bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining peptide recognition specificity and context information for the prediction of the 14‐3‐3‐mediated interactome in S. cerevisiae and H. sapiens
Authors: Panni Simona , Montecchi‐Palazzi Luisa , Kiemer Lars , Cabibbo Andrea , Paoluzi Serena , Santonico Elena , Landgraf Christiane , Volkmer‐Engert Rudolf , Bachi Angela , Castagnoli Luisa , Cesareni Gianni 
Published: November 2010

AbstractLarge‐scale interaction studies contribute the largest fraction of protein interactions information in databases. However, co‐purification of non‐specific or indirect ligands, often results in data sets that are affected by a considerable number of false positives. For the fraction of interactions mediated by short linear peptides, we present here a combined experimental and computational strategy for ranking the reliability of the inferred partners. We apply this strategy to the family of 14‐3‐3 domains. We have first characterized the recognition specificity of this domain family, largely confirming the results of previous analyses, while revealing new features of the preferred sequence context of 14‐3‐3 phospho‐peptide partners. Notably, a proline next to the carboxy side of the phospho‐amino acid functions as a potent inhibitor of 14‐3‐3 binding. The position‐specific information about residue preference was encoded in a scoring matrix and two regular expressions. The integration of these three features in a single predictive model outperforms publicly available prediction tools. Next we have combined, by a naïve Bayesian approach, these “peptide features” with “protein features”, such as protein co‐expression and co‐localization. Our approach provides an orthogonal reliability assessment and maps with high confidence the 14‐3‐3 peptide target on the partner proteins.
A proteome‐scale study on in vivo protein Nα‐acetylation using an optimized method
Authors: Zhang Xumin , Ye Juanying , Engholm‐Keller Kasper , Højrup Peter 
Published: November 2010

AbstractProtein N‐terminal acetylation (Nα‐acetylation) is among the most common modifications in eukaryotes. We previously described a simple method to enrich Nα‐modified peptides using CNBr‐activated Sepharose resin. A limitation of this method is that an optimal ratio of sample to resin had to be determined prior to the analysis since Lys‐containing Nα‐modified peptides may be lost. To address this problem, we hereby present an optimized method by the introduction of double incubation at pH 6.0. We demonstrate with the optimized method that the Nα‐modified peptides can be enriched regardless of whether ε‐NH2 is present or not, and the sample to resin ratio optimization is no longer necessary. Another improvement was accomplished by the inclusion of the singly charged precursor for MS/MS fragmentation to alleviate the shortcoming of the reduced charge state of Nα‐modified peptides. We employed a duplicate experiment using 80 μg samples each and identified 922 IPI annotated and 103 IPI unannotated acetylated N‐termini from 989 proteins, so far the largest acetylated N‐termini data set acquired from a tryptic digest. Furthermore, the reproducibility of the Nα‐acetyl proteome approach was evaluated and its complementarity to the regular proteome approach was analyzed. The unexpected coupling of CNBr‐activated Sepharose to His‐containing peptides via the imidazole group was discovered.
Protective Effects of Mentha haplocalyx Ethanol Extract (MH) in a Mouse Model of Allergic Asthma
Authors: Lee Mee‐Young , Lee Jin‐Ah , Seo Chang‐Seob , Ha Hyekyung , Lee Nam‐Hun , Shin Hyeun‐Kyoo 
Published: November 2010

AbstractMentha haplocalyx Briq., a commonly used herb in traditional Oriental medicine, has a variety of known pharmacological properties. However, neither the protective effects of Mentha haplocalyx ethanol extract (MH) against inflammation of the airway in an asthmatic model nor the mechanisms involved, have previously been reported. In the present study, an ovalbumin (OVA)‐induced mouse model of allergic asthma was used to investigate whether MH was effective against the disease through regulation of airway inflammation. The MH treatment significantly inhibited increases in immunoglobulin (Ig) E and T‐helper 2 (Th2)‐type cytokines such as IL‐4 and IL‐5 in bronchoalveolar lavage fluid (BALF) and lung tissue. Inflammatory cell infiltration of the airway in mice treated with MH was effectively alleviated when compared with infiltration seen in the OVA‐induced group. These data indicated that decreased cytokine levels are the result of the decreased number of invaded leukocytes. Also, the generation of reactive oxygen species (ROS) in BALF was diminished by MH treatment. Taken together, these findings indicate that the administration of MH may have potential therapeutic value in the treatment of inflammatory disease. Copyright © 2010 John Wiley & Sons, Ltd.
ZipfAllocation: an algorithm for static allocation of movies in a cluster of video servers
Authors: Kim SeongKi , Song HaYoon , Han SangYong 
Published: November 2010

AbstractWhen a single video server provides a streaming service, there are many limitations. Thus, clusters of multiple video servers are widely used today to provide better service. How movies are allocated to each server in a cluster is an important and ongoing research topic because the movies are large, and there are so many of them. We have developed a movie allocation algorithm based on the observation that client accesses follow a Zipf distribution. We have developed an algorithm in which servers use their storage to their full capacities, movies are assigned to servers as evenly as possible, servers receive requests as evenly as possible, and all movies are allocated to at least one server. Copyright © 2010 John Wiley & Sons, Ltd.
Safe, multiphase bounds check elimination in Java
Authors: Gampe Andreas , von Ronne Jeffery , Niedzielski David , Vasek Jonathan , Psarris Kleanthis 
Published: November 2010

AbstractAs part of its type‐safety regime, Java's semantics require precise exceptions at runtime when programs attempt out‐of‐bound array accesses. This paper describes a Java implementation that utilizes a multiphase approach to identifying safe array accesses. This approach reduces runtime overhead by spreading the out‐of‐bounds checking effort across multiple phases of compilation and execution: production of mobile code from source code, just‐in‐time (JIT) compilation in the virtual machine, application method invocations, and the execution of individual array accesses. The code producer uses multiple passes (including common subexpression elimination, load elimination, induction variable substitution, speculation of dynamically verified invariants, and inequality constraint analysis) to identify unnecessary bounds checks and prove their redundancy. During class‐loading and JIT compilation, the virtual machine verifies the proofs, inserts code to dynamically validate speculated invariants, and generates code specialized under the assumption that the speculated invariants hold. During each runtime method invocation, the method parameters and other inputs are checked against the speculated invariants, and execution reverts to unoptimized code if the speculated invariants do not hold. The combined effect of the multiple phases is to shift the effort associated with bounds‐checking array access to phases that are executed earlier and less frequently, thus, reducing runtime overhead. Experimental results show that this approach is able to eliminate more bounds checks than prior approaches with minimal overhead during JIT compilation. These results also show the contribution of each of the passes to the overall elimination. Furthermore, this approach increased the speed at which the benchmarks executed by up to 16%. Copyright © 2010 John Wiley & Sons, Ltd.
Crop biotechnology: prospects and opportunities
Authors: DUNWELL J. M. 
Published: November 2010

SUMMARYThis paper is a brief review summarizing some of the important areas of activity in crop biotechnology likely to be exploited over the medium term (10–20 years), with an emphasis on agronomic traits. It provides details on various approaches to improving the tolerance of crops to abiotic and to biotic stresses. Additionally, it describes recent advances in understanding the factors that affect the intrinsic performance of plants, for example, in terms of their photosynthetic efficiency and their genetic composition. The review also provides a short selection of recently granted patents and patent applications, as this information often identifies those subjects that might be commercially exploited over this period. Finally, it provides a summary of the various predictions of the commercial development pipeline based upon a range of transgenes in major crop species.
Modified arytenoid adduction for cancer-related unilateral vocal fold paralysis
Authors: Shi J , Chen S , Chen D , Wang W , Xia S , Zheng H 
Published: November 2010

AbstractObjectives:(1) To evaluate the efficacy of modified arytenoid adduction in the management of patients with symptomatic cancer-related unilateral vocal fold paralysis, and (2) to assess the impact of this treatment on patients' quality of life.Methods:Forty-two patients with cancer-related unilateral vocal fold paralysis underwent modified arytenoid adduction between February 2001 and December 2008. Of these, 37 patients were enrolled in this retrospective study (one patient died of primary disease and four were lost to follow up). Laryngostroboscopy was performed to evaluate vocal fold orientation and mobility. Pre- and post-operative assessment of subjective and objective voice, aerodynamic parameters, and quality of life were also undertaken, and aspiration was subjectively rated.Results:Laryngostroboscopic findings indicated a significant post-operative improvement in vocal fold posterior glottal closure and vertical gap. Significant improvements in voice quality, aerodynamic parameters and quality of life were noted three months post-operatively in all patients (p < 0.01). The overall success rate for swallowing rehabilitation was 94.6 per cent (35/37). Subjective aspiration ratings decreased significantly post-operatively, compared with pre-operative values (p < 0.01). No major complication occurred in any patient, except for dyspnoea in one patient.Conclusion:Modified arytenoid adduction is an effective and reliable medialisation technique which can restore satisfactory voice quality, prevent aspiration and lead to a better quality of life for patients with cancer-related unilateral vocal fold paralysis.
Pasteur in Palestine: The Politics of the Laboratory
Authors: Davidovitch Nadav , Zalashik Rakefet 
Published: November 2010

ArgumentWe examine the creation and functioning of the “Pasteur Institute in Palestine” focusing on the relationship between biological science, health policy, and the creation of a “new society” within the framework of Zionism. Similar to other bacteriological institutes founded by colonial powers, this laboratory was developed in response to public health needs. But it also had a political role. Dr. Leo Böhm, a Zionist physician, strived to establish his institution along the lines of the Zionist aspiration to develop a national entity based on strong scientific foundations. Even though the institute enjoyed several fruitful years of operation, mainly during World War I, it achieved no lasting national or scientific importance in the country. Böhm failed to adapt to new ways of knowledge production, scientifically and socially. The case study of the “Pasteur Institute in Palestine” serves as a prism to view the role of the public health laboratory in the history of Palestine with its ongoing changes of scientific, organizational, and political context.
Zionist Internationalism through Number Theory: Edmund Landau at the Opening of the Hebrew University in 1925
Authors: Corry Leo , Schappacher Norbert 
Published: November 2010

ArgumentThis article gives the background to a public lecture delivered in Hebrew by Edmund Landau at the opening ceremony of the Hebrew University in Jerusalem in 1925. On the surface, the lecture appears to be a slightly awkward attempt by a distinguished German-Jewish mathematician to popularize a few number-theoretical tidbits. However, quite unexpectedly, what emerges here is Landau's personal blend of Zionism, German nationalism, and the proud ethos of pure, rigorous mathematics – against the backdrop of the situation of Germany after World War I. Landau's Jerusalem lecture thus shows how the Zionist cause was inextricably linked to, and determined by political agendas that were taking place in Europe at that time. The lecture stands in various historical contexts - Landau's biography, the history of Jewish scientists in the German Zionist movement, the founding of the Hebrew University in Jerusalem, and the creation of a modern Hebrew mathematical language. This article provides a broad historical introduction to the English translation, with commentary, of the original Hebrew text.
The Kishon Affair: Science, Law, and the Politics of Causation
Authors: Golan Tal 
Published: November 2010

ArgumentThis article describes how science and law were called upon (and failed) to resolve a controversy that created a painful rift between the Israeli State and some of its elite soldiers. The controversy, which came to be known as “the Kishon affair,” erupted in 2000, when veterans of an elite and secretive unit in the Israeli navy claimed that pollution in the Kishon River where they had trained and dived during their military service had been the cause of a rash of cancers. The veterans demanded that the Ministry of Defense take responsibility for their illnesses, finance their medical treatment, and support their families if they die. The military denied the causal connection between the polluted river and the veterans’ cancers and rejected their demands. The dispute quickly escalated into a bitter public controversy, and a high-rank commission comprised of one of Israel's top jurists and two prominent scientists was called upon to study the disputed causal relation and reveal its true nature. However, after nearly three years of intense inquiry the jurist and the scientists reached opposing conclusions: the jurist found a causal connection while the scientists rejected it.
Liberal Civic Education, Religious Commitment, and the Spillover Thesis: What Psychology Can Teach Us
Authors: Phillips John L. , McMillian Laura 
Published: November 2010

AbstractThis article addresses an idea central to liberal debates on civic education: the spillover thesis. Both egalitarian liberals and their religious opponents in these debates claim that liberal civic education creates spillover effects into the way individuals assess the meaning of their own lives. Some religious citizens fear that their politically reasonable conceptions of the good life are being undermined by education that emphasizes the practice of autonomous reasoning. Egalitarian liberals usually acknowledge this risk or cost, but deny that religious citizens should be given special dispensation from the burdens of autonomous reasoning. Some may even hope that conservative religious beliefs will be eroded by the practice of liberal civic education. This article disputes the spillover thesis. Given the best evidence available from the field of cognitive psychology, we challenge the notion that critical personal reflection about public matters is bound to spillover into critical reflection about private moral matters. On the contrary, the evidence suggests that human beings are usually well equipped to compartmentalize and are capable of reasoning in different ways depending on the context. Thus, reasonable citizens of faith are not necessarily unduly burdened by programs of civic education; nor are liberal programs of civic education necessarily going to lead us to a more secular society of autonomous thinkers. The article also speaks to a broader civic humanist tradition in political philosophy that includes Plato, Tocqueville, Rousseau, and Marcus Aurelius. For these authors, the success of a political enterprise is seen to crucially depend on the inculcation of a robust and comprehensive system of private virtue. For without private virtue, there is no public virtue. If we are correctly interpreting the available psychological research, private virtue need not be as crucially relevant for the success of common political enterprises. The inculcation of private moral virtue does not so clearly translate into making good leaders, voters, and public servants.
Double-walled carbon nanotube-based polymer composites for electromagnetic protection
Authors: Pacchini Sébastien , Dubuc David , Flahaut Emmanuel , Grenier Katia 
Published: November 2010

In this paper, we present a microwave absorber based on carbon nanotubes (CNT) dispersed inside a BenzoCycloButen® (BCB) polymer. The high aspect ratio and remarkable conductive characteristics of CNT give rise to good absorbing properties for electromagnetic protecting in microelectronic devices with very low concentration. In this article, nanocomposites are prepared using a solution-mixing method and are then evaluated and modeled by means of coplanar test structures. First, CNT concentrations are quantified by image processing. The nanocomposites implemented with coplanar test waveguides are then characterized using a vector network analyzer from 40 MHz to 20 GHz. An algorithm is developed to calculate the propagation constant “γ”, attenuation constant “α”, and relative effective complex permittivity (ɛreff = ɛreff′ − jɛreff″) for each CNT concentration. The extracted effective parameters are verified using the electromagnetic FEM-based Ansoft's® high frequency structure simulator (HFSS). Power absorption (PA) of 7 dB at 15 GHz is obtained with only 0.37 weight percent of CNT concentration in the polymer matrix. The resulting engineerable and controllable composite provides consequently a novel degree of freedom to design and optimize innovative microwave components.
Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation
Authors: Chan Clara S , Fakra Sirine C , Emerson David , Fleming Emily J , Edwards Katrina J 
Published: November 2010

Abstract
Neutrophilic Fe-oxidizing bacteria (FeOB) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by Gallionella ferruginea or Mariprofundus ferrooxydans. Similar filaments preserved in silica are often identified as FeOB fossils in rocks. Although it is assumed that twisted iron stalks are indicative of FeOB, the stalk's metabolic role has not been established. To this end, we studied the marine FeOB M. ferrooxydans by light, X-ray and electron microscopy. Using time-lapse light microscopy, we observed cells excreting stalks during growth (averaging 2.2 μm h−1). Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy show that stalks are Fe(III)-rich, whereas cells are low in Fe. Transmission electron microscopy reveals that stalks are composed of several fibrils, which contain few-nanometer-sized iron oxyhydroxide crystals. Lepidocrocite crystals that nucleated on the fibril surface are much larger (∼100 nm), suggesting that mineral growth within fibrils is retarded, relative to sites surrounding fibrils. C and N 1s NEXAFS spectroscopy and fluorescence probing show that stalks primarily contain carboxyl-rich polysaccharides. On the basis of these results, we suggest a physiological model for Fe oxidation in which cells excrete oxidized Fe bound to organic polymers. These organic molecules retard mineral growth, preventing cell encrustation. This model describes an essential role for stalk formation in FeOB growth. We suggest that stalk-like morphologies observed in modern and ancient samples may be correlated confidently with the Fe-oxidizing metabolism as a robust biosignature.
Novel Clostridium populations involved in the anaerobic degradation of Microcystis blooms
Authors: Xing Peng , Guo Liang , Tian Wei , Wu Qinglong L 
Published: November 2010

Abstract
Understanding the microbial degradation of Microcystis biomass is crucial for determining the ecological consequences of Microcystis blooms in freshwater lakes. The purpose of this study was to identify bacteria involved in the anaerobic degradation of Microcystis blooms. Microcystis scum was anaerobically incubated for 90 days at three temperatures (15 °C, 25 °C and 35 °C). We used terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes, followed by cloning and sequencing of selected samples, to reveal the community composition of bacteria and their dynamics during decomposition. Clostridium spp. were found to be the most dominant bacteria in the incubations, accounting for 72% of the sequenced clones. Eight new clusters or subclusters (designated CLOS.1–8) were identified in the Clostridium phylogenetic tree. The bacterial populations displayed distinct successions during Microcystis decomposition. Temperature had a strong effect on the dynamics of the bacterial populations. At 15 °C, the initial dominance of a 207-bp T-RF (Betaproteobacteria) was largely substituted by a 227-bp T-RF (Clostridium, new cluster CLOS.2) at 30 days. In contrast, at 25 °C and 35 °C, we observed an alternating succession of the 227-bp T-RF and a 231-bp T-RF (Clostridium, new cluster CLOS.1) that occurred more than four times; no one species dominated the flora for the entire experiment. Our study shows that novel Clostridium clusters and their diverse consortiums dominate the bacterial communities during anaerobic degradation of Microcystis, suggesting that these microbes' function in the degradation process.
Production of Lexical Stress in Non-Native Speakers of American English: Kinematic Correlates of Stress and Transfer
Authors: Chakraborty Rahul , Goffman Lisa 
Published: November 2010

PurposeTo assess the influence of second language (L2) proficiency on production characteristics of rhythmic sequences in the L1 (Bengali) and L2 (English), with emphasis on linguistic transfer. One goal was to examine, using kinematic evidence, how L2 proficiency influences the production of iambic and trochaic words, focusing on temporal and spatial aspects of prosody. A second goal was to assess whether prosodic structure influences judgment of foreign accent.MethodTwenty Bengali–English bilingual individuals, 10 with low proficiency in English and 10 with high proficiency in English, and 10 monolingual English speakers, participated. Lip and jaw movements were recorded while the bilingual participants produced Bengali and English words embedded in sentences. Lower lip movement amplitude and duration were measured in trochaic and iambic words. Six native English listeners judged the nativeness of the bilingual speakers.ResultsEvidence of L1–L2 transfer was observed through duration but not amplitude cues. More proficient L2 speakers varied duration to mark iambic stress. Perceptually, the high-proficiency group received relatively higher native-like accent ratings. Trochees were judged as more native than iambs.ConclusionsEven in the face of L1–L2 lexical stress transfer, nonnative speakers demonstrated knowledge of prosodic contrasts. Movement duration appears to be more amenable than amplitude to modifications.