the presence of ATP. Using mathematical modeling, we were able to reproduce quantitatively the experimentally observed phosphorylation dynamics of the KaiABC clockwork in vitro. We thereby identified a highly non‐linear feedback loop through KaiA inactivation as the key synchronization mechanism of KaiC phosphorylation. By using the novel method of native mass spectrometry, we confirm the theoretically predicted complex formation dynamics and show that inactivation of KaiA is a consequence of sequestration by KaiC hexamers and KaiBC complexes. To test further the predictive power of the mathematical model, we reproduced the observed phase synchronization dynamics on entrainment by temperature cycles. Our model gives strong evidence that the underlying entrainment mechanism arises from a temperature‐dependent change in the abundance of KaiAC and KaiBC complexes.
17 years of integrated research, monitoring, and management of HWA and hemlock ecosystems at Delaware Water Gap National Recreation Area
Authors: Evans Richard
Published: January 2011

Delaware Water Gap National Recreation Area (“the park”) covers 28,000 ha along the Delaware River in Pennsylvania and New Jersey. Eastern hemlock forests cover 2,200 ha (8%) of the park, and are often associated with trout streams and scenic waterfalls. Activities like trout fishing, bird watching, and hiking are concentrated in hemlock forests, and many of these areas are officially designated as “Outstanding Natural Features” having “high intrinsic or unique values.” In 1989 hemlock woolly adelgid (HWA) was detected in the park, and since 1993 the park has conducted a program to address the threats that hemlock woolly adelgid and hemlock decline poses to park resources. This program includes annual monitoring of HWA populations and hemlock tree health in permanent plots, studies of hemlock ecosystems and associated biodiversity, and efforts to suppress HWA infestations and maintain hemlock ecosystems in the park. Questions addressed include: What are the distinctive characteristics of hemlock ecosystems in the park? What effects do HWA infestations have on hemlock health? What is the rate and extent of hemlock decline and mortality? How effective are insecticides and biological controls at suppressing HWA infestations and sustaining hemlock health? What are the ecological effects of hemlock decline?Sustained monitoring and research in the park during the past 17 years have provided answers to these questions and informed management. Streams draining hemlock forests are 1oC–2oC cooler in summer, hydrologically more stable, three times more likely to support trout, and typically support 30% more species of aquatic insects than streams draining hardwood forests. Birds such as blackburnian warblers, black-throated green warblers, and blue-headed vireos are very strongly associated with hemlock forests in the park. Permanent plot trees first became infested with HWA in 1998, and by 2008 no healthy hemlocks remained, and 30% had died. A dendrochronology study in the park concluded that every 1% increase in average plot HWA infestation level resulted in an 8% increase in the likelihood of a tree being in decline. Mathematical models indicate that hemlock mortality in the park will reach 50% by 2015, and 80% between 2020 and 2030. Although we have released over 90,000 biocontrol beetles in the past ten years, they have not controlled HWA populations. Insecticides effectively suppress HWA populations and sustain tree health, and we have treated about 10,000 individual trees to date. Continued hemlock decline will have major effects on park ecosystems and biodiversity.
Simultaneous characterization of the electro-optic, converse-piezoelectric, and electroabsorptive effects in epitaxial (Sr,Ba)Nb2O6 thin films
Authors: Cuniot-Ponsard M. , Desvignes J. M. , Bellemain A. , Bridou F.
Published: January 2011

Implementation of the linear electro-optic (EO) effect in thin film waveguides is expected to allow drastic reductions in the drive voltage, power, and dimensions of devices devoted to light modulation. It should also enable the realization of electrically tunable photonic crystal devices. In this paper we introduce a method which eliminates systematically the sources of the unreliability which strongly affects thin film EO characterization. Based on a Fabry–Perot reflective configuration, the method enables characterizing simultaneously the EO, converse-piezoelectric, and electroabsorptive effects in a film. It provides the magnitude and sign of each of the involved coefficients, and allows accounting for the whole of experimental data versus angle of incidence for both transverse-electric and transverse-magnetic polarizations. At λ=633 nm and room temperature, the results obtained with an epitaxial strontium barium niobate (SrxBa1−xNb2O6, x=0.60) ferroelectric thin film, are: r13=+8.5±1.3 pm/V, r33=+38.9±0.5 pm/V, d33=Δe/ΔV=+21±4 pm/V, and Δko/ΔV=(+9.8±0.6)×10−6, where r13 and r33 are two linear EO coefficients, d33 is a converse-piezoelectric coefficient, and e, ko, V represent, respectively, the film thickness, film ordinary extinction coefficient, and applied voltage. Converse-piezoelectric and electroabsorptive effects are found significant in the film response at a frequency below piezoelectric resonance. Diagonal and effective EO coefficients of the (Sr,Ba)Nb2O6 (SBN) film explored in the present work are larger than those of a crystal of lithium niobate (LN) at the same wavelength λ=633 nm. Taking into account the significant difference in dielectric permittivity between the two materials, advances and potential of LN and SBN thin film paths are compared.
Compact electrostatic beam optics for multi-element focused ion beams: Simulation and experiments
Authors: Mathew Jose V. , Bhattacharjee Sudeep
Published: January 2011

Electrostatic beam optics for a multi-element focused ion beam (MEFIB) system comprising of a microwave multicusp plasma (ion) source is designed with the help of two widely known and commercially available beam simulation codes: AXCEL-INP and SIMION. The input parameters to the simulations are obtained from experiments carried out in the system. A single and a double Einzel lens system (ELS) with and without beam limiting apertures (S) have been investigated. For a 1 mm beam at the plasma electrode aperture, the rms emittance of the focused ion beam is found to reduce from ∼0.9 mm mrad for single ELS to ∼0.5 mm mrad for a double ELS, when S of 0.5 mm aperture size is employed. The emittance can be further improved to ∼0.1 mm mrad by maintaining S at ground potential, leading to reduction in beam spot size (∼10 μm). The double ELS design is optimized for different electrode geometrical parameters with tolerances of ±1 mm in electrode thickness, electrode aperture, inter electrode distance, and ±1o in electrode angle, providing a robust design. Experimental results obtained with the double ELS for the focused beam current and spot size, agree reasonably well with the simulations.
Flattening a puckered cyclohexasilane ring by suppression of the pseudo-Jahn–Teller effect
Authors: Pokhodnya Konstantin , Olson Christopher , Dai Xuliang , Schulz Douglas L. , Boudjouk Philip , Sergeeva Alina P. , Boldyrev Alexander I.
Published: January 2011

We report the experimental and theoretical characterization of neutral Si6X12 (X = Cl, Br) molecules that contain D3d distorted six-member silicon rings due to a pseudo-Jahn–Teller (PJT) effect. Calculations show that filling the intervenient molecular orbitals with electron pairs of adduct suppresses the PJT effect in Si6X12, with the Si6 ring becoming planar (D6h) upon complex formation. The stabilizing role of electrostatic and covalent interactions between positively charged silicon atoms and chlorine atoms of the subject [Si6Cl14]2- dianionic complexes is discussed. The reaction of Si6Cl12 with a Lewis base (e.g., Cl-) to give planar [Si6Cl14]2- dianionic complexes presents an experimental proof that suppression of the PJT effect is an effective strategy in restoring high Si6 ring symmetry. Additionally, the proposed pathway for the PJT suppression has been proved by the synthesis and characterization of novel compounds containing planar Si6 ring, namely, [nBu4N]2[Si6Cl12I2], [nBu4N]2[Si6Br14], and [nBu4N]2[Si6Br12I2]. This work represents the first demonstration that PJT effect suppression is useful in the rational design of materials with novel properties.
A molecular quantum wire of linear carbon chains encapsulated within single-walled carbon nanotube (Cn@SWNT)
Authors: Lim San Hua , Lin Jianyi , Widjaja Effendi , Poh Chee Kok , Luo Zhiqiang , Gao Ping Qi , Shen Zexiang , Zhang Qing , Gong Hao , Feng Yuanping
Published: January 2011

Pure sp-hybridized linear carbon chains possess unique physical properties of one-dimensional (1D) system. However, linear carbon chains are highly unstable and require to be stabilized within a matrix for direct experimental studies. Here we report a plasma-enhanced chemical vapor deposition method to encapsulate and stabilize linear carbon chains (Cn) within vertically aligned SWNTs to form a sp-sp2 hybrid system (Cn@SWNT). Intense Raman signals at ∼1760–1860 cm−1 (L bands) indicate the presence of linear carbon chains within SWNTs. Electron transport of Cn@SWNT bundle exhibits Luttinger-liquid behavior.
Terahertz normal mode relaxation in pentaerythritol tetranitrate
Authors: Pereverzev Andrey , Sewell Thomas D.
Published: January 2011

Normal vibrational modes for a three-dimensional defect-free crystal of the high explosive pentaerythritol tetranitrate were obtained in the framework of classical mechanics using a previously published unreactive potential-energy surface [J. Phys. Chem. B 112, 734 (2008)]. Using these results the vibrational density of states was obtained for the entire vibrational frequency range. Relaxation of selectively excited terahertz-active modes was studied using isochoric-isoergic (NVE) molecular dynamics simulations for energy and density conditions corresponding to room temperature and atmospheric pressure. Dependence of the relaxation time on the initial modal excitation was considered for five excitation energies between 10 and 500 kT and shown to be relatively weak. The terahertz absorption spectrum was constructed directly using linewidths obtained from the relaxation times of the excited modes for the case of 10 kT excitation. The spectrum shows reasonably good agreement with experimental results. Dynamics of redistribution of the excited mode energy among the other normal modes was also studied. The results indicate that, for the four terahertz-active initially excited modes considered, there is a small subset of zero wave vector (k = 0) modes that preferentially absorb the energy on a few-picosecond time scale. The majority of the excitation energy, however, is transferred nonspecifically to the bath modes of the system.
The interplay of nonlinearity and architecture in equilibrium cytoskeletal mechanics
Authors: Wang Shenshen , Shen Tongye , Wolynes Peter G.
Published: January 2011

The interplay between cytoskeletal architecture and the nonlinearity of the interactions due to bucklable filaments plays a key role in modulating the cell's mechanical stability and affecting its structural rearrangements. We study a model of cytoskeletal structure treating it as an amorphous network of hard centers rigidly cross-linked by nonlinear elastic strings, neglecting the effects of motorization. Using simulations along with a self-consistent phonon method, we show that this minimal model exhibits diverse thermodynamically stable mechanical phases that depend on excluded volume, cross-link concentration, filament length, and stiffness. Within the framework set by the free energy functional formulation and making use of the random first order transition theory of structural glasses, we further estimate the characteristic densities for a kinetic glass transition to occur in this model system. Network connectivity strongly modulates the transition boundaries between various equilibrium phases, as well as the kinetic glass transition density.
Gas-liquid phase coexistence in quasi-two-dimensional Stockmayer fluids: A molecular dynamics study
Authors: Ouyang Wen-Ze , Xu Sheng-Hua , Sun Zhi-Wei
Published: January 2011

The Maxwell construction together with molecular dynamics simulation is used to study the gas-liquid phase coexistence of quasi-two-dimensional Stockmayer fluids. The phase coexistence curves and corresponding critical points under different dipole strength are obtained, and the critical properties are calculated. We investigate the dependence of the critical point and critical properties on the dipole strength. When the dipole strength is increased, the abrupt disappearance of the gas-liquid phase coexistence in quasi-two-dimensional Stockmayer fluids is not found. However, if the dipole strength is large enough, it does lead to the formation of very long reversible chains which makes the relaxation of the system very slow and the observation of phase coexistence rather difficult or even impossible.
Force-driven migration of particles in ordered porous media
Authors: Chen Shing Bor
Published: January 2011

Brownian dynamics simulation has been employed to study the behavior of force-driven particle migration in different ordered porous media comprised of periodically interconnected spherical cavities, representing inverted colloidal crystals. The effects of the imposed field strength and direction on the particle mobility and direction are investigated. The simulation results find that in a weak or intermediate field, the mobility normalized by the value in free solvent behaves in a similar way as the normalized diffusivity when the porosity is varied. Under a strong field, the normalized mobility can increase or decrease with the field strength, depending on the field direction relative to the cavity arrangement. If the imposed field is not aligned with any unobstructed pathway, the mobility tensor may become anisotropic and prolonged particle entrapment may also take place.