bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of an integrated approach to science and literacy in elementary school classrooms
Authors: Cervetti Gina N. , Barber Jacqueline , Dorph Rena , Pearson P. David , Goldschmidt Pete G.
Published: April 2012

This study investigates the efficacy of an integrated science and literacy approach at the upper‐elementary level. Teachers in 94 fourth grade classrooms in one Southern state participated. Half of the teachers taught the treatment unit, an integrated science–literacy unit on light and energy designed using a curriculum model that engages students in reading text, writing notes and reports, conducting firsthand investigations, and frequent discussion of key concepts and processes to acquire inquiry skills and knowledge about science concepts, while the other half of the teachers taught a content‐comparable science‐only unit on light and energy (using materials provided by their districts) and provided their regular literacy instruction. Students in the treatment group made significantly greater gains on measures of science understanding, science vocabulary, and science writing. Students in both groups made comparable gains in science reading comprehension. © 2012 Wiley Periodicals, Inc. J Res Sci Teach 49: 631–658, 2012
High performance hard carbon coatings (diamond‐like coatings)
Authors: Vetter Jörg , Ackerman Cyndi , Meunier Frederic , Jarry Olivier , Schumacher Dan , Erkens Georg
Published: April 2012

Different dLc coating types are applied at an industrial scale by sulzer Metco thin Film. The coatings are generated with different coating architecture. Deposition methods are: magnetron sputtering, electron beam evaporation and PA‐cVd. Reactive magnetron sputtering is used to deposit metal containing a‐c:h coatings (a‐c:h:Me), e.g. MAXit W‐ch. Pure a‐c:h coatings as functional top coatings are used for cavidur®, MAXit® AhdLc and special versions of dylyn® coatings. In addition to the pure a‐c:h coatings, doped a‐c:h coatings are also used. The dylyn® family of coatings is comprised of at least one layer a‐c:h:si:O. The dylyn® coatings may be doped with metal (a‐c:h:ti:si:O) to adapt selected properties like electrical conductivity.
Kohlenstoffbasierte Beschichtungen für automotive‐Komponenten
Authors: Huben Theresa , Becker Jürgen
Published: April 2012

Die herausragenden Eigenschaften von kohlenstoffbasierten Beschichtungen sind die geringe Reibung gegen Stahl und die mit der erreichbaren hohen Härte verbundene Verschleißbeständigkeit. In geschmierten Systemen wirken Beschichtungen nur im Bereich der Misch‐ und Grenzreibung, d. h. solange Körper und Gegenkörper noch in Kontakt sind.

Die Eigenschaften von Beschichtungen lassen sich in weiten Bereichen anpassen. Ein zielgerechtes Anpassen setzt voraus, dass das tribologische System hinreichend genau verstanden ist.

Es hat sich gezeigt, dass Beschichtungslösungen nur sub‐optimal sind, wenn die Beschichtung erst „zum Schluss”︁ in das System‐Design eingebracht wird. Ein größerer Nutzen ergibt sich, wenn die konstruktiven Freiräume, die eine Beschichtung eröffnet, schon zu Beginn der Design‐Phase ausgeschöpft werden. Die Beschichtung wird als Konstruktionselement verstanden.

Um die Eignung der gewählten Beschichtung schnell und kostengünstig vorab testen zu können, sind die üblichen Standard ‐ Labortests nicht immer geeignet. Ein Prüfaufbau muss hinreichend anwendungsnah sein, um verwertbare Ergebnisse zu generieren.

Diese Überlegungen werden am Beispiel einer Kolbenbolzenbeschichtung dargelegt. Die Rauheit von Körper und Gegenkörper ist vor allem bei Anwendungen unter hohen Lasten von besonderer Bedeutung für die Anpassung des Schichtsystems. Das hier vorgestellte Beispiel zeigt auch, dass die üblicherweise verwendeten Kenngrößen für Oberflächenrauheit wie Ra und Rz nicht immer ausreichend sind.
Models of spoken‐word recognition
Authors: Weber Andrea , Scharenborg Odette
Published: April 2012

All words of the languages we know are stored in the mental lexicon. Psycholinguistic models describe in which format lexical knowledge is stored and how it is accessed when needed for language use. The present article summarizes key findings in spoken‐word recognition by humans and describes how models of spoken‐word recognition account for them. Although current models of spoken‐word recognition differ considerably in the details of implementation, there is general consensus among them on at least three aspects: multiple word candidates are activated in parallel as a word is being heard, activation of word candidates varies with the degree of match between the speech signal and stored lexical representations, and activated candidate words compete for recognition. No consensus has been reached on other aspects such as the flow of information between different processing levels, and the format of stored prelexical and lexical representations. WIREs Cogn Sci 2012, 3:387–401. doi: 10.1002/wcs.1178

This article is categorized under:

Linguistics > Computational Models of Language
Molecular structure and function of Hv1 channels
Authors: Rebolledo Santiago , Qiu Feng , Peter Larsson H.
Published: April 2012

Voltage‐gated proton (Hv) channels have long been found with electrophysiological tools in many different cell types. However, the molecular identity of Hv channels was not discovered until 2006, when two labs independently demonstrated that the gene HVCN1 that codes for a protein called Hv1 or VSOP generates voltage‐gated proton currents when expressed in heterologous cells. Surprisingly, the sequence of Hv1/VSOP was found to be homologous to the sequence of the voltage‐sensing domain of voltage‐gated K+ channels. Recent studies have led to our present understanding of the structure of Hv1/VSOP channels and the structural underpinnings of some of the functional properties of Hv1/VSOP channels, including voltage sensing, subunit cooperativity, permeation and selectivity, pH dependence, zinc inhibition and modulation by PKC of Hv1/VSOP channels. The cloned Hv1/VSOP channels display most of the properties of native voltage‐gated proton channels. However, the molecular mechanisms underlying some of these properties are still unknown. WIREs Membr Transp Signal 2012, 1:763–777. doi: 10.1002/wmts.49

For further resources related to this article, please visit the WIREs website.

Conflict of interest: The authors declare no conflict of interest.
Calculation of X‐ray tube spectra by means of photon generation yields and a modified Kramers background for side‐window X‐ray tubes
Authors: Rackwitz Vanessa , Panne Ulrich , Hodoroaba Vasile‐Dan
Published: April 2012

Popular X‐ray tube models available in the literature, i.e. ‘Pella’, ‘Ebel’, and ‘Finkelshtein and Pavlova’, are systematically evaluated with the focus on the estimation of the associated uncertainties. Also taken in consideration and compared is our recent semi‐empirical own approach already employed in our lab. This has been working for the common target elements rhodium, molybdenum and tungsten and was further extended in the present work for the target elements copper, chromium and vanadium. By using a modern scanning electron microscope/energy dispersive spectroscopy (SEM/EDS) system this time, higher performances such as stability of the beam current and especially the better energy resolution of the EDS have enabled the reliable extension of our own X‐ray tube spectrum approach into the low‐energy range, due to increasing interest. Hence, also the more challenging X‐ray lines of copper, chromium and vanadium L‐series lying in the energy range below 1–2 keV are included into the model. Such low‐energy L‐lines or, e.g. M‐lines of tungsten, are not treated explicitly by the other existing popular algorithms for the nowadays widely used geometries of side‐window tubes, offering a unique virtue to our present, modern approach. With our own model, a measurement uncertainty of the X‐ray tube spectra (considering the uncertainties associated with the SEM beam current, the detector acceptance solid angle and efficiency of the spectrometer) within 15% has been estimated. The validation of the approach is demonstrated with metrological measurements with a calibrated SEM/EDS system geometrically configured as a side‐window X‐ray tube. Copyright © 2012 John Wiley & Sons, Ltd.
Determining the elemental composition of Calotropis procera using X‐ray Analytical Microscopy
Authors: Attaelmanan Atta Gaffar , Kawam Mohammed Alfarouk
Published: April 2012

Caloptropis procera (Oshar) is a desert plant that did not receive much attention from the science community. The objective of this study was to investigate the elemental composition of the different parts of the plant using an X‐ray analytical microscope, to identify the elements naturally present in the plant and in the future detect the presence of any contaminants absorbed by the plants from the surrounding environment. Stalks, leaves and flowers from three Oshar plants were qualitatively and quantitatively analyzed. Leaves were scanned to establish the elemental spatial distribution within individual leaves. Subsequently, parts of the plants were dried, crushed and pulverized, then analyzed to determine elemental concentrations. The major elements present throughout the plant were Cl, K and Ca with varied concentrations. Other elements (Mg, Si, P, Fe, Sr, Mn and Br) are present in the leaf with various low concentrations of <5%. Major, minor and trace elements present in the various plant parts were determined. The outcome of this study will be used as a pilot for further investigations pertaining to the utilization of the Oshar plant for environmental cleaning purposes. Copyright © 2012 John Wiley & Sons, Ltd.
Reconstructed topography of Southern New England prior to isostatic rebound with implications of total isostatic depression and relative sea level
Authors: Oakley Bryan A. , Boothroyd Jon C.
Published: April 2012

Topographic models of the late Quaternary landscape prior to isostatic rebound aid interpretation of glacial lake-water levels and geomorphic features as well as ice thickness, mantle viscosity and lithospheric strength. The well-established limit of glacial marine inundation in central and northern New England provides a test of total isostatic depression. Relative sea levels reflecting differing magnitudes of isostatic rebound show that published values of isostatic depression in southern New England would inundate the landscape in southern New England with marine water south of the limit of late Pleistocene marine inundation. This suggests that isostatic depression at the terminal margin of the Laurentide Ice Sheet (LIS) was < 35 m, and that previous workers overestimate isostatic depression in southern New England by > 50 m. A first-order estimate of ice thickness based on total isostatic depression and the observed uplift profile in southern New England supports the ‘thin ice’ models in New England. Ice thickness ranged from 100 m at the southeastern margin of the LIS, to > 1000 m at a point 300 km north of the terminal margin. This regional model places constraints on continental ice-sheet and geophysical models that should be considered in the future.
Cambodia's Seasons of Migration
Authors: Shapiro-Phim Toni
Published: April 2012

In classical Khmer dance dramas, the fluidity of gestural and choreographic movement is complemented by the seamlessness with which mythical figures move between the realms of sky, earth, and sea. Such mythical migrations have been the subject of Khmer dance dramas for centuries. In this essay I explore the recent development and performance of one specific danced story of migration and the performers' social realities that complicate their relationship to their art and to this story in particular. I discuss transnational migration's impact on current and future possibilities for Khmer classical dance, and the lessons Cambodia's female dancers take from the fluidity, adaptability, and flexibility required of Khmer choreography as they negotiate their immediate social, cultural, and political upheavals.
Martha Graham's Haunting Body: Autobiography at the Intersection of Writing and Dancing
Authors: Thoms Victoria
Published: April 2012

In this article I employ modern dance pioneer Martha Graham's memoir Blood Memory (1991) to complicate understandings of autobiography. Following a deconstructive perspective (Buse and Stott 1999; Derrida 1994) and taking up feminist critiques of both autobiography (Benstock 1988; Chanfrault-Duchet 2000) and the effects of embodiment (Phelan 1997; Albright 1997), I theorize autobiography as a haunting interstice between writing and the body. I suggest that while the written account is an important means to chart a life, there are forms of autobiography that remain unrepresentable in the frame of writing. This impossibility is most poignant in Blood Memory as Graham struggles to represent the autobiographical significance of the embodied performance yet is haunted by the inability to fully articulate in writing its significance for her. I argue that in encountering the written autobiography we should not disavow this haunting but rather acknowledge its importance as a means of encountering that life.

To trouble tacit assumptions about written autobiography, I ask, How might written autobiography be understood as haunted? And how might dance serve to illustrate its haunted state? Lastly, what are the possible effects of understanding written autobiography as haunted? To address these questions I first consider the unsettled encounter with Graham's Blood Memory. I theorize the effects of this encounter as stemming from the shadowy but persistent presence of Graham's danced oeuvre as an alternative form of autobiography and argue that this oeuvre could also be considered an autobiographical text. Then placing the “proper” written autobiography in dialogue with the danced autobiography, I posit the haunted status of autobiography itself–as always already troubled by multiple and alternative textual productions of self that can be both bodily and written in form. Finally, I suggest the possible effects of considering autobiography in this way.
Dopaminergic amacrine cells express opioid receptors in the mouse retina
Authors: GALLAGHER SHANNON K. , ANGLEN JULIA N. , MOWER JUSTIN M. , VIGH JOZSEF
Published: April 2012

The presence of opioid receptors has been confirmed by a variety of techniques in vertebrate retinas including those of mammals; however, in most reports, the location of these receptors has been limited to retinal regions rather than specific cell types. Concurrently, our knowledge of the physiological functions of opioid signaling in the retina is based on only a handful of studies. To date, the best-documented opioid effect is the modulation of retinal dopamine release, which has been shown in a variety of vertebrate species. Nonetheless, it is not known if opioids can affect dopaminergic amacrine cells (DACs) directly, via opioid receptors expressed by DACs. This study, using immunohistochemical methods, sought to determine whether (1) μ- and δ-opioid receptors (MORs and DORs, respectively) are present in the mouse retina, and if present, (2) are they expressed by DACs. We found that MOR and DOR immunolabeling were associated with multiple cell types in the inner retina, suggesting that opioids might influence visual information processing at multiple sites within the mammalian retinal circuitry. Specifically, colabeling studies with the DAC molecular marker anti-tyrosine hydroxylase antibody showed that both MOR and DOR immunolabeling localize to DACs. These findings predict that opioids can affect DACs in the mouse retina directly, via MOR and DOR signaling, and might modulate dopamine release as reported in other mammalian and nonmammalian retinas.
Clinico-immunological profile and outcome of antiretroviral therapy in HIV-positive children
Authors: Choudhary Nidhi , Gomber Sunil , Narang Manish
Published: April 2012

Objectives

To study the clinico-immunological, nutritional and growth characteristics of HIV-infected children and the impact of antiretroviral therapy (ART) on these parameters.

Design

Retrospective study.

Setting

Out-patient department of a paediatric ART centre, Delhi, India.

Subjects

HIV-positive children registered at the paediatric ART centre of the hospital were enrolled (n 130). Anthropometric measurements were used to classify children into the type of malnutrition according to definitions of the WHO and US Centers for Disease Control and Prevention. Clinical and immunological status of the children was recorded as per WHO guidelines. First-line ART was started based on guidelines of the National AIDS Control Organization. Nutritional status and clinico-immunological characteristics were followed up annually in children receiving ART.

Results

Of children ≤5 years of age (n 54), stunting was noted in 42·5 % contrary to wasting seen in only 12·9 %. In children >5 years of age (n 76), short stature (40·7 %) and underweight (39·4 %) were seen in almost equal proportions. Asymptomatic presentation was noted in 60·0 %. Following ART, a reduction in wasting was noted in 75·0 % of children ≤5 years of age, whereas only 44·4 % of underweight children >5 years of age showed an improvement after therapy. Stunting and short stature continued to persist in all in children (≤5 years and >5 years, respectively). Clinico-immunologically, 67·5 % improved in clinical status and 62·5 % showed immunological improvement.

Conclusions

ART improves the acute parameters of nutritional status like wasting. It also improves the clinical outcome and restores the immune system. At present first-line ART is effective in HIV-positive children.
Vegetarian diets, low-meat diets and health: a review
Authors: McEvoy Claire T , Temple Norman , Woodside Jayne V
Published: April 2012

Objective

To review the epidemiological evidence for vegetarian diets, low-meat dietary patterns and their association with health status in adults.

Design

Published literature review focusing primarily on prospective studies and meta-analyses examining the association between vegetarian diets and health outcomes.

Results

Both vegetarian diets and prudent diets allowing small amounts of red meat are associated with reduced risk of diseases, particularly CHD and type 2 diabetes. There is limited evidence of an association between vegetarian diets and cancer prevention. Evidence linking red meat intake, particularly processed meat, and increased risk of CHD, cancer and type 2 diabetes is convincing and provides indirect support for consumption of a plant-based diet.

Conclusions

The health benefits of vegetarian diets are not unique. Prudent plant-based dietary patterns which also allow small intakes of red meat, fish and dairy products have demonstrated significant improvements in health status as well. At this time an optimal dietary intake for health status is unknown. Plant-based diets contain a host of food and nutrients known to have independent health benefits. While vegetarian diets have not shown any adverse effects on health, restrictive and monotonous vegetarian diets may result in nutrient deficiencies with deleterious effects on health. For this reason, appropriate advice is important to ensure a vegetarian diet is nutritionally adequate especially for vulnerable groups.
Automatic-dependent surveillance–broadcast experimental deployment using system wide information management
Authors: Besada Juan A. , de Miguel Gonzalo , Bernardos Ana M. , Casar José R.
Published: April 2012

This paper describes an automatic-dependent surveillance–broadcast (ADS–B) implementation for air-to-air and ground-based experimental surveillance within a prototype of a fully automated air traffic management (ATM) system, under a trajectory-based-operations paradigm. The system is built using an air-inclusive implementation of system wide information management (SWIM). This work describes the relations between airborne and ground surveillance (SURGND), the prototype surveillance systems, and their algorithms. System's performance is analyzed with simulated and real data. Results show that the proposed ADS–B implementation can fulfill the most demanding surveillance accuracy requirements.
Birth size and physical activity in a cohort of Indian children aged 6–10 years
Authors: Kehoe S. H. , Krishnaveni G. V. , Veena S. R. , Hill J. C. , Osmond C. , Kiran  , Coakley P. , Karat S. C. , Fall C. H. D.
Published: April 2012

There is evidence of a reduction in children's physical activity in India in the last decade. Our objective was to assess whether size and body composition at birth are associated with physical activity in school-aged children. Children from a prospective observational cohort study born in Mysore, South India between 1997 and 1998 (n = 663) had neonatal anthropometric measurements made within 72 h of delivery [weight, mid-upper arm circumference (MUAC), chest, abdomen and head circumference, crown–heel, crown–buttock and leg length, triceps and subscapular skinfolds]. At 6–10 years, children (n = 449) were asked to wear AM7164 or GT1M Actigraph accelerometers for 7 days. Body composition was measured within 6 months of activity monitoring. Arm muscle area at birth and time of activity monitoring was calculated from MUAC and skinfold measurements.

Activity outcome measures were: mean accelerometer counts per minute (cpm); counts per day and proportion of time spent in moderate and vigorous activity. The mean (s.d.) number of days with ⩾500 min of recorded accelerometer data was 7.0 (1.1). Linear regression models showed no significant associations between any of the neonatal anthropometric measures and the activity variables. Body fat percentage at 7.5 years was negatively associated with all activity variables (B = −4.69, CI: −7.31, −2.07 for mean cpm).

In conclusion, this study showed no associations between body size and skinfold thickness at birth and objectively measured physical activity in childhood.
Enhancement of turbulence through lateral spreading in a stratified‐shear flow: Development and assessment of a conceptual model
Authors: MacDonald Daniel G. , Chen Fei
Published: April 2012

A conceptual model for the impact of lateral spreading processes on local stratified‐shear turbulence is presented and evaluated using field data from the rapidly spreading near‐field region of the Merrimack River plume. The conceptual model addresses increases in turbulent kinetic energy associated with the stretching of a Kelvin‐Helmholz billow along its rotational axis. A non‐dimensional relationship is derived with two fit parameters, including a parameter representing the magnitude of mixing under the no spreading case, and a non‐dimensional time scale. For the model to be viable, this time scale, representing the period of time that a Kelvin‐Helmholz billow is subject to stretching should be of the same order as the evolution time scale for the billow. Observational data from field experiments are used to evaluate the two fit parameters, indicating a stretching time scale of the same order as evolution time scales reported in the literature. In addition, application of the model to the field data reduces observed variability. We conclude that spreading is an important mechanism capable of enhancing local stratified‐shear turbulence.
Flow over rough mobile beds: Friction factor and vertical distribution of the longitudinal mean velocity
Authors: Ferreira Rui M. L. , Franca Mário J. , Leal João G. A. B. , Cardoso António H.
Published: April 2012

The main objective of the present study is to identify the impacts of bed mobility on the vertical profile of the mean longitudinal velocity and on resistance in flows over water‐worked beds of poorly sorted mixtures of sand and gravel. Water‐worked beds with sediment transport are explicitly distinguished from immobile beds with imposed sediment feed. Flows with different equilibrium sediment transport rates are generated in a laboratory flume. The initial bed mixtures featured combinations of sand and gravel modes. Data collection included instantaneous velocities measured with Laser Doppler Annemometry. Wall similarity, in the sense of Townsend (1976), is assumed. The parameters of the formulae are discussed within three scenarios comprising different definitions ofu* and ks combined with different conceptions of the Von Kármán constant (κ flow independent or flow dependent). It is shown that the parameters of the formulae that express the velocity profile vary with the Shields number and with the initial bed composition. The variation is independent of the adopted scenario, except in what concerns the formulation of hydraulic smoothening in the presence of sand sizes, which depends on the definition of ks.
Relative role of wind forcing and riverine nutrient input on the extent of hypoxia in the northern Gulf of Mexico
Authors: Feng Y. , DiMarco S. F. , Jackson G. A.
Published: April 2012

Seasonal hypoxia of the northern Gulf of Mexico has been observed for more than 25 years. It is generally accepted that the variation in the areal extent of hypoxia is determined by changes in nutrient addition from the Mississippi River. In this study, we investigate the statistical relation between the hypoxic area and a new variable, the duration of west wind, using the available measurements for the period 1985–2010. Special consideration was paid to the 1993–2010 period, a time when a large shift in the seasonal hypoxia pattern has been reported. When excluding the years in which hurricanes directly impacted the hypoxic area observation, we find that the duration of west wind is correlated with the hypoxic area at r2 = 0.32 for the 1985–2010 period, and r2= 0.52 for the 1993–2010 period. Multilinear regressions using both wind duration and May‐June nitrate loading improve the statistical relationships for both periods tor2 = 0.69 and 0.74 for the long and short time periods, respectively. Mechanistically, the statistical relationships reflect the movement and changes in horizontal river plume position associated with the wind and the influence of stratification on the hypoxic area.
Argo profiles variability of barrier layer in the tropical Indian Ocean and its relationship with the Indian Ocean Dipole
Authors: Qiu Yun , Cai Wenju , Li Li , Guo Xiaogang
Published: April 2012

Interannual variability of the barrier layer (BL) in the southeastern tropical Indian Ocean (SETIO) is examined using temperature and salinity profiles derived from Argo floats since 2004. We show that a quasi‐permanent BL exists off Sumatra with a semi‐annual cycle and a maximum in November. Further, interannual variability of the BL is closely related to the Indian Ocean Dipole (IOD) with the IOD leading the BL by one month. During the 2006 positive IOD (pIOD) season, equatorial easterly‐induced upwelling Kelvin waves raise the isothermal layer (IL) off Sumatra; a salinity‐stratified mixed layer (ML) shoals due to a reduced eastward salty water transport by a weaker Wyrtki Jet, despite an offset by a reduced freshwater flux. Consequently, thinning of the BL is dominated by thinning of the IL. During the 2010 negative IOD (nIOD), similar processes operate but in an opposite direction. As thinning of the BL during a pIOD enhances the thermocline‐ML coupling, our results reveal that an IOD‐induced co‐varying BL in turn enhances the IOD positive feedbacks.
A Note On The Denisova Cave mtDNA Sequence
Authors: Caldararo Niccolo , Guthrie Michael
Published: April 2012

The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Critical nutritional stress among adult tribal populations of West Bengal and Orissa, India.
Authors: Bisai Samiran , Bose Kaushik
Published: April 2012

This paper deals with cross-sectional studies carried out during the period 2004-2007. It is based on eight data sets of tribals of Paschim Medinipur and Bankura Districts of West Bengal and Keonjhar District of Orissa. The tribes include Bhumijs, Kora Mudis, Lodhas, Santals, Bathudis and Savars. Height and weight were measured following standard techniques. The body mass index (BMI) was computed following standard equation. Nutritional status (chronic energy deficiency, CED) was evaluated using internationally accepted cut-off values of BMI. We followed the World Health Organization's classification (1995) of the public health problem of low BMI, based on adult populations worldwide. Our results show that, in general, among the tribes studied:i)Both sexes had very low levels of BMI ii)There existed high rates of CED indicating a critical nutritional condition iii)Women experienced greater nutritional stress iv)The nutritional situation is similar in both West Bengal as well as Orissa.
From Machine Learning to Learning Machines - A Perspective toward Personalized Medicine
Authors: Bhattacharyya Malay
Published: April 2012

We describe how to learn a network using a bottom-up approach by building networks from expression profiles. Then we can analyze these networks with different graph mining approaches and by studying topological behaviors. Finally, how we can achieve personalized medicine from the network biology.
Mining Co-expression Graphs: Applications to MicroRNA Regulation and Disease Analysis
Authors: Bhattacharyya Malay
Published: April 2012

MicroRNAs (miRNAs) are known to translationally repress or post-transcriptionally regulate mRNAs and are responsible for many diseases. We are preparing a comprehensive framework of co-expression analysis to figure out co-expression, differential co-expression and co-expression dynamics within multiple phenotypes in expression profiles. The purpose is to elucidate the disease association of miRNAs via co-regulatory pattern analysis.
Fundamentals of Molecular Biology
Authors: Bhattacharyya Malay
Published: April 2012

We present some basic concepts of molecular biology and the related open problems.
Mapping from Statistical to Biological Proximity
Authors: Bhattacharyya Malay
Published: April 2012

We verify whether the proximity claimed by state-of-the-art statistical similarity measures are indeed biologically appropriate or not. We present some analytical results on it.
Kinetic resolution of racemates under chiral catalysis: connecting the dots
Authors: Chandrasekhar Sosale
Published: April 2012

The current theory of the titled phenomenon is apparently based on an inconsistent use of concentration units, as employed in the derivation of the fundamental equations. Thus, manifestly, whilst the relation between extent of conversion and e.e. is derived with mole fractions, the succeeding kinetic equations employ units of molarity. This invalidates the derivation in the general case. Fortuitously, however, it is applicable in the majority of simple cases, wherein the total number of moles involved in the reaction remains constant. Herein is presented a rigorous approach which is generally valid.
Thermal lens spectroscopy for the differentiation of biodiesel-diesel blends
Authors: Ventura M. , Simionatto E. , Andrade L. H. C. , Lima S. M.
Published: April 2012

Thermal lens (TL) spectroscopy was applied to biofuels to test its potential to distinguish diesel from biodiesel in blended fuels. Both the heat and mass diffusion effects observed using a TL procedure provide significant information about biodiesel concentrations in blended fuels. The results indicate that the mass diffusivity decreases 32% between diesel and the blend with 10% biodiesel added to the diesel. This simple TL procedure has the potential to be used for in loco analyses to certify the mixture and quality of biodiesel-diesel blends.
Monte Carlo code G3sim for simulation of plastic scintillator detectors with wavelength shifter fiber readout
Authors: Mohanty P. K. , Dugad S. R. , Gupta S. K.
Published: April 2012

A detailed description of a compact Monte Carlo simulation code “G3sim” for studying the performance of a plastic scintillator detector with wavelength shifter (WLS) fiber readout is presented. G3sim was developed for optimizing the design of new scintillator detectors used in the GRAPES-3 extensive air shower experiment. Propagation of the blue photons produced by the passage of relativistic charged particles in the scintillator is treated by incorporating the absorption, total internal, and diffuse reflections. Capture of blue photons by the WLS fibers and subsequent re-emission of longer wavelength green photons is appropriately treated. The trapping and propagation of green photons inside the WLS fiber is treated using the laws of optics for meridional and skew rays. Propagation time of each photon is taken into account for the generation of the electrical signal at the photomultiplier. A comparison of the results from G3sim with the performance of a prototype scintillator detector showed an excellent agreement between the simulated and measured properties. The simulation results can be parametrized in terms of exponential functions providing a deeper insight into the functioning of these versatile detectors. G3sim can be used to aid the design and optimize the performance of scintillator detectors prior to actual fabrication that may result in a considerable saving of time, labor, and money spent.
Performance of the M11-L density functional for bandgaps and lattice constants of unary and binary semiconductors
Authors: Peverati Roberto , Truhlar Donald G.
Published: April 2012

The recently developed SOGGA11 and M11-L density functionals have been tested for the prediction of bandgaps and lattice constants by comparing to databases containing 31 bandgaps and 34 lattice constants. To make a comparative assessment we also test several other density functionals against the same databases; in particular, we test the local spin density approximation, PBE, PBEsol, SOGGA, TPSS, revTPSS, and M06-L local density functionals and the HSE screened-exchange hybrid nonlocal density functional; and for a subset of 13 lattice constants we also compare the mean errors to those of the AM05 and WC local density functionals and the HISS and HSEsol nonlocal density functionals. The tests show that, of the ten functionals tested against all 65 data, the SOGGA, PBEsol, and HSE functionals are the most accurate for lattice constants, whereas the HSE, M11-L, and M06-L density functionals are the most accurate for bandgaps. However, the SOGGA11 density functional is the most accurate generalized gradient approximation for bandgaps.
Synthesis and signature of M-E coupling in novel self-assembled CaCu3Ti4O12-NiFe2O4 nanocomposite structure
Authors: Ahlawat Anju , Sathe V. G. , Ganesan V. , Phase D. M. , Satapathy S.
Published: April 2012

Self-assembled epitaxial nanostructures of NiFe2O4 ferrimagnetic material were grown in the matrix of CaCu3Ti4O12 dielectric material by pulsed laser deposition. SEM and AFM studies showed self-assembly of vertical columnar structures of NiFe2O4 in the matrix of CaCu3Ti4O12. The substrate induced strain in this nanocomposite system is insignificant and vertical strain induced by CaCu3Ti4O12 matrix material on the NiFe2O4 rods governs the strain state. Further, vertical strain state in NiFe2O4 is switched from tension to compression as a result of this geometry. A change in magnetization of the composite film is observed around 100 K where the dielectric constant also showed a sudden change.
Reduction in anti-ferromagnetic interactions in ion-beam deposited Fe3O4 thin films
Authors: Kumar Ankit , Pandya Dinesh K. , Chaudhary Sujeet
Published: April 2012

Phase pure Fe3O4 thin films of thickness ∼42 nm have been prepared on the Si(100) substrate by reactive ion beam sputtering in the growth temperature range of 150–250 °C. A high degree of phase purity in the 175 °C sample has been confirmed by the XRD, Raman shift, and R-T measurements. The polycrystalline films show a sharp Verway transition as supported by temperature dependent resistivity, AC susceptibility, and coercivity behavior. The significant feature of these films is the early saturation of their room temperature magnetization at ∼400 mT, indicating the presence of low anti-ferromagnetic competitions in sharp contrast to most of the previous reports. The noticeable reduction of anti-phase boundaries and its dependence on growth temperature has been correlated with the energetic ion-beam deposition process, and explained in terms of the of ionic vacancy migration approach of Eerenstein et al. [Phys. Rev. B 68, 014428 (2003)]. The electronic conduction of these films is governed by near-neighbor hopping above 240 K and Shklovskii-Efros variable range hopping below this transition temperature.
Electronic states and pseudo Jahn-Teller distortion of heavy metal-monobenzene complexes: M(C6H6) (M = Y, La, and Lu)
Authors: Liu Yang , Kumari Sudesh , Roudjane Mourad , Li Shenggang , Yang Dong-Sheng
Published: April 2012

Monobenzene complexes of yttrium (Y), lanthanum (La), and lutetium (Lu), M(C6H6) (M = Y, La, and Lu), were prepared in a laser-vaporization supersonic molecular beam source and studied by pulsed-field ionization zero electron kinetic energy (ZEKE) spectroscopy and ab initio calculations. The calculations included the second-order perturbation, the coupled cluster with single, double, and perturbative triple excitation, and the complete active space self-consistent field methods. Adiabatic ionization energies and metal-benzene stretching frequencies of these complexes were measured for the first time from the ZEKE spectra. Electronic states of the neutral and ion complexes and benzene ring deformation were determined by combining the spectroscopic measurements with the theoretical calculations. The ionization energies of M(C6H6) are 5.0908 (6), 4.5651 (6), and 5.5106 (6) eV, and the metal-ligand stretching frequencies of [M(C6H6)]+ are 328, 295, and 270 cm−1 for M = Y, La, and Lu, respectively. The ground states of M(C6H6) and [M(C6H6)]+ are 2A1 and 1A1, respectively, and their molecular structures are in C2v point group with a bent benzene ring. The deformation of the benzene ring upon metal coordination is caused by the pseudo Jahn-Teller interaction of (12E2+12A1+22E2) ⊗ e2 at C6v symmetry. In addition, the study shows that spectroscopic behaviors of Y(C6H6) and La(C6H6) are similar to each other, but different from that of Lu(C6H6).
Multi-layer coarse-graining polarization model for treating electrostatic interactions of solvated α-conotoxin peptides
Authors: Jiang Nan , Ma Jing
Published: April 2012

A multi-layer coarse-graining (CG) model is presented for treating the electrostatic interactions of solvated α-conotoxin peptides. According to the sensitivity to the electrostatic environment, a hybrid set of electrostatic parameters, such as secondary-structure- and residue-based dipoles, and atom-centered partial charges, are adopted. For the polarization “inert” secondary-structures and residues, the fragment dipole moments are distributed within narrow ranges with the magnitude close to zero. The coarse-graining fragment dipoles are parameterized from a large training set (10 000 configurations) to reproduce the electrostatic features of molecular fragments. In contrast, the electrostatically “sensitive” atoms exhibit large fluctuations of charges with the varied environments. The environment-dependent variable charges are updated in each energetic calculation. The electrostatic interaction of the whole chemical system is hence partitioned into several sub-terms coming from the fragment dipole-dipole, (fragment) dipole-(atom) charge, and atom charge-charge interactions. A large number of test calculations on the relative energies of cyclo-peptide conformers have demonstrated that the multi-layer CG electrostatic model presents better performance than the non-polarized force fields, in comparison with the density-functional theory and the fully polarized force field model. The selection of CG fragment centers, mass or geometric center, has little influence on the fragment-based dipole-dipole interactions. The multi-layer partition of electrostatic polarization is expected to be applied to many biologically interesting and complicated phenomena.
Monte Carlo calculation of electron diffusion coefficient in wurtzite indium nitride
Authors: Wang Shulong , Liu Hongxia , Gao Bo , Cai Huimin
Published: April 2012

This paper presents the theoretical analysis of the diffusivity of electrons in wurtzite (WZ) indium nitride (InN) using an ensemble Monte Carlo (EMC) method. The electron diffusion coefficient D(E,d,ω) as the functions of the electric field (E), doping concentration (d), and frequency (ω) is investigated in detail. The research results show that the maximum zero-field diffusion coefficient is about 250 cm2/s. The diffusion coefficient parallel to the electric field is smaller than that of perpendicular to the electric field. Further investigation shows that the diffusion coefficient decreases greatly at high frequency. Using Einstein equation, we obtain the zero-field mobility and make comparisons with the references.
Improved switching uniformity in resistive random access memory containing metal-doped electrolyte due to thermally agglomerated metallic filaments
Authors: Lee Wootae , Park Jubong , Kim Seonghyun , Woo Jiyong , Shin Jungho , Lee Daeseok , Cha Euijun , Hwang Hyunsang
Published: April 2012

We demonstrate improved switching uniformity in resistive random-access memory (RRAM) containing metal-doped electrolyte due to thermally agglomerated metallic filaments. Rapid thermal annealing (RTA) produced copper-doped carbon (CuC) devices that exhibited better switching parameters, such as on/off resistance and set/reset voltage, than a control device. High-resolution transmission electron microscopy, electron dispersive spectroscopy, and conductive atomic force microscopy revealed that Cu atoms were agglomerated during the RTA process and formed a Cu filament in the CuC film. Consequently, the forming process can be eliminated, which is desirable for practical RRAM applications.
Nanosecond threshold switching of GeTe6 cells and their potential as selector devices
Authors: Anbarasu M. , Wimmer Martin , Bruns Gunnar , Salinga Martin , Wuttig Matthias
Published: April 2012

Time-resolved threshold switching characteristics including transient parameters such as delay time and holding voltage are reported for a nanoscale GeTe6 Ovonic threshold switching (OTS) device. The voltage dependence of the threshold switching process has been studied, revealing switching in less than 5 ns in the fastest case. A constant holding voltage is observed for the different voltage pulses applied, which is an indicative for a stable on state in the amorphous phase. In addition, the potential of GeTe6 devices as OTS selectors is validated.
Enhancement of carrier-mediated ferromagnetism in Zr/Fe-codoped In2O3 films
Authors: Kim H. , Osofsky M. , Auyeung R. C. Y. , Piqué A.
Published: April 2012

Fe/Zr-codoped In2O3 thin films were grown on yttria stabilized zirconia substrates by pulsed laser deposition. The deposited films exhibited ferromagnetism at room temperature with strong magnetic anisotropy, which was influenced by a magnetostriction effect under tensile stress (i.e., c/a > 1). Both the saturation magnetization and anomalous Hall effect (AHE) were enhanced by increasing charge carrier density via Zr-doping. Our observations, including AHE and magnetic anisotropy, provide strong evidence of intrinsic ferromagnetism at room temperature in these materials.
Quantized charge pumping through a carbon nanotube double quantum dot
Authors: Chorley S. J. , Frake J. , Smith C. G. , Jones G. A. C. , Buitelaar M. R.
Published: April 2012

We demonstrate single-electron pumping in a gate-defined carbon nanotube double quantum dot. By periodic modulation of the potentials of the two quantum dots, we move the system around charge triple points and transport exactly one electron or hole per cycle. We investigate the pumping as a function of the modulation frequency and amplitude and observe good current quantization up to frequencies of 18 MHz where rectification effects cause the mechanism to break down.
Relationships between skin follicle characteristics and fibre properties of Suri and Huacaya alpacas and Peppin Merino sheep
Authors: Ferguson M. B. , McGregor B. A. , Behrendt R.
Published: April 2012

We aimed to quantify the number, type and arrangement of skin follicles in Huacaya and Suri alpaca skin and correlate their follicle characteristics with fibre traits of harvested fibre and compared these relationships with those of Merino sheep. Fibre and skin samples were collected from the mid-side of 12 Huacaya alpacas, 24 Suri alpacas and 10 Merino sheep. The mean fibre diameter (MFD ± s.e.) of the Huacaya and Suri were: 35.5 ± 0.9 and 28.3 ± 1.0 μm, respectively. The follicle groups found for alpacas were very different from the normal trio of primary follicles found in sheep and goats. The follicle group of the alpacas consisted of a single primary follicle surrounded by a variable number of secondary follicles. The mean ± s.e. primary follicle density was 3.1 ± 0.3 and 2.7 ± 0.1 follicles/mm2 for Huacaya and Suri, respectively. The mean ± s.e. secondary follicle density (SFD) was 13.7 ± 1.2 and 17.5 ± 0.6 follicles/mm2 for Huacaya and Suri, respectively. The mean ± s.e. ratio of secondary to primary follicles (S/P ratio) was 5.1 ± 0.5 for the Huacaya and 7.3 ± 0.2 for the Suri alpacas. The sheep had higher S/P ratios and SFD, lower MFD and produced significantly heavier fleeces. The key correlations found between traits in alpacas include a negative correlation between SFD and MFD (r = –0.71, P = 0.001) and a negative correlation between S/P ratio and MFD (r = –0.44, P = 0.003) and a positive correlation between S/P ratio and total follicle density (r = 0.38, P = 0.010). The study revealed that important relationships exist between alpaca skin follicle characteristics and fibre characteristics. It was the number of secondary follicles in a group that imparts density and a corresponding reduced MFD.