bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactions between short-term and long-term plasticity: shooting for a moving target
Authors: Pfister Jean-Pascal , Lengyel Máté 
Published: March 2011

AbstractFar from being static transmission units, synapses are highly dynamical elements that change over multiple time scales depending on the history of the neural activity of both the pre- and postsynaptic neuron. Moreover, synaptic changes on different time scales interact: long-term plasticity (LTP) can modify the properties of short-term plasticity (STP) in the same synapse. Most existing theories of synaptic plasticity focus on only one of these time scales (either STP or LTP or late-LTP) and the theoretical principles underlying their interactions are thus largely unknown. Here we develop a normative model of synaptic plasticity that combines both STP and LTP and predicts specific patterns for their interactions. Recently, it has been proposed that STP arranges for the local postsynaptic membrane potential at a synapse to behave as an optimal estimator of the presynaptic membrane potential based on the incoming spikes. Here we generalize this approach by considering an optimal estimator of a non-linear function of the membrane potential and the long-term synaptic efficacy -- which itself may be subject to change on a slower time scale. We find that an increase in the long-term synaptic efficacy necessitates changes in the dynamics of STP. More precisely, for a realistic non-linear function to be estimated, our model predicts that after the induction of LTP, causing long-term synaptic efficacy to increase, a depressing synapse should become even more depressing. That is, in a protocol using trains of presynaptic stimuli, as the initial EPSP becomes stronger due to LTP, subsequent EPSPs should become weakened and this weakening should be more pronounced with LTP. This form of redistribution of synaptic efficacies agrees well with electrophysiological data on synapses connecting layer 5 pyramidal neurons.
Using spatial principles to optimize distributed computing for enabling the physical science discoveries
Authors: Yang Chaowei , Wu Huayi , Huang Qunying , Li Zhenlong , Li Jing 
Published: March 2011

Contemporary physical science studies rely on the effective analyses of geographically dispersed spatial data and simulations of physical phenomena. Single computers and generic high-end computing are not sufficient to process the data for complex physical science analysis and simulations, which can be successfully supported only through distributed computing, best optimized through the application of spatial principles. Spatial computing, the computing aspect of a spatial cyberinfrastructure, refers to a computing paradigm that utilizes spatial principles to optimize distributed computers to catalyze advancements in the physical sciences. Spatial principles govern the interactions between scientific parameters across space and time by providing the spatial connections and constraints to drive the progression of the phenomena. Therefore, spatial computing studies could better position us to leverage spatial principles in simulating physical phenomena and, by extension, advance the physical sciences. Using geospatial science as an example, this paper illustrates through three research examples how spatial computing could (
i
) enable data intensive science with efficient data/services search, access, and utilization, (
ii
) facilitate physical science studies with enabling high-performance computing capabilities, and (
iii
) empower scientists with multidimensional visualization tools to understand observations and simulations. The research examples demonstrate that spatial computing is of critical importance to design computing methods to catalyze physical science studies with better data access, phenomena simulation, and analytical visualization. We envision that spatial computing will become a core technology that drives fundamental physical science advancements in the 21st century.
Radiation damage in protein crystals is reduced with a micron-sized X-ray beam
Authors: Sanishvili Ruslan , Yoder Derek W. , Pothineni Sudhir Babu , Rosenbaum Gerd , Xu Shenglan , Vogt Stefan , Stepanov Sergey , Makarov Oleg A. , Corcoran Stephen , Benn Richard , Nagarajan Venugopalan , Smith Janet L. , Fischetti Robert F. 
Published: March 2011

Radiation damage is a major limitation in crystallography of biological macromolecules, even for cryocooled samples, and is particularly acute in microdiffraction. For the X-ray energies most commonly used for protein crystallography at synchrotron sources, photoelectrons are the predominant source of radiation damage. If the beam size is small relative to the photoelectron path length, then the photoelectron may escape the beam footprint, resulting in less damage in the illuminated volume. Thus, it may be possible to exploit this phenomenon to reduce radiation-induced damage during data measurement for techniques such as diffraction, spectroscopy, and imaging that use X-rays to probe both crystalline and noncrystalline biological samples. In a systematic and direct experimental demonstration of reduced radiation damage in protein crystals with small beams, damage was measured as a function of micron-sized X-ray beams of decreasing dimensions. The damage rate normalized for dose was reduced by a factor of three from the largest (15.6 μm) to the smallest (0.84 μm) X-ray beam used. Radiation-induced damage to protein crystals was also mapped parallel and perpendicular to the polarization direction of an incident 1-μm X-ray beam. Damage was greatest at the beam center and decreased monotonically to zero at a distance of about 4 μm, establishing the range of photoelectrons. The observed damage is less anisotropic than photoelectron emission probability, consistent with photoelectron trajectory simulations. These experimental results provide the basis for data collection protocols to mitigate with micron-sized X-ray beams the effects of radiation damage.
Glasses crystallize rapidly at free surfaces by growing crystals upward
Authors: Sun Ye , Zhu Lei , Kearns Kenneth L. , Ediger Mark D. , Yu Lian 
Published: March 2011

The crystallization of glasses and amorphous solids is studied in many fields to understand the stability of amorphous materials, the fabrication of glass ceramics, and the mechanism of biomineralization. Recent studies have found that crystal growth in organic glasses can be orders of magnitude faster at the free surface than in the interior, a phenomenon potentially important for understanding glass crystallization in general. Current explanations differ for surface-enhanced crystal growth, including released tension and enhanced mobility at glass surfaces. We report here a feature of the phenomenon relevant for elucidating its mechanism: Despite their higher densities, surface crystals rise substantially above the glass surface as they grow laterally, without penetrating deep into the bulk. For indomethacin (IMC), an organic glass able to grow surface crystals in two polymorphs (α and γ), the growth front can be hundreds of nanometers above the glass surface. The process of surface crystal growth, meanwhile, is unperturbed by eliminating bulk material deeper than some threshold depth (
ca.
300 nm for α IMC and less than 180 nm for γ IMC). As a growth strategy, the upward-lateral growth of surface crystals increases the system’s surface energy, but can effectively take advantage of surface mobility and circumvent slow growth in the bulk.
Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from
Aquifex aeolicus
Authors: Pandelia Maria-Eirini , Nitschke Wolfgang , Infossi Pascale , Giudici-Orticoni Marie-Thérèse , Bill Eckhard , Lubitz Wolfgang 
Published: March 2011

Iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. In the oxygen-tolerant Hydrogenase I from
Aquifex aeolicus
such electron “wires” form a relay to a diheme cyt
b
, an integral part of a respiration pathway for the reduction of O
2
to water. Amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. Electron paramagnetic resonance spectra exhibited complex signals that disclose interesting features and spin-coupling patterns; by redox titrations three iron-sulfur clusters were identified in their usual redox states, a [3Fe4S] and two [4Fe4S], but also a unique high-potential (HP) state was found. On the basis of
57
Fe Mössbauer spectroscopy we attribute this HP form to a superoxidized state of the [4Fe4S] center proximal to the [NiFe] site. The unique environment of this cluster, characterized by a surplus cysteine coordination, is able to tune the redox potentials and make it compliant with the [4Fe4S]
3+
state. It is actually the first example of a biological [4Fe4S] center that physiologically switches between 3+, 2+, and 1+ oxidation states within a very small potential range. We suggest that the (1 + /2+) redox couple serves the classical electron transfer reaction, whereas the superoxidation step is associated with a redox switch against oxidative stress.
Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations
Authors: Delemotte Lucie , Tarek Mounir , Klein Michael L. , Amaral Cristiano , Treptow Werner 
Published: March 2011

The response of a membrane-bound Kv1.2 ion channel to an applied transmembrane potential has been studied using molecular dynamics simulations. Channel deactivation is shown to involve three intermediate states of the voltage sensor domain (VSD), and concomitant movement of helix S4 charges 10–15 Å along the bilayer normal; the latter being enabled by zipper-like sequential pairing of S4 basic residues with neighboring VSD acidic residues and membrane-lipid head groups. During the observed sequential transitions S4 basic residues pass through the recently discovered charge transfer center with its conserved phenylalanine residue, F
233
. Analysis indicates that the local electric field within the VSD is focused near the F
233
residue and that it remains essentially unaltered during the entire process. Overall, the present computations provide an atomistic description of VSD response to hyperpolarization, add support to the sliding helix model, and capture essential features inferred from a variety of recent experiments.
DISCOVERY AND COSMOLOGICAL IMPLICATIONS OF SPT-CL J2106-5844, THE MOST MASSIVE KNOWN CLUSTER AT z>1
Authors: Foley R. J. , Andersson K. , Bazin G. , de Haan T. , Ruel J. , Ade P. A. R. , Aird K. A. , Armstrong R. , Ashby M. L. N. , Bautz M. , Benson B. A. , Bleem L. E. , Bonamente M. , Brodwin M. , Carlstrom J. E. , Chang C. L. , Clocchiatti A. , Crawford T. M. , Crites A. T. , Desai S. , Dobbs M. A. , Dudley J. P. , Fazio G. G. , Forman W. R. , Garmire G. , George E. M. , Gladders M. D. , Gonzalez A. H. , Halverson N. W. , High F. W. , Holder G. P. , Holzapfel W. L. , Hoover S. , Hrubes J. D. , Jones C. , Joy M. , Keisler R. , Knox L. , Lee A. T. , Leitch E. M. , Lueker M. , Luong-Van D. , Marrone D. P. , McMahon J. J. , Mehl J. , Meyer S. S. , Mohr J. J. , Montroy T. E. , Murray S. S. , Padin S. , Plagge T. , Pryke C. , Reichardt C. L. , Rest A. , Ruhl J. E. , Saliwanchik B. R. , Saro A. , Schaffer K. K. , Shaw L. , Shirokoff E. , Song J. , Spieler H. G. , Stalder B. , Stanford S. A. , Staniszewski Z. , Stark A. A. , Story K. , Stubbs C. W. , Vanderlinde K. , Vieira J. D. , Vikhlinin A. , Williamson R. , Zenteno A. 
Published: March 2011

ABSTRACT
Using the South Pole Telescope (SPT), we have discovered the most massive known galaxy cluster at z>1, SPT-CL J2106-5844. In addition to producing a strong Sunyaev–Zel'dovich (SZ) effect signal, this system is a luminous X-ray source and its numerous constituent galaxies display spatial and color clustering, all indicating the presence of a massive galaxy cluster. Very Large Telescope and Magellan spectroscopy of 18 member galaxies shows that the cluster is at z = 1.132+0.002
−0.003. Chandra observations obtained through a combined HRC-ACIS GTO program reveal an X-ray spectrum with an Fe K line redshifted by z = 1.18 ± 0.03. These redshifts are consistent with the galaxy colors found in optical, near-infrared, and mid-infrared imaging. SPT-CL J2106-5844 displays extreme X-ray properties for a cluster having a core-excluded temperature of TX
= 11.0+2.6
−1.9 keV and a luminosity (within r
500) of LX
(0.5–2.0 keV) = (13.9 ± 1.0) × 1044 erg s−1. The combined mass estimate from measurements of the SZ effect and X-ray data is M
200 = (1.27 ± 0.21) × 1015 h
−1
70
M
☉. The discovery of such a massive gravitationally collapsed system at high redshift provides an interesting laboratory for galaxy formation and evolution, and is a probe of extreme perturbations of the primordial matter density field. We discuss the latter, determining that, under the assumption of ΛCDM cosmology with only Gaussian perturbations, there is only a 7% chance of finding a galaxy cluster similar to SPT-CL J2106-5844 in the 2500 deg2 SPT survey region and that only one such galaxy cluster is expected in the entire sky.
Faster exact maximum parsimony search with XMP
Authors: White W. Timothy J. , Holland Barbara R. 
Published: March 2011

AbstractMotivation: Despite trends towards maximum likelihood and Bayesian criteria, maximum parsimony (MP) remains an important criterion for evaluating phylogenetic trees. Because exact MP search is NP-complete, the computational effort needed to find provably optimal trees skyrockets with increasing numbers of taxa, limiting analyses to around 25–30 taxa. This is, in part, because currently available programs fail to take advantage of parallelism.Results: We present XMP, a new program for finding exact MP trees that comes in both serial and parallel versions. The serial version is faster in nearly all tests than existing software. The parallel version uses a work-stealing algorithm to scale to hundreds of CPUs on a distributed-memory multiprocessor with high efficiency. An optimized SSE2 inner loop provides additional speedup for Pentium 4 and later CPUs.Availability: C source code and several binary versions are freely available from http://www.massey.ac.nz/~wtwhite/xmp. The parallel version requires an MPI implementation, such as the freely available MPICH2.Contact: w.t.white@massey.ac.nz; barbara.holland@utas.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
Hypothalamic–pituitary–adrenal axis reactivity to social stress and adolescent cannabis use: the TRAILS study
Authors: van Leeuwen Andrea Prince , Creemers Hanneke E. , Greaves‐Lord Kirstin , Verhulst Frank C. , Ormel Johan , Huizink Anja C. 
Published: March 2011

ABSTRACTAims  To investigate the relationship of life‐time and repeated cannabis use with hypothalamic–pituitary–adrenal (HPA) axis reactivity to social stress in a general population sample of adolescents.Design  Adolescents who reported life‐time or repeated cannabis use, life‐time or repeated tobacco use and never use of either cannabis or tobacco were compared with respect to their HPA axis reactivity during the Groningen Social Stress Task (GSST), which was based on the Trier Social Stress Task.Setting  A large prospective population study of Dutch adolescents [the TRacking Adolescents' Individual Lives Survey (TRAILS) study].Participants  A total of 591 adolescents (51% male) who participated in the GSST, which was an additional measurement during the third assessment wave.Measurements  HPA axis stress‐reactivity was indexed by four cortisol samples collected before, during and after the GSST. Furthermore, all adolescents in our study completed self‐reported questionnaires on life‐time and repeated cannabis and tobacco use. Models were adjusted for sex, recent alcohol use, experimental session risk status, socio‐economic status, mood and time of the experimental session.Findings  Life‐time cannabis users had significantly lower stress‐reactivity levels when compared to abstainers [odds ratio (OR) = 0.68, confidence interval (CI) = 0.55–0.85, P < 0.01] and life‐time tobacco users (OR = 0.79, CI = 0.64–0.98, P < 0.05). In addition, repeated cannabis users also exhibited lower stress‐reactivity levels when compared to life‐time ever users of either tobacco or cannabis (OR = 0.74, CI = 0.53–0.98, P < 0.05).Conclusions  Lower hypothalamic–pituitary–adrenal‐axis stress‐reactivity in adolescents is related specifically to life‐time and repeated cannabis use.
Evidence for involvement of Dicer‐like, Argonaute and histone deacetylase proteins in gene silencing in Phytophthora infestans
Authors: VETUKURI RAMESH R. , AVROVA ANNA O. , GRENVILLE‐BRIGGS LAURA J. , VAN WEST PIETER , SÖDERBOM FREDRIK , SAVENKOV EUGENE I. , WHISSON STEPHEN C. , DIXELIUS CHRISTINA 
Published: March 2011

SUMMARYGene silencing may have a direct or indirect impact on many biological processes in eukaryotic cells, and is a useful tool for the determination of the roles of specific genes. In this article, we report silencing in Phytophthora infestans, an oomycete pathogen of potato and tomato. Gene silencing is known to occur in P. infestans, but its genetic basis has yet to be determined. Genes encoding the major components of the RNA interference (RNAi) pathway, Dicer‐like (Pidcl1), Argonaute (Piago1–5) and RNA‐directed RNA polymerase (Pirdr1), were identified in the P. infestans genome by comparative genomics, together with families of other genes potentially involved in gene silencing, such as histone deacetylases, histone methyltransferases, DEAD helicases, chromodomain proteins and a class 1 RNaseIII. Real‐time reverse transcription‐polymerase chain reaction demonstrated transcript accumulation for all candidate genes throughout the asexual lifecycle and plant infection, but at different levels of mRNA abundance. A functional assay was developed in which silencing of the sporulation‐associated Picdc14 gene was released by the treatment of protoplasts with in vitro‐synthesized double‐stranded RNAs homologous to Pidcl1, Piago1/2 and histone deacetylase Pihda1. These results suggest that the components of gene silencing, namely Dicer‐like, Argonaute and histone deacetylase, are functional in P. infestans. Our data demonstrate that this oomycete possesses canonical gene silencing pathways similar to those of other eukaryotes.
Molecular and biochemical characterization of JAK3 deficiency in a patient with severe combined immunodeficiency over 20 years after bone marrow transplantation: implications for treatment
Authors: Bozzi F. , Lefranc G. , Badolato R. , Schumacher R. F. , Khalil G. , Loiselet J. , Bresciani S. , O'Shea J. J. , Vezzoni P. , Notarangelo L. D. , Candotti F. 
Published: March 2011

Summary. Severe combined immunodeficiency (SCID) comprises a heterogenous group of disorders that are fatal unless treated by bone marrow transplantation (BMT). The most common form of SCID (T−B+ SCID) is due to mutations of either the common gamma chain (γc) or of γc‐coupled JAK3 kinase.We report an unusual JAK3 defect in a female who was successfully treated >20 years ago with a BMT using her HLA‐identical father as the donor. Persistence of genetically and biochemically defective autologous B cells, associated with reconstitution of cellular and humoral immunity, suggests that integrity of the γc‐JAK3 signalling pathway is not strictly required for immunoglobulin production.
Identification of sole parvalbumin as a major allergen: study of cross‐reactivity between parvalbumins in a Spanish fish‐allergic population
Authors: Perez‐Gordo M. , Cuesta‐Herranz J. , Maroto A. S. , Cases B. , Ibáñez M. D. , Vivanco F. , Pastor‐Vargas C. 
Published: March 2011

SummaryBackground
Fish allergy is becoming an important health problem in Spain, a country with the third highest level of fish consumption after Japan and Portugal. The most common fish allergens are parvalbumins. In our area, the most widely consumed fish species are lean, such as whiff (Lepidorhombus whiffiagonis) and sole (Solea solea). Adverse reactions to fish are usually related to these species, a fact that is largely unknown to allergists in other countries.Objective
The aim of this study was to identify and purify the major allergen implicated in allergic response to sole and evaluate the IgE cross‐reactivity of purified parvalbumins from whiff and sole, which are phylogenetically close, and more distant species (i.e. cod and salmon).Methods
Eighteen Spanish fish‐allergic patients with a positive history of type I allergy to fish were recruited from the clinic. Total protein extracts and purified parvalbumins from whiff and sole were tested for their IgE‐binding properties by combining two‐dimensional Western blotting and mass spectrometry. The extent of cross‐reactivity between these parvalbumins along with cod and salmon parvalbumins was investigated by IgE ELISA inhibition assay.Results
An IgE‐binding spot of approximately 14 kDa was identified as parvalbumin and confirmed as a major allergen in sole extract, which is recognized by almost 70% of the patients. Whiff parvalbumin was recognized by 83.4% of the patients. High cross‐reactivity was determined for all purified parvalbumins by IgE inhibition assay.Conclusions and Clinical Relevance
Sole and whiff parvalbumin were confirmed as major allergens. The parvalbumins of sole, whiff, cod and salmon were highly cross‐reactive, thus suggesting a high amino acid sequence identity between them. Cite this as: M. Perez‐Gordo, J. Cuesta‐ Herranz, A. S. Maroto, B. Cases, M. D. Ibáñez, F. Vivanco and C. Pastor‐Vargas, Clinical & Experimental Allergy, 2011 (41) 750–758.
Embryonic stem cell factors undifferentiated transcription factor‐1 (UFT‐1) and reduced expression protein‐1 (REX‐1) are widely expressed in human skin and may be involved in cutaneous differentiation but not in stem cell fate determination
Authors: Reinisch Christina M. , Mildner Michael , Petzelbauer Peter , Pammer Johannes 
Published: March 2011

SummaryUndifferentiated transcription factor‐1 (UTF‐1) and reduced expression protein‐1 (REX‐1) are used as markers for the undifferentiated state of pluripotent stem cells. Because no highly specific cytochemical marker for epidermal stem cells has yet been identified, we investigated the expression pattern of these markers in human epidermis and skin tumours by immunohistochemistry and in keratinocyte cell cultures. Both presumed stem cell markers were widely expressed in the epidermis and skin appendages. Distinct expression was found in the matrix cells of the hair shaft. Differentiation of human primary keratinocytes (KC) in vitro strongly downregulated UTF‐1 and REX‐1 expression. In addition, REX‐1 was upregulated in squamous cell carcinomas, indicating a possible role of this transcription factor in malignant tumour formation. Our data point to a role for these proteins not only in maintaining KC stem cell populations, but also in proliferation and differentiation of matrix cells of the shaft and also suprabasal KC.