bluuebunny/crossref_metadata_2025_split huggingface dataset:
A polymetamorphic protein
Authors: Stewart Katie L. , Dodds Eric D. , Wysocki Vicki H. , Cordes Matthew H. J. 
Published: March 2013

AbstractArc repressor is a homodimeric protein with a ribbon‐helix–helix fold. A single polar‐to‐hydrophobic substitution (N11L) at a solvent‐exposed position leads to population of an alternate dimeric fold in which 310 helices replace a β‐sheet. Here we find that the variant Q9V/N11L/R13V (S‐VLV), with two additional polar‐to‐hydrophobic surface mutations in the same β‐sheet, forms a highly stable, reversibly folded octamer with approximately half the✠α‐helical content of wild‐type Arc. At low protein concentration and low ionic strength, S‐VLV also populates both dimeric topologies previously observed for N11L, as judged by NMR chemical shift comparisons. Thus, accumulation of simple hydrophobic mutations in Arc progressively reduces fold specificity, leading first to a sequence with two folds and then to a manifold bridge sequence with at least three different topologies. Residues 9–14 of S‐VLV form a highly hydrophobic stretch that is predicted to be amyloidogenic, but we do not observe aggregates of higher order than octamer. Increases in sequence hydrophobicity can promote amyloid aggregation but also exert broader and more complex effects on fold specificity. Altered native folds, changes in fold coupled to oligomerization, toxic pre‐amyloid oligomers, and amyloid fibrils may represent a near continuum of accessible alternatives in protein structure space.
Improving ranking of models for protein complexes with side chain modeling and atomic potentials
Authors: Viswanath Shruthi , Ravikant D. V. S. , Elber Ron 
Published: March 2013

AbstractAn atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re‐ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re‐ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Salvianolic acid B inhibits the amyloid formation of human islet amyloid polypeptideand protects pancreatic beta‐cells against cytotoxicity
Authors: Cheng Biao , Gong Hao , Li Xiaochao , Sun Yue , Chen Hong , Zhang Xin , Wu Qian , Zheng Ling , Huang Kun 
Published: March 2013

AbstractThe misfolding of human islet amyloid polypeptide (hIAPP) is regarded as one of the causative factors of type 2 diabetes mellitus (T2DM). Salvia miltiorrhiza (Danshen), one of the most commonly used of traditional Chinese medicines, is often used in Compound Recipes for treating diabetes, however with unclear mechanisms. Since salvianolic acid B (SalB) is the most abundant bioactive ingredient of salvia miltiorrhiza water‐extract. In this study, we tested whether SalB has any effect on the amyloidogenicity of hIAPP. Our results clearly suggest that SalB can significantly inhibit the formation of hIAPP amyloid and disaggregate hIAPP fibrils. Furthermore, photo‐crosslinking based oligomerization studies suggest SalB significantly suppresses the toxic oligomerization of hIAPP monomers. Cytotoxicity protection effects on pancreatic INS‐1 cells by SalB were also observed using MTT‐based assays, potentially due to the inhibition on the membrane disruption effects and attenuated mitochondria impairment induced by hIAPP. These results provide evidence that SalB may further be studied on the possible pharmacological treatment for T2DM. Proteins 2013. © 2012 Wiley Periodicals, Inc.
LabCaS: Labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields
Authors: Fan Yong‐Xian , Zhang Yang , Shen Hong‐Bin 
Published: March 2013

AbstractThe calpain family of Ca2+‐dependent cysteine proteases plays a vital role in many important biological processes which is closely related with a variety of pathological states. Activated calpains selectively cleave relevant substrates at specific cleavage sites, yielding multiple fragments that can have different functions from the intact substrate protein. Until now, our knowledge about the calpain functions and their substrate cleavage mechanisms are limited because the experimental determination and validation on calpain binding are usually laborious and expensive. In this work, we aim to develop a new computational approach (LabCaS) for accurate prediction of the calpain substrate cleavage sites from amino acid sequences. To overcome the imbalance of negative and positive samples in the machine‐learning training which have been suffered by most of the former approaches when splitting sequences into short peptides, we designed a conditional random field algorithm that can label the potential cleavage sites directly from the entire sequences. By integrating the multiple amino acid features and those derived from sequences, LabCaS achieves an accurate recognition of the cleave sites for most calpain proteins. In a jackknife test on a set of 129 benchmark proteins, LabCaS generates an AUC score 0.862. The LabCaS program is freely available at: http://www.csbio.sjtu.edu.cn/bioinf/LabCaS. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Rapid field application of hydraulic tomography for resolving aquifer heterogeneity in unconsolidated sediments
Authors: Brauchler R. , Hu R. , Hu L. , Jiménez S. , Bayer P. , Dietrich P. , Ptak T. 
Published: March 2013

Key Points
Rapid field application of hydraulic tomography
Further development of hydraulic attenuation tomography
Comparison of direct‐push profiling and hydraulic tomography
Guidelines for Surgeons on Establishing Projects in Low‐Income Countries
Authors: Grimes Caris E. , Maraka Jane , Kingsnorth Andrew N. , Darko Rudolph , Samkange Christopher A. , Lane Robert H. S. 
Published: March 2013

AbstractBackgroundThere is increasing interest by surgeons in high‐income countries to support colleagues in low‐income countries to improve the provision of surgical care, particularly in rural areas. Such interest may be demonstrated by single individuals, short‐term surgical missions, or establishment of partnerships. Such altruistic efforts may cause problems unless properly planned and carried out.MethodsWe reviewed the available literature and consulted widely to establish consensus guidelines for any surgeon considering participating in an initiative to improve surgical care in low‐income countries.ResultsA series of recommendations is presented. These include ensuring that projects are appropriate, that there is an emphasis on training local healthcare providers in all aspects of perioperative care, that outcomes are monitored, and that initiatives work with local and regional training programs.ConclusionsWith adherence to these recommendations, we hope that future partnerships and missions can maximize their effectiveness and minimize the risks of potential harm done.
The melody of the immature brain
Authors: Sieben K. , Hartung H. , Wolff A. , Hanganu-Opatz I. 
Published: March 2013

Abstract
The periodicity of brain activity became ob­vious even after the first attempt to capture it, with Hans Berger noting in 1929 that the “electroencephalogram represents a con­tinuous curve with continuous oscillations”. This rhythmicity of neural activity, the ‘melo­dy’ of the brain, has since gained interest as an energy-efficient strategy for the organisa­tion and communication both within and be­tween brain regions. While it is now known that these oscillations actively contribute to sensory perception and cognition in the adult brain, their function during development is still largely unknown. Recent experimental data revealed the ability of immature human and rodent brain to generate various patterns of electrical activity. Their properties and un­derlying mechanisms may vary among dif­ferent brain areas. However, these early pat­terns of activity seem to facilitate the refine­ment of cortical maps involved in sensory perception as well as mnemonic and execu­tive processing. Here we review recent stud­ies, which characterize the early oscillatory activity and demonstrate its impact on brain development.
Addressing barriers to safe abortion
Authors: Culwell Kelly R. , Hurwitz Manuelle 
Published: March 2013

AbstractThe latest World Health Organization data estimate that the total number of unsafe abortions globally has increased to 21.6 million in 2008. There is increasing recognition by the international community of the importance of the contribution of unsafe abortion to maternal mortality. However, the barriers to delivery of safe abortion services are many. In 68 countries, home to 26% of the world's population, abortion is prohibited altogether or only permitted to save a woman's life. Even in countries with more liberal abortion legal frameworks, additional social, economic, and health systems barriers and the stigma surrounding abortion prevent adequate access to safe abortion services and postabortion care. While much has been achieved to reduce the barriers to comprehensive abortion care, much remains to be done. Only through the concerted action of public, private, and civil society partners can we ensure that women have access to services that are safe, affordable, confidential, and stigma free.
Servitization: Disentangling the impact of service business model innovation on manufacturing firm performance
Authors: Kastalli Ivanka Visnjic , Van Looy Bart 
Published: March 2013

AbstractAs manufacturing businesses operate in an ever more competitive, global economy where products are easily commoditized, innovating by adding services to the core product offering has become a popular strategy. Contrary to the economic benefits expected, recent findings pinpoint implementation hurdles that lead to a potential performance decline, the so‐called ‘servitization paradox’. In this paper, we analyze this paradox by disentangling the value creation and value appropriation processes of 44 national subsidiaries of a global manufacturing firm turned product‐service provider, in the 2001–2007 period. Our findings show that the firm under study is able to successfully transcend the inherent substitution of products by services and to enact complementary sales dynamics between the two activities. Moreover, labor‐intensive services such as maintenance, which imply higher levels of customer proximity, further enhance product sales. Empirical results also reveal a positive yet non‐linear relationship between the scale of service activities and profitability: while initial levels of servicing result in a steep increase in profitability, a period of relative decline is observed before the positive relationship between the scale of services and profitability re‐emerges. These findings suggest the presence of initial short‐term gains but also indicate the existence of a ‘profitability’ hurdle; profitable growth seems feasible only to the extent that investments in service capability are translated into economies of scale. In helping to clarify the performance implications of service innovation, our findings suggest pathways to sustainable growth through servitization for manufacturing firms.
1-REGULAR CAYLEY GRAPHS OF VALENCY 7
Authors: LI JING JIAN , ZHANG GENG RONG , LING BO 
Published: March 2013

AbstractA graph $\mit{\Gamma} $ is called $1$-regular if $ \mathsf{Aut} \mit{\Gamma} $ acts regularly on its arcs. In this paper, a classification of $1$-regular Cayley graphs of valency $7$ is given; in particular, it is proved that there is only one core-free graph up to isomorphism.
Genetic structure ofLycorma delicatula(Hemiptera: Fulgoridae) populations in Korea: implication for invasion processes in heterogeneous landscapes
Authors: Park Marana , Kim Kyung-Seok , Lee Joon-Ho 
Published: March 2013

AbstractLycorma delicatula(White) was identified in 2004 as an invasive pest in South Korea, where it causes serious damage to vineyard crops. To investigate the population structure and dispersal pattern ofL. delicatulain South Korea, we estimated the population genetic structure and gene flow among nine locations across the country using seven microsatellite markers. AlthoughL. delicatulaspread throughout most of its geographical range in South Korea within 5–7 years following invasion, its populations show evidence of genetic structuring across the range with a low but significant globalFST(genetic differentiation across all populations) of 0.0474. Bayesian-based clustering analysis indicates the presence of at least three genetically unique populations in South Korea, including populations in northeastern South Korea, which show a distinct genetic background. However, isolation by distance suggests that populations in South Korea have not yet reached genetic equilibrium. Estimates of the historical rate of gene flow (Nem) indicate that relatively high rates of flow have been maintained among populations within the western region, which may indicate recent range expansion. A population assignment test using the first-generation migrant detection method suggested that long-distance dispersal ofL. delicatulamay have occurred over large areas of South Korea. More complex dispersal patterns may have occurred duringL. delicatulainvasion of heterogeneous landscapes in South Korea.
INTRA-CORPORATE CONSPIRACY: AN INTRIGUING PROSPECT
Authors: Witting Christian 
Published: March 2013

AbstractThis paper considers whether unlawful means conspiracy might have a role to play in extending liability from insolvent companies to those who stand behind them. A reason for thinking that the tort might have such a role is that, where an agreement to injure exists, liability can be found not only in those who commit unlawful acts but in any other persons who take steps to further the conspiracy. The paper argues, furthermore, that courts should accept that unlawful means conspiracy might be committed between even the smallest company and its controlling shareholder. This would strengthen the propositions that the company is a separate legal person with its own rights and responsibilities and that it is competent to deal with all comers, including its controller.
BOUNDARY ANGULAR DERIVATIVES OF GENERALIZED SCHUR FUNCTIONS
Authors: BOLOTNIKOV VLADIMIR , WANG TENGYAO , WEISS JOSHUA M. 
Published: March 2013

AbstractCharacterization of generalized Schur functions in terms of their Taylor coefficients was established by Krein and Langer [‘Über einige Fortsetzungsprobleme, die eng mit der Theorie hermitescher Operatoren im Raume${\Pi }_{\kappa } $zusammenhängen. I. Einige Funktionenklassen und ihre Darstellungen’,Math. Nachr. 77(1977), 187–236]. We establish a boundary analogue of this characterization.
HYPERCOMMUTING VALUES IN ASSOCIATIVE RINGS WITH UNITY
Authors: DE FILIPPIS VINCENZO , SCUDO GIOVANNI 
Published: March 2013

AbstractLet $K$ be a commutative ring with unity, $R$ an associative $K$-algebra of characteristic different from $2$ with unity element and no nonzero nil right ideal, and $f({x}_{1} , \ldots , {x}_{n} )$ a multilinear polynomial over $K$. Assume that, for all $x\in R$ and for all ${r}_{1} , \ldots , {r}_{n} \in R$ there exist integers $m= m(x, {r}_{1} , \ldots , {r}_{n} )\geq 1$ and $k= k(x, {r}_{1} , \ldots , {r}_{n} )\geq 1$ such that $\mathop{[{x}^{m} , f({r}_{1} , \ldots , {r}_{n} )] }\nolimits_{k} = 0$. We prove that: (1) if $\text{char} (R)= 0$ then $f({x}_{1} , \ldots , {x}_{n} )$ is central-valued on $R$; and (2) if $\text{char} (R)= p\gt 2$ and $f({x}_{1} , \ldots , {x}_{n} )$ is not a polynomial identity in $p\times p$ matrices of characteristic $p$, then $R$ satisfies ${s}_{n+ 2} ({x}_{1} , \ldots , {x}_{n+ 2} )$ and for any ${r}_{1} , \ldots , {r}_{n} \in R$ there exists $t= t({r}_{1} , \ldots , {r}_{n} )\geq 1$ such that ${f}^{{p}^{t} } ({r}_{1} , \ldots , {r}_{n} )\in Z(R)$, the center of $R$.
Anodal transcranial direct current stimulation increases brain intracellular pH and modulates bioenergetics
Authors: Rae Caroline D. , Lee Vincent H.-C. , Ordidge Roger J. , Alonzo Angelo , Loo Colleen 
Published: March 2013

AbstractTranscranial direct current stimulation is an emerging treatment for brain disorders but its mode of action is not well understood. We applied 10 min 1 mA anodal transcranial direct current stimulation (tDCS) inside the bore of a 3 T MRI scanner to the left dorsolateral prefrontal cortex of 13 healthy volunteers (aged 19–28 yr) in a blinded, sham-controlled, cross-over design. Brain bioenergetics were measured from the left temporo-frontal region using 31P magnetic resonance spectroscopy before, during and for 20 min following tDCS. Brain pH rose during tDCS and remained elevated afterwards. Phosphomonoesters were significantly decreased while inorganic phosphate (Pi) also fell. Partial-least squares discriminant analysis of the data revealed two significantly different subject groups: one where phosphocreatine (PCr), ATP and Pi fell along with a larger increase in pH and one where PCr and ATP increased along with a smaller increase in pH and a slower and more sustained decrease in Pi. Group membership was predicted by baseline pH and ATP. We interpreted the effects of tDCS as driving two biochemical processes: cellular consumption of ATP causing hydrolysis of PCr via the creatine kinase reaction driving the increase in pH; synthesis of ATP and PCr by mitochondria with concomitant drop in Pi and phosphomonoester levels.
Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing
Authors: Lundin Sverker , Gruselius Joel , Nystedt Björn , Lexow Preben , Käller Max , Lundeberg Joakim 
Published: March 2013

AbstractHere we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries are degraded, sub-sampled and arrested at timed intervals to achieve pools of differing average length, each of which is indexed with a new tag. By this process, indices of sample origin, molecular origin and degree of degradation is incorporated in order to achieve a nested hierarchical structure, later to be utilized in the data processing to order the reads over a longer distance than the sequencing system originally allows. With this protocol we show how continuous regions beyond 3000 bp can be decoded by an Illumina sequencing system and we illustrate the potential applications by calling variants of the lambda genome, analysing TP53 in cancer cell lines and targeting a variable canine mitochondrial region.
The Role of Fat Grafting in the Treatment of Posttraumatic Maxillofacial Deformities
Authors: Arcuri Francesco , Brucoli Matteo , Baragiotta Nicola , Stellin Livia , Giarda Mariangela , Benech Arnaldo 
Published: March 2013

Purpose The first autologous adipose tissue grafting was performed by Neuber in 1893 with an open approach. In the early 1980s, Illouz and Fournier introduced closed liposuction. In the 1990s, Coleman published a new method of atraumatic fat transplantation. Recently, immunohistochemical studies of the extracellular matrix of the lipoaspirate showed the presence of adipose-derived stem cells. The purpose of this study is to describe the role of fat grafting in the management of posttraumatic facial deformities. Methods The study population was composed of all patients who underwent facial fat grafting between March 2008 and November 2010 as a secondary reconstructive procedure after an initial unsatisfactory treatment of the skeletal fractures. We analyzed the postoperative morphological changes by comparing the grafted side of the face to the contralateral side with the aid of a software package. Results Nineteen patients were surgically treated with fat transplantation for facial asymmetry due to a pathological postoperative healing of the soft tissue. Clinical examination and software analysis showed adequate postoperative facial balance without major complications. Conclusion Fat grafting is a very powerful tool to correct posttraumatic maxillofacial deformities and to ensure a long-term follow-up. Although we have achieved excellent clinical results in our reconstructive clinical cases, we are convinced that more complex prospective studies, enriched by long-term radiological controls, are needed to fully understand the biological behavior of the transplanted fat in the posttraumatic face.
Haemodynamic effects, safety, and pharmacokinetics of human stresscopin in heart failure with reduced ejection fraction†
Authors: Gheorghiade Mihai , Greene Stephen J. , Ponikowski Piotr , Maggioni Aldo P. , Korewicki Jerzy , Macarie Cezar , Metra Marco , Grzybowski Jacek , Bubenek‐Turconi Serban‐Ion , Radziszewski Waldemar , Olson Allan , Bueno Orlando F. , Ghosh Atalanta , Deckelbaum Lawrence I. , Li Lilian Y. , Patel Ayan R. , Koester Andreas , Konstam Marvin A. 
Published: March 2013

AimsHuman stresscopin is a corticotropin‐releasing factor (CRF) type 2 receptor (CRFR2) selective agonist and a member of the CRF peptide family. Stimulation of CRFR2 improves cardiac output and left ventricular ejection fraction (LVEF) in patients with stable heart failure (HF) with reduced LVEF. We examined the safety, pharmacokinetics, and effects on haemodynamics and serum biomarkers of intravenous human stresscopin acetate (JNJ‐9588146) in patients with stable HF with LVEF ≤35% and cardiac index (CI) ≤2.5 L/min/m2.Methods and resultsSixty‐two patients with HF and LVEF ≤35% were instrumented with a pulmonary artery catheter and randomly assigned (ratio 3:1) to receive an intravenous infusion of JNJ‐9588146 or placebo. The main study was an ascending dose study of three doses (5, 15, and 30 ng/kg/min) of study drug or placebo administered in sequential 1 h intervals (3 h total). Statistically significant increases in CI and reduction in systemic vascular resistance (SVR) were observed with both the 15 ng/kg/min (2 h time point) and 30 ng/kg/min (3 h time point) doses of JNJ‐9588146 without significant changes in heart rate (HR) or systolic blood pressure (SBP). No statistically significant reductions in pulmonary capillary wedge pressure (PCWP) were seen with any dose tested in the primary analysis, although a trend towards reduction was seen.ConclusionIn HF patients with reduced LVEF and CI, ascending doses of JNJ‐9588146 were associated with progressive increases in CI and reductions in SVR without significant effects on PCWP, HR, or SBP.Trial registration: NCT01120210