bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational changes in DNA‐binding proteins: Relationships with precomplex features and contributions to specificity and stability
Authors: Mizuguchi Kenji , Ahmad Shandar 
Published: October 2013

ABSTRACTBoth Proteins and DNA undergo conformational changes in order to form functional complexes and also to facilitate interactions with other molecules. These changes have direct implications for the stability and specificity of the complex, as well as the cooperativity of interactions between multiple entities. In this work, we have extensively analyzed conformational changes in DNA‐binding proteins by superimposing DNA‐bound and unbound pairs of protein structures in a curated database of 90 proteins. We manually examined each of these pairs, unified the authors' annotations, and summarized our observations by classifying conformational changes into six structural categories. We explored a relationship between conformational changes and functional classes, binding motifs, target specificity, biophysical features of unbound proteins, and stability of the complex. In addition, we have also investigated the degree to which the intrinsic flexibility can explain conformational changes in a subset of 52 proteins with high quality coordinate data. Our results indicate that conformational changes in DNA‐binding proteins contribute significantly to both the stability of the complex and the specificity of targets recognized by them. We also conclude that most conformational changes occur in proteins interacting with specific DNA targets, even though unbound protein structures may have sufficient information to interact with DNA in a nonspecific manner. Proteins 2014; 82:841–857. © 2013 Wiley Periodicals, Inc.
Infantile spinale Muskelatrophie: mehr als eine Motoneuronerkrankung?
Authors: Rudnik-Schöneborn S. , Lorson C.L. , Shababi M. 
Published: October 2013

Zusammenfassung
Die infantile spinale Muskelatrophie (SMA) – bedingt durch homozygote Mutationen im Survival-motor-neuron-1(SMN1)-Gen – ist durch eine Degeneration von motorischen Neuronen im Vorderhorn des Rückenmarks und im Hirnstamm charakterisiert. Die Folge eines SMN-Proteinmangels ist eine progrediente Muskelatrophie mit proximal betonten Lähmungen der Willkürmuskulatur und motorischen Hirnnervenausfällen. In den letzten Jahren mehren sich klinische Beobachtungen und Berichte von Tiermodellen, dass eine SMN-Proteinreduktion zusätzlich zu unterschiedlichen Funktionsstörungen anderer Organsysteme führt. Diese betreffen insbesondere das periphere, zentrale und autonome Nervensystem, die Entwicklung des Herzes, die Funktion des Verdauungstrakts und metabolische Veränderungen. Um sinnvolle und effiziente Therapiestrategien zu entwickeln und um weiteren Komplikationen begegnen zu können, die sich z. B. bei einer längeren Überlebensdauer v. a. von schwer betroffenen Patienten ergeben können, ist es erforderlich, dass jede mögliche Organpathologie systematisch untersucht wird. Der Vergleich mit SMA-Mausmodellen ist hierfür außerordentlich hilfreich, wenn auch die phänotypischen Auswirkungen nicht vollständig auf den Menschen übertragbar sind.
Genetische Diagnostik und Beratung bei Arthrogryposis
Authors: Heller R. , Hoffmann K. 
Published: October 2013

Zusammenfassung
Es werden wichtige Probleme in der Diagnostik bei Patienten mit Arthrogryposis dargestellt und Definitionen eingeführt. Danach werden praktische Ansätze für die Diagnostik und humangenetische Betreuung vorgeschlagen.
THE COMMUTATIVITY OF EVIDENCE: A PROBLEM FOR CONCILIATORY VIEWS OF PEER DISAGREEMENT
Authors: Gardiner Georgi 
Published: October 2013

AbstractConciliatory views of peer disagreement hold that when an agent encounters peer disagreement she should conciliate by adjusting her doxastic attitude towards that of her peer. In this paper I distinguish different ways conciliation can be understood and argue that the way conciliationism is typically understood violates the principle of commutativity of evidence. Commutativity of evidence holds that the order in which evidence is acquired should not influence what it is reasonable to believe based on that evidence. I argue that when an agent encounters more than one peer, and applies the process of conciliation serially, the order she encounters the peers influences the resulting credence. I argue this is a problem for conciliatory views of disagreement, and suggest some responses available to advocates of conciliation.
RECITAL 12 OF THE RECAST REGULATION: A NEW HOPE?
Authors: Camilleri Simon P 
Published: October 2013

AbstractThis article seeks to consider the EU's new approach to arbitration as set out in Recital 12 of the Brussels I Regulation (Recast). The article first considers the Court of Justice of the European Union'sWest Tankersdecision and the foremost English authority applying that case (The Wadi Sudr) in order to provide some background to the problem which gave rise to Recital 12. Following this, the article goes on to consider whether Recital 12 does in fact act as a solution to the problem created by theWest Tankersdecision.
DIGGING DEEP: PROPERTY RIGHTS IN SUBTERRANEAN SPACE AND THE CHALLENGE OF CARBON CAPTURE AND STORAGE
Authors: Morgan Jill 
Published: October 2013

AbstractA burgeoning international interest in Carbon Capture and Storage (CCS) as a means of mitigating the effects of climate change has raised a number of novel legal issues, one of which concerns ownership of the underground sites in which captured carbon dioxide can be stored. This paper considers the extent of a surface landowner's rights above and below land and explores the treatment of underground space within the context of CCS in relation to differing jurisdictions. Particular attention is paid to legal principles applied in the United Kingdom and the United States, and consideration is also given to relevant legislation in Australia and Canada.
Further contributions to the lichen genus Leptogium in southern South America
Authors: JØRGENSEN Per M. , BUCK William R. 
Published: October 2013

AbstractTwo new species in Leptogium are described and illustrated from the Cape Horn region: L. auriculatum and L. adnatum both grow on wet rocks, the former by a river, the latter on coastal rocks. In addition to the special habitat the latter is easily identified on the closely appressed thallus which centrally often have densely packed squamules in intricately folded structures. Leptogium auriculatum is characterized by the regular, rounded lobes with thickened margins carrying granular isidia. The total number of Leptogium species known in the region at present is 19, including the previously doubtful L. patagonicum Zahlbr., which is here confirmed as a distinct species.
Pyrenocarpous lichens (except Trypetheliaceae) in Rondônia
Authors: APTROOT André , CÁCERES Marcela Eugenia da Silva 
Published: October 2013

AbstractThe following new species of pyrenocarpous lichens are described from Rondônia: Agonimia tenuiloba: corticolous, thallus with minute flabellate lobes developing goniocysts; ascomata smooth, grey, ellipsoidal; ascospores densely muriform, 30–50(–76)×20–35 µm. Anisomeridium lateriticum: saxicolous; conidiomata sessile, pyriform, ostiole with brown and hyaline septate setae; conidia simple to 1-septate, 8–11×2·0–2·5 µm. Anisomeridium triseptatum: corticolous, ascomata with lateral ostioles; ascospores (1–)3-septate, 25–30×7·5–10·0 µm, often with gelatinous appendages. Mycomicrothelia megaspora: ascospores ornamented, 1-septate, (27–)29–35(–40)×8–12 µm, often with a gelatinous layer 6–15 µm thick. Porina linearispora: corticolous; thallus green, shiny; ascomata immersed, 0·2–0·3 mm; ascospores filiform, (7–)9(–13)-septate, 75–90×1·5–2·0 µm. Porina maxispora: corticolous; thallus green, matt; ascomata immersed, 0·5–0·7 mm; ascospores filiform, (17–)23–35-septate, 95–110×4·5–5·5 µm. Porina novemseptatoides: saxicolous; thallus very thin, brown, glossy; ascomata superficial, 0·1–0·2 mm; ascospores fusiform, (7–)9-septate, 21–24×4·5–5·0 µm, with a c. 5 µm thick gelatinous layer. Porina termitophila: terricolous; thallus greyish green; ascomata emergent, 0·15–0·20 mm; ascospores fusiform, 1–3-septate, 13–15×2·5–3·0 µm. Pyrenula bispora: corticolous, thallus whitish, ascomata dispersed; hamathecium inspersed; ascospores 2 per ascus, muriform, 55–75×19–23 µm. Pyrenula leptaleoides: corticolous; thallus green to pale brown; ascomata deeply immersed in bark, with long necks fused in joint ostioles visible as brown dots on the surface; ascospores 23–27×8–11 µm, with rather angular lumina. Pyrenula rhomboidea: corticolous; thallus olive-brown; ascomata single, immersed; ascospores irregularly uniseriate, clavate-rhomboidal, 11–13×3·5–4·0 µm.A key is provided to all species of pyrenocarpous lichens (except Trypetheliaceae) found in Rondônia. Nearly all species are new reports for Rondônia. Aspidothelium glabrum, Pyrenula leucotrypa and P. micheneri are newly reported for South America. The usually foliicolous Strigula nitidula is reported for the first time from bark.The high lichen diversity is explained by the poor soils, supporting an only moderately dense forest where enough light can reach the tree trunks at ground level to support a rich flora of crustose lichens usually confined to the upper trunks.
Genetic diversity of sterile culturedTrebouxiaphotobionts associated with the lichen-forming fungusXanthoria parietinavisualized with RAPD-PCR fingerprinting techniques
Authors: NYATI Shyam , WERTH Silke , HONEGGER Rosmarie 
Published: October 2013

AbstractPhotobiont diversity within populations ofXanthoria parietinawas studied at the species level by means of ITS analyses and at the subspecific level with fingerprinting techniques (RAPD-PCR) applied to sterile cultured algal isolates. Populations from coastal, rural and urban sites from NW, SW and central France and from NE Switzerland were investigated. Between 8 and 63 samples per population, altogether 150 isolates, were subjected to phenetic and ordination analyses. Epiphytic samples ofX. parietinaassociated with different genotypes ofTrebouxia decoloransbut saxicolous samples containedT. arboricola. For comparison theT. gelatinosaphotobiont of a small population ofTeloschistes chrysophthalmus(4 samples) was investigated. ITS sequences ofT. decoloransisolates from different geographic locations were largely similar. In all populations a surprisingly high diversity of genotypes was observed inTrebouxiaisolated from lichen thalli growing side by side. AsTrebouxiaspp. are assumed to be asexually reproducing haplonts, the genetic background of this diversity is discussed. Fingerprinting techniques are a powerful tool for obtaining valuable insights into the genetic diversity within the algal partner of lichen-forming fungi at the population level, provided that sterile cultured isolates are available.
Fact or fiction? Welfare cuts and fiscal adjustments
Authors: Wenzelburger Georg 
Published: October 2013

AbstractGovernments in the industrialised western democracies have repeatedly been advised to curb the welfare state when adjusting public finances in order to stabilise public debt in the long run and to create economic growth. This recommendation has been founded on a vast body of research on fiscal adjustments, which has come to the conclusion that cutting social expenditures leads to expansionary and more sustainable budget consolidations. This paper adds to the existing literature suggesting a more nuanced view, which challenges the simplicity of the “cutting-welfare” advice: first, we find that whereas less social spending is indeed associated with expansionary and successful adjustments, this is not the case for overall welfare state generosity. Second, disaggregating the welfare state in its components reveals that a reduction of pension generosity is indeed related to successful adjustments whereas reducing unemployment generosity does not seem to play a major role.
Cyclophilin A: a key player for human disease
Authors: Nigro P , Pompilio G , Capogrossi M C 
Published: October 2013

AbstractCyclophilin A (CyPA) is a ubiquitously distributed protein belonging to the immunophilin family. CyPA has peptidyl prolyl cis-trans isomerase (PPIase) activity, which regulates protein folding and trafficking. Although CyPA was initially believed to function primarily as an intracellular protein, recent studies have revealed that it can be secreted by cells in response to inflammatory stimuli. Current research in animal models and humans has provided compelling evidences supporting the critical function of CyPA in several human diseases. This review discusses recently available data about CyPA in cardiovascular diseases, viral infections, neurodegeneration, cancer, rheumatoid arthritis, sepsis, asthma, periodontitis and aging. It is believed that further elucidations of the role of CyPA will provide a better understanding of the molecular mechanisms underlying these diseases and will help develop novel pharmacological therapies.
High rate capability caused by surface cubic spinels in Li-rich layer-structured cathodes for Li-ion batteries
Authors: Song Bohang , Liu Hongwei , Liu Zongwen , Xiao Pengfei , Lai Man On , Lu Li 
Published: October 2013

AbstractModified Li-rich layered cathode Li(Li0.2Mn0.54Ni0.13Co0.13)O2 has been synthesized by a simple strategy of using surface treatment with various amounts (0–30 wt.%) of Super P (carbon black). Based on detailed characterizations from X-ray diffraction (XRD), high resolution transmission electron microscope (HRTEM), X-ray photoelectron spectroscopy (XPS) and electrochemical impedance spectroscopy (EIS), it is suggested that the phase transformation from Li2MnO3-type of structure to spinel-like phase take place at the surface regions of particles during post annealing process at 350°C, leading to increase in both first coulombic efficiency and rate capability, from 78% and 100 mAh·g−1 (charge capacity at 2500 mA·g−1) of the pristine material to 93.4% and 200 mAh·g−1. The evidences of spinel formation and the reasons for electrochemical enhancement are systematically investigated.
Secret of the major birch pollen allergen Bet v 1: identification of the physiological ligand
Authors: Seutter von Loetzen Christian , Hoffmann Thomas , Hartl Maximilian J. , Schweimer Kristian , Schwab Wilfried , Rösch Paul , Hartl-Spiegelhauer Olivia 
Published: October 2013

The major birch pollen allergen Bet v 1 is the main elicitor of airborne type I allergies and belongs to the PR-10 family (pathogenesis-related proteins 10). Bet v 1 is the most extensively studied allergen, and is well characterized at a biochemical and immunological level; however, its physiological function remains elusive. In the present study, we identify Q3OS (quercetin-3-O-sophoroside) as the natural ligand of Bet v 1. We isolated Q3OS bound to Bet v 1 from mature birch pollen and confirmed its binding by reconstitution of the Bet v 1–Q3OS complex. Fluorescence and UV–visible spectroscopy experiments, as well as HSQC (heteronuclear single-quantum coherence) titration, and the comparison with model compounds, such as quercetin, indicated the specificity of Q3OS binding. Elucidation of the binding site by NMR combined with a computational model resulted in a more detailed understanding and shed light on the physiological function of Bet v 1. We postulate that the binding of Q3OS to Bet v 1 plays an important, but as yet unclear, role during the inflammation response and Bet v 1 recognition by IgE.
Analysis, design and implementation of an improved two‐switch zero‐current zero‐voltage pulse‐width modulation forward converter
Authors: Soltanzadeh Karim , Dehghani Majid , Khalilian Hosein 
Published: October 2013

In this study, an improved two‐switch zero‐current zero‐voltage switching pulse‐width modulation (ZCZVS‐PWM) forward converter, which employs a simple resonant lossless snubber circuit, is introduced. A simple resonant snubber circuit consists of a capacitor, an inductor and two diodes. In proposed converter, switch Q1 operates under exactly zero‐current switching at turn‐on, and exactly zero‐voltage switching (ZVS) at turn‐off, and switch Q2 operates under exactly ZCZVS at turn‐on, and ZVS at turn‐off, and the all‐passive semiconductor devices operate under soft‐switching at turn‐on and turn‐off. The proposed converter has no current and voltage spikes in the switches in comparison with the hard‐switching forward converter counterpart and is suitable for high switching frequency and high‐power operation. The proposed converter is analysed and various operating modes of the improved two‐switch ZCZVS‐PWM forward converter are discussed. Analysis and design considerations are presented and the prototype experimental results of a 160 W (32 V/5 A) proposed converter operating at 300 kHz switching frequency, confirm the validity of theoretical analysis.
The London Symphony Orchestra: The First Decade Revisited
Authors: McVeigh Simon 
Published: October 2013

ABSTRACTThe early history of the London Symphony Orchestra and its association with Richter and Elgar have been well documented, yet there is much still to be learnt about the 1904 break with the autocratic Henry Wood and about the artistic and commercial decisions facing the new self-governing orchestra. From the start, the LSO confidently allied itself with international standards and cosmopolitan repertoire, and a roster of celebrated conductors to match. But financial security was less easily gained. Detailed analysis of the finances of the prestigious subscription series shows initial eclecticism giving way to concentration on the Austro-German canon in reaction to commercial and social pressures. British music came in and out of focus, despite the nationalistic mood of the time, and the analysis places in sharp relief the successes and failures of the link with Elgar. Furthermore, in an extraordinary sacrifice of self-interest, the freelance members decided to renounce normal fees for the subscription series in order to gain lucrative engagements elsewhere: thus the orchestra acted more as an agency than as a stable business proposition. Nevertheless, the innovative governance structure, underpinning a combination of resolute management, entrepreneurial energy and communal decision-making, eventually proved a viable and sustainable model that has remained influential up to this day.
‘Putting the BBC and T. Beecham to Shame’: The Macnaghten–Lemare Concerts, 1931–7
Authors: Fuller Sophie 
Published: October 2013

ABSTRACTThis article explores and contextualizes the Macnaghten–Lemare concerts, a London concert series run for six seasons in the 1930s by the violinist Anne Macnaghten and the conductor Iris Lemare, with the help of the composer Elisabeth Lutyens and others. Notable for their performances of the work of emerging British composers such as Benjamin Britten and Elizabeth Maconchy, the concerts are also remarkable for the central role played by women – as performers, organizers and composers – and for the space they provided for the unconventional and ignored. Drawing on interviews with Macnaghten and Lemare as well as extensive archival research, the article provides details of the 20 concerts and argues for their hitherto overlooked importance in understanding the British concert life of this decade.
HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data
Authors: Hochreiter Sepp 
Published: October 2013

Abstract
Identity by descent (IBD) can be reliably detected for long shared DNA segments, which are found in related individuals. However, many studies contain cohorts of unrelated individuals that share only short IBD segments. New sequencing technologies facilitate identification of short IBD segments through rare variants, which convey more information on IBD than common variants. Current IBD detection methods, however, are not designed to use rare variants for the detection of short IBD segments. Short IBD segments reveal genetic structures at high resolution. Therefore, they can help to improve imputation and phasing, to increase genotyping accuracy for low-coverage sequencing and to increase the power of association studies. Since short IBD segments are further assumed to be old, they can shed light on the evolutionary history of humans. We propose HapFABIA, a computational method that applies biclustering to identify very short IBD segments characterized by rare variants. HapFABIA is designed to detect short IBD segments in genotype data that were obtained from next-generation sequencing, but can also be applied to DNA microarray data. Especially in next-generation sequencing data, HapFABIA exploits rare variants for IBD detection. HapFABIA significantly outperformed competing algorithms at detecting short IBD segments on artificial and simulated data with rare variants. HapFABIA identified 160 588 different short IBD segments characterized by rare variants with a median length of 23 kb (mean 24 kb) in data for chromosome 1 of the 1000 Genomes Project. These short IBD segments contain 752 000 single nucleotide variants (SNVs), which account for 39% of the rare variants and 23.5% of all variants. The vast majority—152 000 IBD segments—are shared by Africans, while only 19 000 and 11 000 are shared by Europeans and Asians, respectively. IBD segments that match the Denisova or the Neandertal genome are found significantly more often in Asians and Europeans but also, in some cases exclusively, in Africans. The lengths of IBD segments and their sharing between continental populations indicate that many short IBD segments from chromosome 1 existed before humans migrated out of Africa. Thus, rare variants that tag these short IBD segments predate human migration from Africa. The software package HapFABIA is available from Bioconductor. All data sets, result files and programs for data simulation, preprocessing and evaluation are supplied at http://www.bioinf.jku.at/research/short-IBD.
GM(1, 1) forecast under function cot x transformation
Authors: Ye Jing , Li Bingjun , Liu Fang 
Published: October 2013

Purpose
– This paper aims to find an effective and standardized function transformation method to apply in both high-growth original data sequences and low-growth original data sequences, which can improve the accuracy of model prediction in GM(1, 1) forecast.

Design/methodology/approach
– In GM(1, 1) forecast, many original data sequences need to meet the quasi-exponential characteristic by methods of function transformation. However, many methods of function transformation have complex transformation processes or narrow application range. On the basis of the research results of Ye and Li, the paper presents a standardized approach based on to original data sequences and designs four situations of the standardized approach. By using high-growth and low-growth original data sequences as the objects, respectively, the paper verifies the effectiveness of the proposed method and compares the forecasting effects of GM(1, 1) based on function transformation with the original GM(1, 1).

Findings
– Most of the results show that function transformations can improve the accuracy of the conventional GM(1, 1) forecast, and transform is a powerful tool to effectively process original data sequence of GM(1, 1) modeling.

Practical implications
– GM(1, 1) forecast have been widely used in many fields such as agriculture, economy, meteorology, and geology. The proposed method in this paper can effectively apply to prediction of high-growth original data sequences and low-growth original data sequences, to some extent, enrich and deepen application of GM(1, 1) forecast.

Originality/value
– The paper succeeds in providing a standardized approach based on and designs four intensity levels for different data sequences based on the standardized approach.