bluuebunny/crossref_metadata_2025 huggingface dataset:
Accounting for functional loss in Alzheimer's disease and dementia with Lewy bodies: Beyond cognition
Authors: Hamilton Joanne M. , Salmon David P. , Raman Rema , Hansen Lawrence A. , Masliah Eliezer , Peavy Guerry M. , Galasko Douglas
Published: July 2013

Background

The relative contributions of cognitive, motor, and behavioral deficits to the impairment of physical or instrumental activities of daily living (ADLs) may differ in patients with dementia with Lewy bodies (DLB) and Alzheimer's disease (AD).

Methods

Multiple linear regression analyses were used to identify the amount of variability in physical self‐maintenance and instrumental ADL ratings predicted by cognitive, motor, and behavioral indices separately for patients with autopsy‐diagnosed DLB (n = 39) or AD (n = 39).

Results

Motor dysfunction accounted for significant variance in physical ADLs in DLB (R2 change = 0.17), whereas behavioral (R2 change = 0.23) and motor dysfunction (R2 change = 0.13) accounted for significant variance in AD. Motor (R2 change = 0.32) and cognitive (R2 change = 0.10) dysfunction accounted for significant variance in instrumental ADLs in DLB, whereas cognitive (R2 change = 0.36) and behavioral (R2 change = 0.12) dysfunction accounted for significant variance in AD.

Conclusions

Cognitive, motor, and behavioral deficits contribute differently to ADL changes in DLB and AD. Thus, treatments designed to ameliorate a certain aspect of AD or DLB (e.g., cognitive dysfunction) may have a larger impact on everyday functioning in one disorder than the other.
Progression from ductal carcinoma in situ to invasive breast cancer: Revisited
Authors: Cowell Catherine F. , Weigelt Britta , Sakr Rita A. , Ng Charlotte K.Y. , Hicks James , King Tari A. , Reis-Filho Jorge S.
Published: July 2013

Ductal carcinoma in situ (DCIS) is an intraductal neoplastic proliferation of epithelial cells that is separated from the breast stroma by an intact layer of basement membrane and myoepithelial cells. DCIS is a non‐obligate precursor of invasive breast cancer, and up to 40% of these lesions progress to invasive disease if untreated. Currently, it is not possible to predict accurately which DCIS would be more likely to progress to invasive breast cancer as neither the significant drivers of the invasive transition have been identified, nor has the clinical utility of tests predicting the likelihood of progression been demonstrated. Although molecular studies have shown that qualitatively, synchronous DCIS and invasive breast cancers are remarkably similar, there is burgeoning evidence to demonstrate that intra‐tumor genetic heterogeneity is observed in a subset of DCIS, and that the process of progression to invasive disease may constitute an ‘evolutionary bottleneck’, resulting in the selection of subsets of tumor cells with specific genetic and/or epigenetic aberrations. Here we review the clinical challenge posed by DCIS, the contribution of the microenvironment and genetic aberrations to the progression from in situ to invasive breast cancer, the emerging evidence of the impact of intra‐tumor genetic heterogeneity on this process, and strategies to combat this heterogeneity.
Gate-keeping and localizing in scientific translation publishing: the case of Richard Taylor andScientific Memoirs
Authors: OLOHAN MAEVE
Published: July 2013

Growing interest in studying translation through a sociological lens and the relative lack of attention by translation scholars to the production of scientific translations provide impetus and rationale for this case study. Richard Taylor's editorial work for theScientific Memoirsperiodical is examined, with a particular focus on his conception of the utility of translation in the service of scientific advancement in Britain. The roles of gate-keeper and localizer of scientific material are attributed to Taylor, roles which he exercised through promotion of scientific translation, selection of texts to publish and editorial interventions in translations. The historical case study sheds light on activities of editing, translating and publishing science in mid-nineteenth-century Britain but is also illustrative of research areas where the interests of translation scholars and historians of science may converge. By centring attention on Taylor's editorial role, some of the material and social contingencies of this publishing activity are highlighted, enabling us to gain a deeper appreciation of scientific translation as sociohistorical practice.
The sculpture of the Heroon of Perikle at Limyra: the making of a Lycian king
Authors: Şare Tuna
Published: July 2013

As one of the many monumental tombs of fourth-century BC Anatolia, the Heroon of Perikle at Limyra is usually overshadowed by the earlier and better preserved Nereid Monument of Xanthos. Its owner, Perikle, is seen as either a mediocre pro-Achaemenid dynast or a fan of his namesake, the Athenian strategos, a view reflected in previous assessments of the stylistic pedigree of the tomb’s ornamentation. But a re-examination of the Heroon’s sculptural programme that places the cella friezes, karyatids and akroteria within their historical context shows the tomb to be Perikle’s announcement of his status as the first military king of Lycia. The Heroon of Perikle reflects associations with both the buildings of the Athenian Akropolis and Persian iconography, but these elements were appropriated to serve the political agenda of Perikle and his later hero cult.
EXPERIMENTS IN ECONOMICS AND PHILOSOPHY
Authors: Konow James , Schwitzgebel Eric , Bicchieri Cristina , Dana Jason , Jiménez-Buedo María
Published: July 2013

Not so long ago, many economists and philosophers felt that their disciplines had no use for experimental methods. An experimental study was, by its nature, ‘not economics’ or ‘not philosophy’ – psychology maybe. Opinion has changed dramatically. This issue of Economics and Philosophy represents a collection of recent contributions to experimental research that explicitly deal with empirical findings or methodological questions in the intersection of the two disciplines. To the best of our knowledge, it is the first such collection dedicated to addressing these common interests.
Structural and Functional Changes of the Cingulate Gyrus following Traumatic Brain Injury: Relation to Attention and Executive Skills
Authors: Merkley Tricia L. , Larson Michael J. , Bigler Erin D. , Good Daniel A. , Perlstein William M.
Published: July 2013

Impairments of attention and executive functions are common sequelae of traumatic brain injury (TBI). The anterior cingulate is implicated in conflict-related task performance, such as the Stroop, and is susceptible to TBI-related injury due to its frontal location and proximity to the rough surface of the falx cerebri. We investigated the relationship between cingulate cortex volume and performance on tasks of selective attention and cognitive flexibility (single-trial Stroop and Auditory Consonant Trigrams [ACT]). Participants consisted of 12 adults with severe TBI and 18 controls. T1-weighted volumetric MRI data were analyzed using automated cortical reconstruction, segmentation, parcellation, and volume measurement. Cortical volume reductions were prominent bilaterally in frontal, temporal, and inferior parietal regions. Specific regional reduction of the cingulate cortex was observed only for cortical volume of right caudal anterior cingulate (cACC). The TBI group performed significantly worse than control participants on the Stroop and ACT tasks. Findings suggest that atrophy of the right cACC may contribute to reduced performance on executive function tasks, such as the Stroop and ACT, although this is likely but one node of an extensive brain network involved in these cognitive processes. (JINS, 2013,19, 1–12)
Learn to Think for Yourself: Impelled by UPIC to open new ways of composing
Authors: Bourotte Rodolphe , Delhaye Cyrille
Published: July 2013

Originally designed by Xenakis to free him from traditional music notation while allowing a faithful execution of his musical thought, UPIC (Unité Polyagogique Informatique du CEMAMu) was quickly diverted from its original functions. Even if Xenakis recommended to apprentice composers who came to study with him ‘listen to a lot of music and write’ (Serrou 2003: 20), this machine, since its inception, has enabled a large number of people to access music composition, because it does not require any preliminary theoretical training. Based on this observation we ask how UPIC, capable of converting a drawing into sound in real-time, upset the perception of musical pedagogy not only in Europe but also worldwide, through the many workshops/concerts offered to a wide audience. Exchanges and emulation around this invention are discussed as well.

After describing the technical development of this tool and, by extension, Xenakis's pedagogical thinking, we will highlight some of the most significant encounters between the machine and the public thanks to many unpublished sources found in the archives of the Centre Iannis Xenakis (CIX) recently deposited at the University of Rouen. We will highlight the pedagogical correlation between sound theory, gesture and image involved in the composition of a UPIC score. We will also approach other software applications that combine drawing and sound.
Promotion of exclusive breast-feeding at scale within routine health services: impact of breast-feeding counselling training for community health workers in Recife, Brazil
Authors: Coutinho Sonia B , Lira Pedro IC , Lima Marilia C , Frias Paulo G , Eickmann Sophie H , Ashworth Ann
Published: July 2013

Objective

Breast-feeding counselling has been identified as the intervention with the greatest potential for reducing child deaths, but there is little experience in delivering breast-feeding counselling at scale within routine health systems. The study aim was to compare rates of exclusive breast-feeding associated with a breast-feeding counselling intervention in which community health agents (CHA) received 20 h of training directed at counselling and practical skills with rates pre-intervention when CHA received 4 h of didactic teaching.

Design

Cross-sectional surveys of breast-feeding practices were conducted pre- and post-intervention in random samples of 1266 and 1245 infants aged 0–5·9 months, respectively.

Setting

Recife, Brazil, with a population of 2 million.

Subjects

CHA (n 1449) of Brazil's Family Health Programme were trained to provide breast-feeding counselling at home visits.

Results

Rates of exclusive breast-feeding improved when CHA were trained to provide breast-feeding counselling and were significantly higher by 10–13 percentage points at age 3–5·9 months when compared with pre-intervention rates (P < 0·05). Post-intervention point prevalence of exclusive breast-feeding for infants aged <4 months was 63 % and for those aged <6 months was 50 %.

Conclusions

Multifunctional CHA were able to deliver breast-feeding counselling at scale within a routine health service and this was associated with a significant increase in rates of exclusive breast-feeding. The study reinforces the need to focus training on counselling and practical skills; a key component was an interactive style that utilized the knowledge and experience of CHA. The findings are relevant to the call by international organizations to scale up breast-feeding counselling.
FORUM: A WORLD OF IDEAS: NEW PATHWAYS IN GLOBAL INTELLECTUAL HISTORY,C.1880–1930
Authors: GÄNGER STEFANIE , LEWIS SU LIN
Published: July 2013

This forum explores new directions in global intellectual history, engaging with the methodologies of global and transnational history to move beyond conventional territorial boundaries and master narratives. The papers focus on the period between the last decades of the nineteenth century and the first decades of the twentieth, an era in which the growth of cities, burgeoning print cultures and new transport and communications technology enabled the accelerated circulation and exchange of ideas throughout the globe. The proliferation of conferences, world fairs, and international congresses, the growing professionalization and definition of academic disciplines, and the enhanced circulation of scholarly journals and correspondence enabled intellectuals around the world to converse in shared vocabularies. Much of the scholarship on early twentieth-century intellectual history in the non-Western world has been viewed through the binary relationships of metropole and colony, or as nationalist reactions to colonial domination. This cluster widens the framework to consider the way in which intellectuals formed scholarly networks and gathered multiple influences to articulate new visions of community and society within a wider world of ideas. The multiplicity of imperial and transnational pathways allowed not only for “centers of calculation” in colonial metropoles, but also for points of convergence and encounter outside Europe. As these papers show, the routes by which ideas travelled brought forth a global republic of letters, composed of diverse “centers” for the collection and production of knowledge by intellectuals operating in different parts of the world.
UNDER THE INFLUENCE? TRANSLATIONS AND TRANSGRESSIONS IN LATE OTTOMAN IMPERIAL THOUGHT
Authors: ARSAN ANDREW
Published: July 2013

This essay focuses upon a single speech by the Ottoman man of religion Shaykh Ahmad Tabbarah. Though short, it allows us to reconsider the ways in which we have framed intellectual production beyond Europe in the nineteenth and twentieth centuries. For even as scholars have queried the diffusionist sweep of earlier narratives, asserting the intellectual agency of non-Western thinkers, they have continued to lay the emphasis on the ways the latter customized European thought to local exigencies. Tabbarah, however, engaged in two-way translations and transgressions. Arraying French sources into a Khaldunian narrative even as he slotted statistics into conventional rhetorical forms, he imbued the secular with the religious, and the religious with the secular. Resolutely refusing to choose between these various elements, he laced them together into a compound creation, which drew its strength from the confluence of two seemingly incommensurable bodies of thought.
THE INDIAN PSYCHOLOGICAL ASSOCIATION, THE BIRTH OF THE MODERN DISCIPLINE AND “THE DESTINY OF ONE NATION”, 1905–1947
Authors: LASKIN ARIA
Published: July 2013

In the age of decolonization, Indian psychology engaged with and nationalized itself within global networks of ideas. While psychology was eventually applied by public intellectuals in explicitly political arenas, this essay focuses on the initial mobilization of the discipline's early Indian experts, led by the founder of the Indian Psychological Association, Narendranath Sengupta. Although modern critics have harshly judged early Indian psychologists for blind appropriation of European concepts, an analysis of the networks through which the science of psychology was developed challenges this oversimplification. Early Indian psychologists developed their discipline within a simultaneously transnational and nationalistic context, in which European ideas overlapped with ancient texts, creating a deliberately “Indian” brand of psychology. As the discipline of psychology exploded across the world, Indian psychologists developed a science ofswaraj, enabling synergies between modern psychological doctrine, philosophy and ancient texts. This paper explores the networks of ideas within which modern Indian psychology was developed, the institutional and civil environment in which it matured, and the framework through which it engaged with and attempted to claim credence within transnational scientific networks.
Technique for reduction of noise resistance in a balanced low-noise amplifier for beam-steering applications
Authors: Smith David M.P. , Woestenburg Bert E.M.
Published: July 2013

This paper, following up on the previous work, investigates the effect of the input coupler's load termination of a balanced amplifier in a beam-steering system. The noise generated in this load termination deteriorates the amplifier noise resistance, which increases the noise temperature due to a varying active reflection coefficient at the antenna ports as a function of scan angle. In reducing this effect, the balanced configuration is made more favorable for radio astronomy applications. By lowering the value of the impedance termination on the fourth port of the quadrature coupler an improvement in noise temperature sensitivity is achieved at the cost of reduced power matching.
Why haven't we made an efficacious vaccine for malaria?
Authors: Wykes Michelle N
Published: July 2013

The malaria parasite has an extraordinary ability to evade the immune system, which may explain the failure of malaria vaccines to date. It is high time to think seriously of new treatments for this disease.
Cancer heterogeneity—a multifaceted view
Authors: Melo Felipe De Sousa E , Vermeulen Louis , Fessler Evelyn , Medema Jan Paul
Published: July 2013

Cancers of various organs have been categorized into distinct subtypes after increasingly sophisticated taxonomies. Additionally, within a seemingly homogeneous subclass, individual cancers contain diverse tumour cell populations that vary in important cancer‐specific traits such as clonogenicity and invasive potential. Differences that exist between and within a given tumour type have hampered significantly both the proper selection of patients that might benefit from therapy, as well as the development of new targeted agents. In this review, we discuss the differences associated with organ‐specific cancer subtypes and the factors that contribute to intra‐tumour heterogeneity. It is of utmost importance to understand the biological causes that distinguish tumours as well as distinct tumour cell populations within malignancies, as these will ultimately point the way to more rational anti‐cancer treatments.EMBO reports advance online publication 12 July 2013; doi:10.1038/embor.2013.92
Modulation of Post-Antibiotic Bacterial Community Reassembly and Host Response by Candida albicans
Authors: Erb Downward John R. , Falkowski Nicole R. , Mason Katie L. , Muraglia Ryan , Huffnagle Gary B.
Published: July 2013

The introduction of Candida albicans into cefoperazone-treated mice results in changes in bacterial community reassembly. Our objective was to use high-throughput sequencing to characterize at much greater depth the specific changes in the bacterial microbiome. The colonization of C. albicans significantly altered bacterial community reassembly that was evident at multiple taxonomic levels of resolution. There were marked changes in the levels of Bacteriodetes and Lactobacillaceae. Lachnospiraceae and Ruminococcaceae, the two most abundant bacterial families, did not change in relative proportions after antibiotics, but there were marked genera-level shifts within these two bacterial families. The microbiome shifts occurred in the absence of overt intestinal inflammation. Overall, these experiments demonstrate that the introduction of a single new microbe in numerically inferior numbers into the bacterial microbiome during a broad community disturbance has the potential to significantly alter the subsequent reassembly of the bacterial community as it recovers from that disturbance.
Phosphorus oxychloride as an efficient coupling reagent for the synthesis of esters, amides and peptides under mild conditions
Authors: Chen Hu , Xu Xunfu , Liu Liu Leo , Tang Guo , Zhao Yufen
Published: July 2013

A mild method is described for the conversion of carboxylic acids into esters, amides, as well as peptides without racemization through carboxyl activation by the reagent combination of POCl3and DMAP.
When worlds collide: inositol pyrophosphates and phosphoinositides intersect at the plasma membrane
Authors: Erneux Christophe , Elong Edimo William's
Published: July 2013

Highly phosphorylated inositol pyrophosphates are present in the cells of many organisms such as yeast, Dictyostelium and mammals. They can act as signal molecules in growth factor and insulin signalling both in cultured cells and in intact mice. Their action involves protein pyrophosphorylation or binding to multiple protein interactors such as PH (pleckstrin homology)-domain-containing proteins. One key enzyme in their synthesis, PPIP5K (diphosphoinositol pentakisphosphate kinase) 1/2, can phosphorylate InsP6 and 5-InsP7 to 1-InsP7 and InsP8 respectively. Stephen Shears's laboratory reported in this issue of the Biochemical Journal that PPIP5K1's unexpectedly high affinity for PtdIns(3,4,5)P3, which is synthesized at the plasma membrane, provides a recruitment mechanism for this enzyme in response to growth factor receptor activation. In competition experiments, they observed that PtdIns(3,4,5)P3 binding to PPIP5K1 could be displaced by inositol pyrophosphates and that PPIP5K1 substrates were more potent inhibitors than PPIP5K1 products. Those findings reveal a mechanism for localized depletion of InsP6 and 5-InsP7 at the plasma membrane and further translocation of PtdIns(3,4,5)P3-binding PH-domain-containing proteins.
Multiscale analysis in momentum space for quasi-periodic potential in dimension two
Authors: Karpeshina Yulia , Shterenberg Roman
Published: July 2013

We consider a polyharmonic operator \documentclass[12pt]{minimal}\begin{document}$H=(-\Delta)^l+V({\vec{x}})$\end{document}H=(−Δ)l+V(x⃗) in dimension two with l ⩾ 2, l being an integer, and a quasi-periodic potential \documentclass[12pt]{minimal}\begin{document}$V({\vec{x}})$\end{document}V(x⃗). We prove that the absolutely continuous spectrum of H contains a semiaxis and there is a family of generalized eigenfunctions at every point of this semiaxis with the following properties. First, the eigenfunctions are close to plane waves \documentclass[12pt]{minimal}\begin{document}$e^{i\langle {\vec{\varkappa }},{\vec{x}}\rangle }$\end{document}ei⟨ϰ⃗,x⃗⟩ at the high energy region. Second, the isoenergetic curves in the space of momenta \documentclass[12pt]{minimal}\begin{document}${\vec{\varkappa }}$\end{document}ϰ⃗ corresponding to these eigenfunctions have a form of slightly distorted circles with holes (Cantor type structure). A new method of multiscale analysis in the momentum space is developed to prove these results.
Monte Carlo validation experiments for the gas Cherenkov detectors at the National Ignition Facility and Omega
Authors: Rubery M. S. , Horsfield C. J. , Herrmann H. , Kim Y. , Mack J. M. , Young C. , Evans S. , Sedillo T. , McEvoy A. , Caldwell S. E. , Grafil E. , Stoeffl W. , Milnes J. S.
Published: July 2013

The gas Cherenkov detectors at NIF and Omega measure several ICF burn characteristics by detecting multi-MeV nuclear γ emissions from the implosion. Of primary interest are γ bang-time (GBT) and burn width defined as the time between initial laser-plasma interaction and peak in the fusion reaction history and the FWHM of the reaction history respectively. To accurately calculate such parameters the collaboration relies on Monte Carlo codes, such as GEANT4 and ACCEPT, for diagnostic properties that cannot be measured directly. This paper describes a series of experiments performed at the High Intensity γ Source (HIγS) facility at Duke University to validate the geometries and material data used in the Monte Carlo simulations. Results published here show that model-driven parameters such as intensity and temporal response can be used with less than 50% uncertainty for all diagnostics and facilities.
Debye-type dielectric relaxation in glass-forming 3-methylthio-1-hexanol
Authors: Gao Yanqin , Bi Dongyang , Li Xin , Liu Riping , Tian Yongjun , Wang Li-Min
Published: July 2013

The dielectric relaxation of a substituted monohydroxy alcohol, 3-methylthio-1-hexanol, is studied in the highly viscous regime near the glass transition. The Debye relaxation is detected in the dielectric spectra showing the slowest and strongest relaxation dynamics. The calorimetric and dielectric measurements of the liquid and the mixtures with a Debye liquid (2-ethyl-1-hexanol) and a non-Debye liquid (2-ethylhexylamine) reproduce the dynamic characters of the relaxations in monohydroxy alcohols. The Debye relaxation strength and time of 3-methylthio-1-hexanol do not change much compared with 2-ethyl-1-hexanol, while the structural relaxation strength shows a considerable enhancement accompanied by an increase in relaxation time, indicative of a reduction in the dynamic separation between the Debye and structural relaxations. The experimental results allow for the examination of the structural models proposed for the Debye relaxation.
Simulations reveal that the HIV-1 gp120-CD4 complex dissociates via complex pathways and is a potential target of the polyamidoamine (PAMAM) dendrimer
Authors: Nandy Bidisha , Bindu D. Hima , Dixit Narendra M. , Maiti Prabal K.
Published: July 2013

The polyamidoamine (PAMAM) dendrimer prevents HIV-1 entry into target cells in vitro. Its mechanism of action, however, remains unclear and precludes the design of potent dendrimers targeting HIV-1 entry. We employed steered molecular dynamics simulations to examine whether the HIV-1 gp120-CD4 complex is a target of PAMAM. Our simulations mimicked single molecule force spectroscopy studies of the unbinding of the gp120-CD4 complex under the influence of a controlled external force. We found that the complex dissociates via complex pathways and defies the standard classification of adhesion molecules as catch and slip bonds. When the force loading rate was large, the complex behaved as a slip bond, weakening gradually. When the loading rate was small, the complex initially strengthened, akin to a catch bond, but eventually dissociated over shorter separations than with large loading rates. PAMAM docked to gp120 and destabilized the gp120-CD4 complex. The rupture force of the complex was lowered by PAMAM. PAMAM disrupted salt bridges and hydrogen bonds across the gp120-CD4 interface and altered the hydration pattern of the hydrophobic cavity in the interface. In addition, intriguingly, PAMAM suppressed the distinction in the dissociation pathways of the complex between the small and large loading rate regimes. Taken together, our simulations reveal that PAMAM targets the gp120-CD4 complex at two levels: it weakens the complex and also alters its dissociation pathway, potentially inhibiting HIV-1 entry.
Evolution of particle size and interparticle magnetic interactions with thickness in co-sputtered Cu79Co21 nanogranular thin films
Authors: Kumar Dinesh , Chaudhary Sujeet , Pandya Dinesh K.
Published: July 2013

The fitting of magnetoresistance data of Cu79Co21 films co-sputtered at room temperature reveals the presence of bimodal distribution of Co-particles. With the increase of film thickness from 25 to 100 nm, whereas smaller particle (2.5 nm) distribution remains unaffected, the bigger one grows monotonically to 4.9 nm. Detailed temperature and field dependent investigations of the magnetoresistance and magnetization behavior of these films establish a correlation between film thickness, size, and fraction of bigger particles, which is interpreted on the basis of operative growth process. The ability of controlling the interparticle magnetic interactions among the superparamagnetic particles, blocking temperature, and coercivity is demonstrated.
Carrier density modulation in graphene underneath Ni electrode
Authors: Moriyama T. , Nagashio K. , Nishimura T. , Toriumi A.
Published: July 2013

We investigate the transport properties of graphene underneath metal to reveal whether the carrier density in graphene underneath source/drain electrodes in graphene field-effect transistors is fixed. The resistance of the graphene/Ni double-layered structure has shown a graphene-like back-gate bias dependence. In other words, the electrical properties of graphene are not significantly affected by its contact with Ni. This unexpected result may be ascribed to resist residuals at the metal/graphene interface, which may reduce the interaction between graphene and metals. In a back-gate device fabricated using the conventional lithography technique with an organic resist, the carrier density modulation in the graphene underneath the metal electrodes should be considered when discussing the metal/graphene contact.
Calculation of core-level excitation in some MAX-phase compounds
Authors: Wang Liaoyuan , Rulis Paul , Ching W. Y.
Published: July 2013

We report first-principles spectroscopic calculation of core level excitations in five MAX-phase compounds. The spectra of Ti-K edges in Ti2AlC and Ti2AlN, C-K edge in Ti2AlC, N-K edge in Ti2AlN, and Nb-K edge in Nb2AlC are calculated and found to be in good agreement with reported experimental measurements. Based on this agreement, the Al-K and Al-L3 edges in the same five phases plus the Cr-K and C-K edges in Cr2AlC and the C-K edge in Nb2AlC are calculated as theoretical predictions. We further analyze the anisotropy in the calculated spectra to gain additional insights on the structure-properties relationships in these MAX-phase compounds. These results are further discussed in the context of the local atomic environments of the M, A, and X elements in MAX-phase compounds and in relation to their fundamental electronic structures.
Automation of the guiding center expansion
Authors: Burby J. W. , Squire J. , Qin H.
Published: July 2013

We report on the use of the recently developed Mathematica package VEST (Vector Einstein Summation Tools) to automatically derive the guiding center transformation. Our Mathematica code employs a recursive procedure to derive the transformation order-by-order. This procedure has several novel features. (1) It is designed to allow the user to easily explore the guiding center transformation's numerous non-unique forms or representations. (2) The procedure proceeds entirely in cartesian position and velocity coordinates, thereby producing manifestly gyrogauge invariant results; the commonly used perpendicular unit vector fields e1,e2 are never even introduced. (3) It is easy to apply in the derivation of higher-order contributions to the guiding center transformation without fear of human error. Our code therefore stands as a useful tool for exploring subtle issues related to the physics of toroidal momentum conservation in tokamaks.
The energy transfer in the TEMP-4M pulsed ion beam accelerator
Authors: Isakova Y. I. , Pushkarev A. I. , Khaylov I. P.
Published: July 2013

The results of a study of the energy transfer in the TEMP-4M pulsed ion beam accelerator are presented. The energy transfer efficiency in the Blumlein and a self-magnetically insulated ion diode was analyzed. Optimization of the design of the accelerator allows for 85% of energy transferred from Blumlein to the diode (including after-pulses), which indicates that the energy loss in Blumlein and spark gaps is insignificant and not exceeds 10%–12%. Most losses occur in the diode. The efficiency of energy supplied to the diode to the energy of accelerated ions is 8%–9% for a planar strip self-magnetic MID, 12%–15% for focusing diode and 20% for a spiral self-magnetic MID.
Phase field modeling of current density distribution and effective electrical conductivity in complex microstructures
Authors: Jin Yongmei M.
Published: July 2013

Phase field model is developed to simulate local current density distribution and macroscopic effective electrical conductivity in complex microstructures. Heterogeneous conductivity tensor in multi-grain and/or multi-phase microstructures is explicitly described by phase field variables without direct tracking of interfaces or boundaries. Microscopic anisotropic Ohm's law is solved efficiently using Fourier transform technique. These advantageous features allow this model to seamlessly integrate with other phase field models of microstructure evolutions. Application examples are presented to demonstrate the model's capability and potential, including polycrystals, solder joints, and two-phase alloys.
Quantum interference in DNA bases probed by graphene nanoribbons
Authors: Jeong Heejeong , Seul Kim Han , Lee Sung-Hoon , Lee Dongho , Hoon Kim Yong , Huh Nam
Published: July 2013

Based on first-principles nonequilibrium Green's function calculations, we demonstrate quantum interference (QI) effects on the tunneling conductance of deoxyribonucleic acid bases placed between zigzag graphene nanoribbon electrodes. With the analogy of QI in hydrocarbon ring structures, we hypothesize that QI can be well preserved in the π-π coupling between the carbon-based electrode and a single DNA base. We demonstrate indications of QI, such as destructively interfered anti-resonance or Fano-resonance, that affect the variation of tunneling conductance depending on the orientation of a base. We find that guanine, with a 10-fold higher transverse conductance, can be singled out from the other bases.
Study on an alternating current electrothermal micropump for microneedle-based fluid delivery systems
Authors: Zhang Rumi , Jullien Graham A. , Dalton Colin
Published: July 2013

In this paper, we report on a modeling study of an AC electrothermal (ACET) micropump with high operating pressures as well as fast flow rates. One specific application area is for fluid delivery using microneedle arrays which require higher pressures and faster flow rates than have been previously reported with ACET devices. ACET is very suitable for accurate actuation and control of fluid flow, since the technique has been shown to be very effective in high conductivity fluids and has the ability to create a pulsation free flow. However, AC electrokinetic pumps usually can only generate low operating pressures of 1 to 100 Pa, where flow reversal is likely to occur with an external load. In order to realize a high performance ACET micropump for continuous fluid delivery, applying relatively high AC operating voltages (20 to 36 Vrms) to silicon substrate ACET actuators and using long serpentine channel allows the boosting of operating pressure as well as increasing the flow rates. Fast pumping flow rates (102–103 nl/s) and high operating pressures (1–12 kPa) can be achieved by applying both methods, making them of significant importance for continuous fluid delivery applications using microneedle arrays and other such biomedical devices.
Laser irradiation of carbon nanotube films: Effects and heat dissipation probed by Raman spectroscopy
Authors: Mialichi J. R. , Brasil M. J. S. P. , Iikawa F. , Veríssimo C. , Moshkalev S. A.
Published: July 2013

We investigate the thermal properties of thin films formed by single- and multi-walled carbon nanotubes submitted to laser irradiation using Raman scattering as a probe of both the tube morphology and the local temperature. The nanotubes were submitted to heating/cooling cycles attaining high laser intensities (∼1.4 MW/cm2) under vacuum and in the presence of an atmosphere, with and without oxygen. We investigate the heat diffusion of the irradiated nanotubes to their surroundings and the effect of laser annealing on their properties. The presence of oxygen during laser irradiation gives rise to an irreversible increase of the Raman efficiency of the carbon nanotubes and to a remarkable increase of the thermal conductivity of multi-walled films. The second effect can be applied to design thermal conductive channels in devices based on carbon nanotube films using laser beams.
Tunable bandgap in BiFeO3 nanoparticles: The role of microstrain and oxygen defects
Authors: Mocherla Pavana S. V. , Karthik C. , Ubic R. , Ramachandra Rao M. S. , Sudakar C.
Published: July 2013

We demonstrate a tunable bandgap from 2.32 eV to 2.09 eV in phase-pure BiFeO3 by controlling the particle size from 65 nm to 5 nm. Defect states due to oxygen and microstrain show a strong dependence on BiFeO3 particle size and have a significant effect on the shape of absorbance curves. Oxygen-defect induced microstrain and undercoordinated oxygen on the surface of BiFeO3 nanoparticles are demonstrated via HRTEM and XPS studies. Microstrain in the lattice leads to the reduction in rhombohedral distortion of BiFeO3 for particle sizes below 30 nm. The decrease in band gap with decreasing particle size is attributed to the competing effects of microstrain, oxygen defects, and Coulombic interactions.
Note: Using an optical phase–locked loop in heterodyne velocimetry
Authors: Tao Tianjiong , Wang Xiang , Ma Heli , Liu Shenggang , Li Xinzhu , Weng Jidong
Published: July 2013

An optical phase–locked loop was introduced in heterodyne velocimetry to lock the differential frequency between a fiber laser and an external cavity diode laser. An uncertainty less than 1 MHz of the locked beat frequency was achieved during several microseconds, corresponding to a velocity uncertainty at 0.1 m/s level for 1550 nm light. In this way, a measurement with higher precision and better time resolution simultaneously can be obtained during a transient process. Three proof–of–principles shots were performed to measure elastic wave–induced vibrations on surfaces of steel films with submillimeter thicknesses. The surface velocity fluctuations were probed with amplitudes of about 2 m/s and periods of tens of nanoseconds, and propagating times and sound velocities of waves were also well analyzed at a time scale 0.5 μs. A velocity resolution of 0.1 m/s level and a temporal resolution of a few nanoseconds were achieved in these measurements.
Communication: Active-space decomposition for molecular dimers
Authors: Parker Shane M. , Seideman Tamar , Ratner Mark A. , Shiozaki Toru
Published: July 2013

We have developed an active-space decomposition strategy for molecular dimers that allows for the efficient computation of the dimer's complete-active-space wavefunction while only constructing the monomers’ active-space wavefunctions. Dimer states are formed from linear combinations of direct products of localized orthogonal monomer states and Hamiltonian matrix elements are computed directly without explicitly constructing the product space. This decomposition is potentially exact in the limit where a full set of monomer states is included. The adiabatic states are then found by diagonalizing the dimer Hamiltonian matrix. We demonstrate the convergence of our method to a complete-active-space calculation of the full dimer with two test cases: the benzene and naphthalene dimers.
Effect of boron incorporation on the structural and photoluminescence properties of highly-strained InxGa1-xAs/GaAs multiple quantum wells
Authors: Wang Qi , Jia Zhigang , Ren Xiaomin , Yan Yingce , Bian Zhiqiang , Zhang Xia , Cai Shiwei , Huang Yongqing
Published: July 2013

In this research, 5-period highly-strained BInGaAs/GaAs multiple quantum wells (MQWs) have been successfully grown at 480-510ºC by LP-MOCVD. Room-temperature photoluminescence (RT-PL) measurements of BInGaAs/GaAs MQWs showed the peak wavelength as long as 1.17 μm with full-width at half maximum (FWHM) of only 29.5 meV. In addition, a slight blue-shift (∼18 meV) of PL peak energy of InxGa1-xAs/GaAs MQWs was observed after boron incorporation. It has been found boron incorporation (<2%) was mainly dominated by a negative effect even though it can effectively reduce the compressive strain, i.e., it degraded the structural properties and PL efficiency of MQWs containing relatively less indium. Only at the lowest temperature growth (i.e., indium content x > 40%), the positive effect of boron incorporation prevailed, i.e., boron incorporation completely suppressed the thickness undulation and lead to the improvement of PL properties.
Extracellular matrix of secondary lymphoid organs impacts on B-cell fate and survival
Authors: Song Jian , Lokmic Zerina , Lämmermann Tim , Rolf Julia , Wu Chuan , Zhang Xueli , Hallmann Rupert , Hannocks Melanie-Jane , Horn Nathalie , Ruegg Markus A. , Sonnenberg Arnoud , Georges-Labouesse Elisabeth , Winkler Thomas H. , Kearney John F. , Cardell Susanna , Sorokin Lydia
Published: July 2013

Significance

We describe a unique extracellular matrix (ECM) niche in the spleen, the marginal zone (MZ), that supports a specialized population of MZ B lymphocytes that respond rapidly to blood-borne antigens and are therefore crucial for the first line of immune defense. We show, for the first time, that both the novel 3D structure and the biochemical composition of the ECM impacts on B-cell fate and survival. Similar pericellular ECM networks occur in thymus, bone marrow, and lymph node; hence, our data are likely to have broader ramifications to the fate and survival of other immune cells.
Promoting genital autonomy by exploring commonalities between male, female, intersex, and cosmetic female genital cutting
Authors: Svoboda J. Steven
Published: July 2013

All forms of genital cutting – female genital cutting (FGC), intersex genital cutting, male genital cutting (MGC), and even cosmetic forms of FGC – are performed in a belief that they will improve the subject’s life. Genital autonomy is a unified principle that children should be protected from genital cutting that is not medically necessary. Safeguarding genital autonomy encompasses helping societies and individuals to explore wounds common across different forms of genital cutting regarding gender, power, the quest for cultural belonging, and social and sexual control. A desire to prevent alternative sexualities helps explain the origins of MGC’s medicalization starting in the nineteenth century, as well as the roots of the failed attempt to similarly medicalize FGC. The child with ‘ambiguous’ genitalia brings us face to face with the failure of the attempted alignment of sex and gender. Medical ethics, law, and human rights suggest a path forward toward genital autonomy.
Exotic smooth structures on topological fiber bundles II
Authors: Goette Sebastian , Igusa Kiyoshi
Published: July 2013

We use a variation of a classical construction of A. Hatcher to construct virtually all stable exotic smooth structures on compact smooth manifold bundles whose fibers have sufficiently large odd dimension (at least twice the base dimension plus 3). Using a variation of the Dwyer-Weiss-Williams smoothing theory which we explain in a separate joint paper with Bruce Williams, we associate a homology class in the total space of the bundle to each exotic smooth structure and show that the image of this class in the homology of the base is the Poincaré dual of the relative higher Igusa-Klein (IK) torsion invariant. This answers the question, in the relative case, of which cohomology classes can occur as relative higher torsion classes.
Perspectives on an alternative career path in regulatory science
Authors: Fields F. Owen
Published: July 2013

Perspectives are provided on an alternative career path in regulatory science for those currently involved in basic biology research. This path is compared and contrasted with basic research, and factors to be examined if one is considering such a path are discussed.
pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling
Authors: Gil Víctor A. , Guallar Víctor
Published: July 2013

Summary: We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms.

Availability: The source code (under MIT license), installer, test suites and benchmarks can be found at https://pele.bsc.es/ under the tools section.

Contact:  victor.guallar@bsc.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modeling nucleosome position distributions from experimental nucleosome positioning maps
Authors: Schöpflin Robert , Teif Vladimir B. , Müller Oliver , Weinberg Christin , Rippe Karsten , Wedemann Gero
Published: July 2013

Motivation: Recent experimental advancements allow determining positions of nucleosomes for complete genomes. However, the resulting nucleosome occupancy maps are averages of heterogeneous cell populations. Accordingly, they represent a snapshot of a dynamic ensemble at a single time point with an overlay of many configurations from different cells. To study the organization of nucleosomes along the genome and to understand the mechanisms of nucleosome translocation, it is necessary to retrieve features of specific conformations from the population average.

Results: Here, we present a method for identifying non-overlapping nucleosome configurations that combines binary-variable analysis and a Monte Carlo approach with a simulated annealing scheme. In this manner, we obtain specific nucleosome configurations and optimized solutions for the complex positioning patterns from experimental data. We apply the method to compare nucleosome positioning at transcription factor binding sites in different mouse cell types. Our method can model nucleosome translocations at regulatory genomic elements and generate configurations for simulations of the spatial folding of the nucleosome chain.

Availability: Source code, precompiled binaries, test data and a web-based test installation are freely available at http://bioinformatics.fh-stralsund.de/nucpos/

Contact:  gero.wedemann@fh-stralsund.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
The Economic Expansion of an Elite Business Family of French Origin in Central Mexico in the First Half of the Twentieth Century
Authors: Galindo Jose
Published: July 2013

This article describes how a French family, the Jeans, built and expanded its wealth in Central Mexico in the first half of the twentieth century. It explains how this family, using a different strategy than other French businessmen who settled in that region, began in textiles and diversified into the financial and housing sectors. The article also explores whether the Mexican Revolution and the early agrarian reform programs affected their properties and/or economic activities. Finally, the article explains how a branch of this family linked into the most powerful media family in Mexico and persisted among the Mexican economic elite until today.