bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of purpose in life in healthy identity formation: A grounded model
Authors: Bronk Kendall Cotton
Published: January 2012

Researchers contend that committing to an inspiring purpose in life is an important component of healthy identity development for adolescents; however, little research has focused on how identity and purpose develop together. Therefore, the study followed a sample of eight adolescent purpose exemplars for five years in order to develop a grounded model of the way these two constructs interact. Findings suggest that for adolescent purpose exemplars, the processes of identity formation and purpose development reinforce one another; the development of purpose supports the development of identity, and the development of identity reinforces purposeful commitments. Furthermore, in the adolescent purpose exemplars' lives, the purpose and identity constructs largely overlap in such a way that what individuals hope to accomplish in their lives serves as the basis of the adults they hope to become. Implications of these findings are discussed.
Purpose plus: Supporting youth purpose, control, and academic achievement
Authors: Pizzolato Jane Elizabeth , Brown Elizabeth Levine , Kanny Mary Allison
Published: January 2012

Research in the past decade suggests that a persistent achievement gap between students from low‐income minority backgrounds and higher‐income white backgrounds may be rooted in theories of student motivation and youth purpose. Yet limited research exists regarding the role of purpose on positive youth development as it pertains to academic achievement. Using a sample of 209 high school students, this study examines the effectiveness of an intervention designed to promote purpose development and internal control over academic success in high school students from a low‐socioeconomic‐status community. Findings reveal that a short‐term intervention was effective in significantly increasing internal control over academic success and purpose in life for students participating in the intervention group. In addition, analysis of academic achievement for students who experienced positive gains in internal control and purpose demonstrates significant gains in academic achievement as measured by grade point average. Implications are made for further study of internal control and life purpose as a means of academic intervention in the effort to address the achievement gap.
Contributions of Jayme Luiz Szwarcfiter to graph theory and computer science
Authors: Lucchesi Cláudio Leonardo
Published: January 2012

This is an account of Jayme’s contributions to graph theory and computer science. Due to restrictions in length, it is not possible to provide an in-depth coverage of every aspect of Jayme’s extensive scientific activities. Thus, I describe in detail only some of his principal contributions, touch upon some, and merely list the other articles.

I found it easier to write the article in the first person, as though it is an account of a previously given lecture.
A note on Kasparov products
Authors: Grensing Martin
Published: January 2012

Combining Kasparov's generalization of a theorem of Voiculescu and Cuntz's description of KK-theory in terms of quasihomomorphisms (sections one and two), we give a simple construction of the Kasparov product (section three). This construction will be generalized in [Gre] to give a version of the product for so-called locally convex Kasparov modules over locally convex algebras in order to treat products of certain universal cycles.
Family- and school-based correlates of energy balance-related behaviours in 10–12-year-old children: a systematic review within the ENERGY (EuropeaN Energy balance Research to prevent excessive weight Gain among Youth) project
Authors: Verloigne Maïté , Van Lippevelde Wendy , Maes Lea , Brug Johannes , De Bourdeaudhuij Ilse
Published: January 2012

Objective

To identify family- and school-based correlates of specific energy balance-related behaviours (physical activity, sedentary behaviour, breakfast consumption, soft drink consumption) among 10–12-year-olds, using the EnRG framework (Environmental Research framework for weight Gain prevention).

Design

A literature review to identify observational studies exploring at least one family- or school-based correlate of the specific behaviours, resulting in seventy-six articles.

Setting

Eighteen studies were conducted in Europe, forty-one studies in North America and seventeen studies in Australasia.

Subjects

Healthy children aged 10–12 years.

Results

Parental and maternal physical activity, doing physical activities with parents and parental logistic support were identified as the most important, positive correlates of physical activity. Parental rules was the most important correlate of sedentary behaviour and was inversely related to it. School socio-economic status was positively related to physical activity and inversely related to sedentary behaviour. The available studies suggested a positive relationship between soft drink availability at home and consumption. Soft drink availability and consumption at school were the most important school-based correlates of soft drink consumption. A permissive parenting style was related to more soft drink consumption and less breakfast consumption.

Conclusions

An important role has been awarded to parents, suggesting parents should be involved in obesity prevention programmes. Despite the opportunities a school can offer, little research has been done to identify school-environmental correlates of energy balance-related behaviours in this age group. Obesity prevention programmes can focus on the most important correlates to maximize the effectiveness of the programme. Future research should aim at longitudinal studies.
Dietary adequacy and dietary quality of Inuit in the Canadian Arctic who smoke and the potential implications for chronic disease
Authors: Rittmueller Stacey E , Roache Cindy , Sharma Sangita
Published: January 2012

Objective

To compare dietary intake and quality among adult Inuit by smoking status.

Design

A cross-sectional study using data from a validated quantitative FFQ.

Setting

Three isolated communities in Nunavut, Canada.

Subjects

Adult Inuit (n208), aged between 19 and 79 years, from randomly selected households.

Results

Average energy intake did not differ between male smokers (n22) and non-smokers (n14; 16 235 kJ and 13 503 kJ;P= 0·18), but was higher among female smokers (n126) compared with non-smokers (n46; 12 704 kJ and 8552 kJ;P< 0·0001). Average daily nutrient intakes were similar among men and higher among female smokers compared with non-smokers for all nutrients (P≤ 0·05) exceptn-3 fatty acids, vitamin A, vitamin D and Se. Female smokers had lower intake densities of thiamin, niacin, vitamin B6, folate, Mg, Na (P≤ 0·05), protein,n-3 fatty acids, cholesterol, Fe (P≤ 0·01), vitamin B12and Se (P≤ 0·001). Between 20 % and 50 % of male and female smokers were below the Dietary Reference Intake (DRI) for Ca, folate, Mg and vitamins A and K, and more than 50 % were below the DRI for fibre and vitamin E. The proportion of smokers below the DRI was lower for all nutrients, except fibre and folate among men. Among smokers, non-nutrient-dense foods and traditional foods contributed less to energy (−2·1 % and −2·0 %, respectively).

Conclusions

Adult smokers consumed fewer nutrient-dense, traditional foods, but had increased energy intake, which likely contributed to fewer dietary inadequacies compared with non-smokers. Promoting traditional food consumption supplemented with market-bought fruits and vegetables is important to improve dietary quality, especially among smokers.
What's in a hump? Re-examining the hunchback in the Villa-Albani-Torlonia
Authors: Trentin Lisa
Published: January 2012

The private collection of the Villa Albani-Torlonia in Rome holds the only surviving large-scale sculpture of a hunchback [fig. i]. Although this hunchback has been intensely studied, it remains enigmatic. The hunchback is generally agreed to be Roman and dated to the second century CE on the basis of its portrait head, particularly in the drilling technique of its hairstyle, though the realism of its misshapen and ugly body is in the direct tradition of works of the third century BCE.

Whether this hunchback is an original of its time or a copy of a now lost Greek work is still contentious. Since its discovery in the Baths of Caracalla, the figure has been identified as the famous Greek fabulist Aesop, who, according to literary tradition, may have been a hunchback. Although several scholars have suggested new possibilities for the identity of this hunchback, including the proposition that it is a Roman original representing a jester of the imperial court, its association with Aesop has remained. But is its identity necessarily key to understanding its significance? This article intends to move away from the identification of this figure to consider the hunchback primarily as a type, rather than a person, and shifts the emphasis to its context within a bathhouse.
The politics of classical allusion at the end of the eighteenth century: radical or redundant?
Authors: Hiscock Matthew
Published: January 2012

My epigraphs offer a stark contrast in their basic assumptions about the place of classical allusion in eighteenth century writing. The second, published only last year in a series devoted to classical reception, implies that allusion – whether conscious or unconscious – is always ‘significant’; the first, fifteen years old and from the first number of theInternational Journal of the Classical Tradition, suggests that it is largely incidental and superficial. To be fair to Kennedy, the passage quoted above comes from an abbreviated history of classicism from the Hellenistic period to the twentieth century which could not be expected to offer a nuanced account of the nature of classical allusion in the various periods it discusses; but the basic question remains: is classical allusion in the eighteenth century ornamental or essential?
The origin of metic status at Athens
Authors: Watson James
Published: January 2012

It is widely held as uncontroversial that throughout the classical period male inhabitants of Attica were divided between three distinct categories – Athenian citizens, metics (regularly translated as ‘resident aliens’) and slaves – and that Athenian society had, therefore, a tripartite structure. The opportunities available to and requirements demanded of a man depended on his category. Those foreigners permanently resident in Attica – those with the legal status of ‘metic’ – were, unlike slaves, free, but, unlike citizens, they could not own land, vote in the Assembly, or serve as adikastesor as a magistrate; in addition, metics were required to pay a poll tax (themetoikion) and to have a citizen sponsor (prostates). In this paper I seek to challenge not the nature of the distinction between citizens and metics but instead the assumption that the distinction was made throughout the classical period. I suggest that the growth of the Athenian citizen population after the Persian invasion of 480–479 demands that the origin of metic status be situated around the middle of the fifth century, and that the occasion on which the Athenianpolisfirst defined metic status is likely to have been the occasion on which it first took an interest in restricting who might become a citizen: in 451/0, with the passing of Perikles' citizenship law.
Kelvin‐Helmholtz billows generated at a cirrus cloud base within a tropopause fold/upper‐level frontal system
Authors: Luce Hubert , Nishi Noriyuki , Caccia Jean‐Luc , Fukao Shoichiro , Yamamoto Masayuki K. , Mega Tomoaki , Hashiguchi Hiroyuki , Tajiri Takuya , Nakazato Masahisa
Published: January 2012

For the first time, trains of Kelvin‐Helmholtz billows of ∼100–1500 m in depth persisting for about 60 hours at the south extremity of a tropopause fold are reported. The structures were monitored by the VHF Middle and Upper atmosphere radar (Shigaraki, 34.85°N, 136.10°E) in November 2008 at the base of cirriform clouds simultaneously detected by a Ka‐band radar. ECWMF reanalysis data indicate that these clouds were advected and spread out by the sub‐tropical jet‐stream from a tropical storm area while dry and cold air penetrated beneath the upper‐level front. The KH billows were likely continuously generated over horizontal extent of several thousand kilometers for several days without evidence of breaking into three‐dimensional turbulence. Rather than radiative effects, our observations suggest that cooling by sublimation of ice particles precipitating in the frontal layer contributed to their generation. These results should motivate further studies on the interaction between clouds and shear instabilities.
A model based method for obtaining the open/closed field line boundary from the cusp auroral 6300 Å[OI] red line
Authors: Johnsen M. G. , Lorentzen D. A. , Holmes J. M. , Løvhaug U. P.
Published: January 2012

Ground based optical instruments are invaluable tools for studies of processes associated with the cusps and auroral morphology. In this work we present a method for obtaining the magnetic latitude of the open/closed field line boundary (OCB) from the cusp 6300 Å[OI] auroral red line using a meridian scanning photometer. The method which is based on a pre‐defined reference cusp aurora produced by the GLOW model is examined with respect to uncertainties, and we describe how a set of equations describing the error is constructed. The method is applicable to data from optical instruments located at high latitude observation sites such as Svalbard and Antarctica. Equations describing both errors and the mapping altitude for transforming the OCB from instrument centered coordinates to magnetic latitude for instrumentation located in Svalbard (Longyearbyen) are presented. Further, by applying the GLOW model we present results illustrating the great variability in the altitude profile of the atomic oxygen 6300 Å[OI] red line emission in the cusp. A simple calculation showing how a poleward neutral wind will change the latitudinal shape of the cusp aurora is also performed.
Process‐evaluation of tropospheric humidity simulated by general circulation models using water vapor isotopologues: 1. Comparison between models and observations
Authors: Risi Camille , Noone David , Worden John , Frankenberg Christian , Stiller Gabriele , Kiefer Michael , Funke Bernd , Walker Kaley , Bernath Peter , Schneider Matthias , Wunch Debra , Sherlock Vanessa , Deutscher Nicholas , Griffith David , Wennberg Paul O. , Strong Kimberly , Smale Dan , Mahieu Emmanuel , Barthlott Sabine , Hase Frank , García Omaira , Notholt Justus , Warneke Thorsten , Toon Geoffrey , Sayres David , Bony Sandrine , Lee Jeonghoon , Brown Derek , Uemura Ryu , Sturm Christophe
Published: January 2012

The goal of this study is to determine how H2O and HDO measurements in water vapor can be used to detect and diagnose biases in the representation of processes controlling tropospheric humidity in atmospheric general circulation models (GCMs). We analyze a large number of isotopic data sets (four satellite, sixteen ground‐based remote‐sensing, five surface in situ and three aircraft data sets) that are sensitive to different altitudes throughout the free troposphere. Despite significant differences between data sets, we identify some observed HDO/H2O characteristics that are robust across data sets and that can be used to evaluate models. We evaluate the isotopic GCM LMDZ, accounting for the effects of spatiotemporal sampling and instrument sensitivity. We find that LMDZ reproduces the spatial patterns in the lower and mid troposphere remarkably well. However, it underestimates the amplitude of seasonal variations in isotopic composition at all levels in the subtropics and in midlatitudes, and this bias is consistent across all data sets. LMDZ also underestimates the observed meridional isotopic gradient and the contrast between dry and convective tropical regions compared to satellite data sets. Comparison with six other isotope‐enabled GCMs from the SWING2 project shows that biases exhibited by LMDZ are common to all models. The SWING2 GCMs show a very large spread in isotopic behavior that is not obviously related to that of humidity, suggesting water vapor isotopic measurements could be used to expose model shortcomings. In a companion paper, the isotopic differences between models are interpreted in terms of biases in the representation of processes controlling humidity.
Evidence of direct correlation between out-of-plane lattice parameter and metal-insulator transition temperature in oxygen-depleted manganite thin films
Authors: Orgiani P. , Petrov A. Yu. , Ciancio R. , Galdi A. , Maritato L. , Davidson B. A.
Published: January 2012

We report on the role of oxygen content alone on structural and transport properties of La0.65Sr0.35MnO3−δ (LSMO) thin films. Identical films were deposited side-by-side during a single deposition run and subsequently post-annealed separately in vacuum to systematically vary the oxygen content. All films remained coherently strained to the SrTiO3 substrate, with no broadening of rocking curve widths after post-anneal. As oxygen content decreases, the LSMO unit cell expands while the metal-insulator transition temperature TMI decreases. A linear correlation between the out-of-plane lattice parameter and the metal-insulator transition temperature was observed.
The effect of elementary reactions on solitary waves in dusty plasmas
Authors: Tahraoui A. , Annou R.
Published: January 2012

The conditions of existence of solitons have been determined by Wang et al. [Phys. Lett. A 339, 96 (2005)], in negative ions containing dusty plasmas where Boltzmannian ions and electrons are assumed. The study is revisited taking into account actual elementary reactions in plasma conditions, viz., particles attachment by grains as well as neutrals and electron impact ionization of neutrals. Dust charge variation is self-consistently introduced leading to the Boltzmannian approximation relaxation.
One-shot spectrometer for several elements using an integrated conical crystal analyzer
Authors: Morishita Kohei , Hayashi Kouichi , Nakajima Kazuo
Published: January 2012

Time-resolved x-ray spectrometry using an ultrastrong x-ray source such as an x-ray free electron laser is one of the new trends in the field of x-ray physics. To achieve such time-resolved measurement, the development of an one-shot spectrometer with a wide wavelength range, high efficiency, and good energy resolution is an essential prerequisite. Here we developed an integrated conical Ge crystal analyzer consisting of several conical rings, which were connected using spline surfaces to form a single body using our previously developed hot deformation technique, which can form a Si or Ge wafer into an arbitrary and accurate shape. We simultaneously focused several characteristic lines from an alloy sample onto different positions on a small x-ray charge-coupled device with very high image brightness (gain relative to planar analyzer: 100) and a good spatial resolution of 9–13 eV. The small radius of curvature of the crystal (28–50 mm) enabled us to realize a very short sample-detector distance of 214.4 mm. The present result shows the possibility of realizing a new focusing x-ray crystal spectrograph that can control the focal position as desired.
Complex evolution of the electronic structure of Cr with temperature
Authors: Adhikary Ganesh , Bindu R. , Patil Swapnil , Maiti Kalobaran
Published: January 2012

Employing state-of-the-art high resolution photoemission spectroscopy, we studied the electronic structure evolution of Cr with temperature. Experimental results reveal signature of a pseudogap much below the spin density wave transition temperature. A sharp peak appears near the Fermi level at low temperatures presumably related to the orbital Kondo effect. These results provide possible origin of the complex electronic properties observed in this system.
Preparation of Ohmic contacts to GaAs/AlGaAs-core/shell-nanowires
Authors: Wirths S. , Mikulics M. , Heintzmann P. , Winden A. , Weis K. , Volk Ch. , Sladek K. , Demarina N. , Hardtdegen H. , Grützmacher D. , Schäpers Th.
Published: January 2012

Ohmic contacts to GaAs/AlGaAs core/shell nanowires are prepared by using a Ni/AuGe/Ni/Au layer system. In contrast to Ohmic contacts to planar GaAs/AlGaAs layer systems here, relatively low alloying temperatures are used in cylindrical geometry. Lowest resistances are found for annealing temperatures of 320 °C and 340 °C. For annealing temperatures exceeding 360 °C, the nanowires degraded completely. Nanowires annealed under optimized conditions preserved their Ohmic characteristics even down to temperatures of 4 K.
Ultraviolet and infrared femtosecond laser induced periodic surface structures on thin polymer films
Authors: Rebollar Esther , Vázquez de Aldana Javier R. , Pérez-Hernández José A. , Ezquerra Tiberio A. , Moreno Pablo , Castillejo Marta
Published: January 2012

This work demonstrates the formation of femtosecond laser induced periodic surface structures (LIPSS) by multipulse irradiation with the fundamental and 3rd harmonic of a linearly polarized Ti:sapphire laser (795 and 265 nm) on thin films of the polymers poly (ethylene terephthalate), poly (trimethylene terephthalate), and poly (carbonate bisphenol A) prepared by spin-coating. LIPSS, inspected by atomic force microscopy, are formed upon multiple pulse UV and IR irradiation with wavelength-sized period in a narrow range of fluences below the ablation threshold. Control and tunability of the size and morphology of the periodic structures become thus possible ensuring photochemical integrity of polymer films.
Micro-imprinted prism substrate for self-aligned short channel organic transistors on a flexible substrate
Authors: Jeon Jin , Tee Benjamin C.-K. , Murmann Boris , Bao Zhenan
Published: January 2012

Using a simple micro-imprinting process on flexible substrates, we demonstrate fabrication of self-aligned short channel organic thin film transistors (OTFTs) with significantly reduced parasitic capacitance. The surface topology resulting from the imprinted prism-like structures enables accurate alignment of both the gate and source-drain electrodes. The parasitic overlap capacitance was reduced by 80%, which enables twice higher transition frequency (fT = 10.1 kHz) compared with conventional top-contact OTFT devices. The prism-OTFTs were applied to both p-type (pentacene) and n-type (C60) organic semiconductors to implement low voltage complementary inverters.
Is N-doped SrO magnetic? A first-principles view
Authors: Wu Hua
Published: January 2012

N-doped SrO seems to be one of the model systems for d0 magnetism, in which magnetism (or ideally, ferromagnetism) was ascribed to the localized N 2p spins mediated by delocalized O 2p holes. Here, we offer a different view, using density functional calculations. We find that N-doped SrO with solely substitutional N impurities as widely assumed in the literature is unstable and instead that a pairing state of substitutional and interstitial N impurities is significantly more stable and has a much lower formation energy than the former by 6.7 eV. The stable (Nsub−Nint)2− dimers behave like a charged (N2)2− molecule and have each a molecular spin = 1. However, their spin-polarized molecular levels lie well inside the wide band gap of SrO, and thus, the exchange interaction is negligibly weak. As a consequence, N-doped SrO could not be ferromagnetic but paramagnetic.
Perceptions of barriers to discussing and testing for sexually transmitted infections in a convenience sample of general practice patients
Authors: Baker Joanne R. , Arnold-Reed Diane E. , Brett Tom , Hince Dana A. , O'Ferrall Ilse , Bulsara Max K.
Published: January 2012

We aimed to identify patient perceptions of barriers to discussing sexually transmitted infections (STIs) at the primary care level. An anonymous questionnaire was available to patients (16–70 years) in the waiting room of four metropolitan Perth general practices. Results are based on 370 participant views (9.5% of the potential target population). Patients felt comfortable discussing STIs with their general practitioner (GP) and their level of comfort would be enhanced if they knew their GP had a special interest or qualification in sexual health. Willingness to discuss issues increased or remained unchanged if the GP took time to explain it to them or was a good listener. Patients were willing to discuss STIs if they were a new patient and irrespective of the GP’s gender and age. Fewer patients were willing to discuss STIs if they knew the GP socially. Patients who had sex with a new partner were willing to request a STI test from their GP. Patients were not embarrassed if discussion was initiated in a consultation unrelated to sexual health and did not mind discussing the topic in the presence of a partner or parent, though this depended on circumstances. Waiting room STI test advertising did not affect patient comfort level. Patients would involve their GP when seeking information about STIs. Patients have fewer barriers to discussing sexual health matters than perceived by GPs.
Assessing the impacts of livestock production on biodiversity in rangeland ecosystems
Authors: Alkemade Rob , Reid Robin S. , van den Berg Maurits , de Leeuw Jan , Jeuken Michel
Published: January 2012

Biodiversity in rangelands is decreasing, due to intense utilization for livestock production and conversion of rangeland into cropland; yet the outlook of rangeland biodiversity has not been considered in view of future global demand for food. Here we assess the impact of future livestock production on the global rangelands area and their biodiversity. First we formalized existing knowledge about livestock grazing impacts on biodiversity, expressed in mean species abundance (MSA) of the original rangeland native species assemblages, through metaanalysis of peer-reviewed literature. MSA values, ranging from 1 in natural rangelands to 0.3 in man-made grasslands, were entered in the IMAGE-GLOBIO model. This model was used to assess the impact of change in food demand and livestock production on future rangeland biodiversity. The model revealed remarkable regional variation in impact on rangeland area and MSA between two agricultural production scenarios. The area of used rangelands slightly increases globally between 2000 and 2050 in the baseline scenario and reduces under a scenario of enhanced uptake of resource-efficient production technologies increasing production [high levels of agricultural knowledge, science, and technology (high-AKST)], particularly in Africa. Both scenarios suggest a global decrease in MSA for rangelands until 2050. The contribution of livestock grazing to MSA loss is, however, expected to diminish after 2030, in particular in Africa under the high-AKST scenario. Policies fostering agricultural intensification can reduce the overall pressure on rangeland biodiversity, but additional measures, addressing factors such as climate change and infrastructural development, are necessary to totally halt biodiversity loss.
Extensive X-linked adaptive evolution in central chimpanzees
Authors: Hvilsom Christina , Qian Yu , Bataillon Thomas , Li Yingrui , Mailund Thomas , Sallé Bettina , Carlsen Frands , Li Ruiqiang , Zheng Hancheng , Jiang Tao , Jiang Hui , Jin Xin , Munch Kasper , Hobolth Asger , Siegismund Hans R. , Wang Jun , Schierup Mikkel Heide
Published: January 2012

Surveying genome-wide coding variation within and among species gives unprecedented power to study the genetics of adaptation, in particular the proportion of amino acid substitutions fixed by positive selection. Additionally, contrasting the autosomes and the X chromosome holds information on the dominance of beneficial (adaptive) and deleterious mutations. Here we capture and sequence the complete exomes of 12 chimpanzees and present the largest set of protein-coding polymorphism to date. We report extensive adaptive evolution specifically targeting the X chromosome of chimpanzees with as much as 30% of all amino acid replacements being adaptive. Adaptive evolution is barely detectable on the autosomes except for a few striking cases of recent selective sweeps associated with immunity gene clusters. We also find much stronger purifying selection than observed in humans, and in contrast to humans, we find that purifying selection is stronger on the X chromosome than on the autosomes in chimpanzees. We therefore conclude that most adaptive mutations are recessive. We also document dramatically reduced synonymous diversity in the chimpanzee X chromosome relative to autosomes and stronger purifying selection than for the human X chromosome. If similar processes were operating in the human–chimpanzee ancestor as in central chimpanzees today, our results therefore provide an explanation for the much-discussed reduction in the human–chimpanzee divergence at the X chromosome.
Education of a model student
Authors: Novikoff Timothy P. , Kleinberg Jon M. , Strogatz Steven H.
Published: January 2012

A dilemma faced by teachers, and increasingly by designers of educational software, is the trade-off between teaching new material and reviewing what has already been taught. Complicating matters, review is useful only if it is neither too soon nor too late. Moreover, different students need to review at different rates. We present a mathematical model that captures these issues in idealized form. The student’s needs are modeled as constraints on the schedule according to which educational material and review are spaced over time. Our results include algorithms to construct schedules that adhere to various spacing constraints, and bounds on the rate at which new material can be introduced under these schedules.
Analysis of Gal4-directed transcription activation using Tra1 mutants selectively defective for interaction with Gal4
Authors: Lin Ling , Chamberlain Lynn , Zhu Lihua J. , Green Michael R.
Published: January 2012

Promoter-specific transcriptional activators (activators) stimulate transcription through direct interactions with one or more components of the transcription machinery, termed the “target.” The identification of direct in vivo targets of activators has been a major challenge. Previous studies have provided evidence that the Tra1 subunit of the yeast SAGA (Spt-Ada-Gcn5-acetyltransferase) complex is the target of the yeast activator Gal4. However, several other general transcription factors, in particular the mediator complex, have also been implicated as Gal4 targets. Here we perform a large-scale genetic screen to derive and characterizetra1alleles that are selectively defective for interaction with Gal4 in vivo [Gal4interactiondefective (GID) mutants]. In contrast to WT Tra1, Tra1 GID mutants are not recruited by Gal4 to the promoter and cannot support Gal4-directed transcription, demonstrating the essentiality of the Gal4–Tra1 interaction. In yeast strains expressing a Tra1 GID mutant, binding of Gal4 to the promoter is unexpectedly also diminished, indicating that Gal4 and Tra1 bind cooperatively. Consistent with cooperative binding, we demonstrate that the Gal4–Tra1 interaction occurs predominantly on the promoter and not off DNA. Finally, we show that although Tra1 is targeted by other activators, these interactions are unaffected by GID mutations, revealing an unanticipated specificity of the Gal4–Tra1 interaction.
Negative and competitive social interactions are related to heightened proinflammatory cytokine activity
Authors: Chiang Jessica J. , Eisenberger Naomi I. , Seeman Teresa E. , Taylor Shelley E.
Published: January 2012

Research has consistently documented that social relationships influence physical health, a link that may implicate systemic inflammation. We examined whether daily social interactions predict levels of proinflammatory cytokines IL-6 and the soluble receptor for tumor necrosis factor-α (sTNFαRII) and their reactivity to a social stressor. One-hundred twenty-two healthy young adults completed daily diaries for 8 d that assessed positive, negative, and competitive social interactions. Participants then engaged in laboratory stress challenges, and IL-6 and sTNFαRII were collected at baseline and at 25- and 80-min poststressor, from oral mucosal transudate. Negative social interactions predicted elevated sTNFαRII at baseline, and IL-6 and sTNFαRII 25-min poststressor, as well as total output of sTNFαRII. Competitive social interactions predicted elevated baseline levels of IL-6 and sTNFαRII and total output of both cytokines. These findings suggest that daily social interactions that are negative and competitive are associated prospectively with heightened proinflammatory cytokine activity.
Agonist of growth hormone-releasing hormone reduces pneumolysin-induced pulmonary permeability edema
Authors: Lucas Rudolf , Sridhar Supriya , Rick Ferenc G. , Gorshkov Boris , Umapathy Nagavedi S. , Yang Guang , Oseghale Aluya , Verin Alexander D. , Chakraborty Trinad , Matthay Michael A. , Zemskov Evgeny A. , White Richard , Block Norman L. , Schally Andrew V.
Published: January 2012

Aggressive treatment with antibiotics in patients infected withStreptococcus pneumoniaeinduces release of the bacterial virulence factor pneumolysin (PLY). Days after lungs are sterile, this pore-forming toxin can still induce pulmonary permeability edema in patients, characterized by alveolar/capillary barrier dysfunction and impaired alveolar liquid clearance (ALC). ALC is mainly regulated through Na+transport by the apically expressed epithelial sodium channel (ENaC) and the basolaterally expressed Na+/K+-ATPase in type II alveolar epithelial cells. Because no standard treatment is currently available to treat permeability edema, the search for novel therapeutic candidates is of high priority. We detected mRNA expression for the active receptor splice variant SV1 of the hypothalamic polypeptide growth hormone-releasing hormone (GHRH), as well as for GHRH itself, in human lung microvascular endothelial cells (HL-MVEC). Therefore, we have evaluated the effect of the GHRH agonist JI-34 on PLY-induced barrier and ALC dysfunction. JI-34 blunts PLY-mediated endothelial hyperpermeability in monolayers of HL-MVEC, in a cAMP-dependent manner, by means of reducing the phosphorylation of myosin light chain and vascular endothelial (VE)-cadherin. In human airway epithelial H441 cells, PLY significantly impairs Na+uptake, but JI-34 restores it to basal levels by means of increasing cAMP levels. Intratracheal instillation of PLY into C57BL6 mice causes pulmonary alveolar epithelial and endothelial hyperpermeability as well as edema formation, all of which are blunted by JI-34. These findings point toward a protective role of the GHRH signaling pathway in PLY-induced permeability edema.
STAT5 is a potent negative regulator of TFH cell differentiation
Authors: Johnston Robert J. , Choi Youn Soo , Diamond Jeffrey A. , Yang Jessica A. , Crotty Shane
Published: January 2012

Follicular helper T cells (TFH cells) constitute the CD4+ T cell subset that is specialized to provide help to germinal center (GC) B cells and, consequently, mediate the development of long-lived humoral immunity. TFH cell differentiation is driven by the transcription factor Bcl6, and recent studies have identified cytokine and cell–cell signals that drive Bcl6 expression. However, although TFH dysregulation is associated with several major autoimmune diseases, the mechanisms underlying the negative regulation of TFH cell differentiation are poorly understood. In this study, we show that STAT5 inhibits TFH cell differentiation and function. Constitutive STAT5 signaling in activated CD4+ T cells selectively blocked TFH cell differentiation and GCs, and IL-2 signaling was a primary inducer of this pathway. Conversely, STAT5-deficient CD4+ T cells (mature STAT5fl/fl CD4+ T cells transduced with a Cre-expressing vector) rapidly up-regulated Bcl6 expression and preferentially differentiated into TFH cells during T cell priming in vivo. STAT5 signaling failed to inhibit TFH cell differentiation in the absence of the transcription factor Blimp-1, a direct repressor of Bcl6 expression and TFH cell differentiation. These results demonstrate that IL-2, STAT5, and Blimp-1 collaborate to negatively regulate TFH cell differentiation.
Using biologically interrelated experiments to identify pathway genes inArabidopsis
Authors: Kim Kyungpil , Jiang Keni , Teng Siew Leng , Feldman Lewis J. , Huang Haiyan
Published: January 2012

Motivation:  Pathway genes are considered as a group of genes that work cooperatively in the same pathway constituting a fundamental functional grouping in a biological process. Identifying pathway genes has been one of the major tasks in understanding biological processes. However, due to the difficulty in characterizing/inferring different types of biological gene relationships, as well as several computational issues arising from dealing with high-dimensional biological data, deducing genes in pathways remain challenging.

Results: In this work, we elucidate higher level gene–gene interactions by evaluating the conditional dependencies between genes, i.e. the relationships between genes after removing the influences of a set of previously known pathway genes. These previously known pathway genes serve as seed genes in our model and will guide the detection of other genes involved in the same pathway. The detailed statistical techniques involve the estimation of a precision matrix whose elements are known to be proportional to partial correlations (i.e. conditional dependencies) between genes under appropriate normality assumptions. Likelihood ratio tests on two forms of precision matrices are further performed to see if a candidate pathway gene is conditionally independent of all the previously known pathway genes. When used effectively, this is a promising approach to recover gene relationships that would have otherwise been missed by standard methods. The advantage of the proposed method is demonstrated using both simulation studies and real datasets. We also demonstrated the importance of taking into account experimental dependencies in the simulation and real data studies.

Contact:  hhuang@stat.berkeley.edu; ljfeldman@berkeley.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Crystallization of the C-terminal domain of the bacteriophage T7 fibre protein gp17
Authors: Garcia-Doval Carmela , van Raaij Mark J.
Published: January 2012

Bacteriophage T7 attaches to its host using the C-terminal domains of its six fibres, which are trimers of the gp17 protein. A C-terminal fragment of gp17 consisting of amino acids 371–553 has been expressed, purified and crystallized. Crystals of two forms were obtained, belonging to space groupP212121(unit-cell parametersa= 61.2,b= 86.0,c= 118.4 Å) and space groupC2221(unit-cell parametersa= 68.3,b= 145.6,c= 172.1 Å). They diffracted to 1.9 and 2.0 Å resolution, respectively. Both crystals are expected to contain one trimer in the asymmetric unit. Multiwavelength anomalous dispersion phasing with a mercury derivative is in progress.
Strong population genetic structure and its management implications in the mud carp Cirrhinus molitorella, an indigenous freshwater species subject to an aquaculture and culture‐based fishery
Authors: Nguyen T. T. T. , Sunnucks P.
Published: January 2012

This study investigated population genetic structure and diversity of mud carp Cirrhinus molitorella, a species widely used in aquaculture and culture‐based fisheries in China and Mekong River riparian countries. Seven newly developed and one published microsatellite DNA markers were used to analyse samples from six wild locations, four hatchery broodstocks and one farmed site from the Mekong, Red and Pearl Rivers. Significant genetic structure was detected in C. molitorella, with isolation‐by‐distance being a strong force in the Mekong. Pair‐wise FST, Fisher's exact tests for population differentiation, permutation tests and individual‐based structure analysis all support the recognition of a sample originating from Toul Krasaing Lake (Cambodia) and one between Kratie and Stung Treng (Cambodia) as distinct from the remainder of the sampled range. Samples from the main upper Mekong and the Nam Khan River were significantly differentiated, but on a time scale inferred to be short (i.e. by genetic drift, not sufficient for evolution of new microsatellite alleles). The Mekong stock of C. molitorella was strongly differentiated from those from the Red and Pearl Rivers, inferred to be on an evolutionary time scale. Finer‐scale sampling is warranted to further improve the understanding of genetic interactions among fish from the Mekong and its tributaries. Detailed studies on the ecology of C. molitorella (e.g. migration pathways and preferred spawning habitats) would provide useful information to explain the patterns of genetic structure detected here, and deepen insights about evolutionary distinctiveness of the population units.
Palestinian Children: Authors of Collective Memory
Authors: Habashi Janette
Published: January 2012

This article investigates the premise that Palestinian children are the authors of collective memory. Palestinian society employs an oral tradition that propagates the collective experience among different generations in which the individual dimensions of each is apparent. The oral history for Palestinian children not only illustrates past events, it also provides the tool for grasping the present and traversing the future. In this ethnographic study, 12 Palestinian children from cities, villages and refugee camps in the West Bank were interviewed. The children demonstrated active roles in reconstructing previous collective memory in relation to their own experiences and vigorously restructured the collective memory as a prerequisite for passing it to the next generation.
What is active acromegaly and which parameters do we have?
Authors: Neggers S. J. C. M. M. , Biermasz N. R. , van der Lely A. J.
Published: January 2012

Disease activity of acromegaly can be measured in many ways. Growth hormone (GH) and insulin‐like growth factor 1 (IGF1) concentrations are the main biochemical markers used to measure the response to treatment. Both GH and IGF1 have been associated with prognosis, in particular mortality. In this review, we discuss the available parameters to assess disease activity in acromegaly.
Low persistence of a monocarpic invasive plant in historical sites biases our perception of its actual distribution
Authors: Pergl Jan , Pyšek Petr , Perglová Irena , Jarošík Vojtěch
Published: January 2012

Aim As accurate and up‐to‐date distribution data for plant species are rarely available, cumulative records over long periods of time are frequently used for mapping distributions, without taking into account that species do not persist in their historical localities forever. However, persistence is highly relevant in changing modern landscapes, especially for invasive species that dynamically spread in unstable human‐made habitats. We studied how an invasive species,Heracleum mantegazzianum, persists at sites once colonized and how its ability to persist affects its distribution.

Location The Czech Republic.

Methods We visited 521 localities ofH. mantegazzianumoccurrence reported in the literature and herbaria to determine whether the species still occurs at these sites. By usingG‐tests and classification trees, we explored the roles of various factors affecting its persistence at a site.

Results Of the total number of 521 historical sites at which the species has occurred since the end of the 19th century, it persists at only 124 (23.8%). The persistence rate differs with respect to habitat type and is highest in meadows and forest margins. Analysis using classification trees indicated that the factors that best explain persistence are: type of habitat (with meadow and forest margins over‐represented); urbanity (with a higher persistence outside urban areas); proximity to the place of the species’ introduction into the country; metapopulation connectivity; and distance to the nearest neighbouring population.

Main conclusions The use of cumulative historical records as a measure of species distribution, which is common in invasion literature, can seriously overestimate the actual distribution of alien plant species with low persistence. In the case of alien species such asH. mantegazzanium, which is non‐clonal and reproduces only by seed, estimates of distribution and spread based on historical data are informative about potentially suitable habitat but may be unreliable as indicators of current occurrence and invasion dynamics.
Limitations on orchid recruitment: not a simple picture
Authors: McCORMICK MELISSA K. , LEE TAYLOR D. , JUHASZOVA KATARINA , BURNETT ROBERT K. , WHIGHAM DENNIS F. , O’NEILL JOHN P.
Published: January 2012

Mycorrhizal fungi have substantial potential to influence plant distribution, especially in specialized orchids and mycoheterotrophic plants. However, little is known about environmental factors that influence the distribution of mycorrhizal fungi. Previous studies using seed packets have been unable to distinguish whether germination patterns resulted from the distribution of appropriate edaphic conditions or the distribution of host fungi, as these cannot be separated using seed packets alone. We used a combination of organic amendments, seed packets and molecular assessment of soil fungi required by three terrestrial orchid species to separate direct and indirect effects of fungi and environmental conditions on both seed germination and subsequent protocorm development. We found that locations with abundant mycorrhizal fungi were most likely to support seed germination and greater growth for all three orchids. Organic amendments affected germination primarily by affecting the abundance of appropriate mycorrhizal fungi. However, fungi associated with the three orchid species were affected differently by the organic amendments and by forest successional stage. The results of this study help contextualize the importance of fungal distribution and abundance to the population dynamics of plants with specific mycorrhizal requirements. Such phenomena may also be important for plants with more general mycorrhizal associations.