bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of the RCSB Protein Data Bank website
Authors: Bourne Philip E. , Beran Bojan , Bi Chunxiao , Bluhm Wolfgang F. , Dimitropoulos Dimitris , Feng Zukang , Goodsell David S. , Prlić Andreas , B. Quinn Gregory , W. Rose Peter , Westbrook John , Yukich Benjamin , Young Jasmine , Zardecki Christine , Berman Helen M. 
Published: June 2011

AbstractThe Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education by providing an essential resource of information about biomolecular structures. As a member of the Worldwide Protein Data Bank (wwPDB), the RCSB PDB curates and annotates the data about the experimentally determined three‐dimensional structures of proteins and nucleic acids that are deposited into the PDB archive. The RCSB PDB also provides online resources to access the data in the archive, including a relational database supporting simple and complex query and reporting, visualization tools, structure‐sequence comparison tools, access to the associated literature, and educational services. In the 11 years (1999–2010) since RCSB PDB has been in operation, the amount of data in the archive has increased six‐fold, along with an increase in the complexity of structures being determined and in the number of experimental methods used. The evolution required by RCSB PDB to meet these challenges provides insight into the motivation and challenges of developing and maintaining a major biological resource, particularly the one used in understanding the molecular details of living systems in both normal and disease states. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 782–789 DOI: 10.1002/wcms.57This article is categorized under:

Computer and Information Science > Chemoinformatics
DNA insertion in and wrapping around carbon nanotubes
Authors: Contreras‐Torres Flavio F. , Martínez‐Lorán Erick 
Published: June 2011

AbstractThe interaction of carbon nanotubes (CNTs) with biomolecules has been a subject of great interest during the last decades, for the wide range of applications profiting their novel properties; particularly, it has been pointed out their ability to interact with living cells for different purposes. The study of the interactions between CNTs and DNA is an active research subject, given the remarkable properties of the DNA molecule and its potential use in biologic materials. Theoretical calculations have become an essential task in the study of such interactions; hence, computational simulations provide a powerful tool, which in turn yields powerful insights on the underlying phenomena of nanoscale processes occurring on these composites. This work reviews some of the latest efforts on theoretical simulations of DNA functionalized CNTs composites. Among the different theoretical approaches used in computational modeling of nanocomposites there are some that were found not fitted for analyzing CNTs, given the large number of molecules present in an ordinary CNT; often these routines are very resource consuming and long computation times are frequently required for accurate analysis. Recent works using density functional theory (DFT) and molecular dynamics (MD) have proven to be of great value when dealing with DNA modified CNTs. We discuss some of the latest results of these treatments, namely, on the DNA insertion in and wrapping around single‐walled carbon nanotubes (SWNTs) and envision some of their current applications such as nanocarriers for therapeutical uses, selective imaging, and biological sensing. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 902–919 DOI: 10.1002/wcms.60This article is categorized under:

Structure and Mechanism > Computational Materials Science
Model-checking timed automata with deadlines with Uppaal
Authors: Gómez Rodolfo 
Published: June 2011

Abstract

Timed automata with deadlines (TAD) are a form of timed automata that admit a more natural representation of urgent actions, with the additional advantage of avoiding the most common form of timelocks. We offer a compositional translation of a practically useful subset of TAD to timed safety automata (the well-known variant of timed automata where time progress conditions are expressed by invariants). More precisely, we translate networks of TAD to the modeling language of
Uppaal
, a state-of-the-art verification tool for timed automata. We also describe an implementation of this translation, which allows
Uppaal
to aid the design and analysis of TAD models.
Nafamostat mesilate can prevent adhesion, invasion and peritoneal dissemination of pancreatic cancer thorough nuclear factor kappa‐B inhibition
Authors: Fujiwara Yuki , Furukawa Kenei , Haruki Koichiro , Shimada Yohta , Iida Tomonori , Shiba Hiroaki , Uwagawa Tadashi , Ohashi Toya , Yanaga Katsuhiko 
Published: June 2011

AbstractBackgroundConstitutive activation of nuclear factor kappa‐B (NF‐κB) contributes to the aggressive behavior of pancreatic cancer. Over‐expression of downstream target genes of NF‐κB such as intercellular adhesion molecule‐1 (ICAM‐1), interleukin‐8 (IL‐8), vascular endothelial growth factor (VEGF) and matrix metalloproteinase‐9 (MMP‐9) leads to the promotion of cell adhesion, angiogenesis, invasion and metastasis. We previously reported that nafamostat mesilate, a synthetic serine protease inhibitor, blocks NF‐κB activation in pancreatic cancer. We hypothesized that nafamostat mesilate may inhibit cell adhesion, angiogenesis, invasion and metastases in peritoneal dissemination of pancreatic cancer.MethodsIn vitro, we assessed inhibition of NF‐κB, phosphorylated IκBα, ICAM‐1, VEGF and MMP‐9 activity by nafamostat mesilate using human pancreatic cancer cell lines (AsPC‐1, BxPC‐3 and PANC‐1). Changes in adhesion and invasion abilities of cancer cells were then evaluated by nafamostat mesilate treatment. In vivo, the efficacy of nafamostat mesilate treatment was assessed using peritoneal dissemination of pancreatic cancer in mice.ResultsIn vitro, nafamostat mesilate inhibited activities of NF‐κB, phosphorylated IκBα, ICAM‐1, VEGF and MMP‐9. Moreover, nafamostat mesilate not only inhibited cell adhesion and invasion but also increased the sensitivity of anoikis. In vivo, tumor growth using AsPC‐1 cells of the treatment group was significantly slower, and survival rate was significantly better, than those in control group (p < 0.05).ConclusionNafamostat mesilate reduced peritoneal metastasis and prolonged survival of pancreatic cancer‐bearing mice.
Functional imaging in muscular diseases
Authors: Amarteifio Erick , Nagel Armin Michael , Kauczor Hans-Ulrich , Weber Marc-André 
Published: June 2011

AbstractObjectiveThe development of morphological and functional imaging techniques has improved the diagnosis of muscular disorders.MethodsWith the use of whole-body magnetic resonance imaging (MRI) the possibility of imaging the entire body has been introduced. In patients with suspected myositis, oedematous and inflammatory changed muscles can be sufficiently depicted and therefore biopsies become more precise.ResultsFunctional MR methods visualise different aspects of muscular (patho)physiology: muscular sodium (Na+) homeostasis can be monitored with23Na MRI; the muscular energy and lipid metabolism can be monitored using31P and1H MR spectroscopy.23Na MRI has reached an acceptable value in the diagnosis and follow-up of patients with muscular Na+channelopathies that are characterised by myocellular Na+overload and consecutive muscle weakness. Besides MRI, low mechanical index contrast-enhanced ultrasound (CEUS) methods have also been introduced. For evaluation of myositis, CEUS is more efficient in the diagnostic work-up than usual b-mode ultrasound, because CEUS can detect the inflammatory-induced muscular hyperperfusion in acute myositis. Moreover, the arterial perfusion reserve in peripheral arterial disease can be adequately examined using CEUS.ConclusionModern muscular imaging techniques offer deeper insights in muscular (patho)physiology than just illustrating unspecific myopathic manifestations like oedematous or lipomatous changes, hypertrophy or atrophy.
Rate of readmission and mortality risks of schizophrenia patients who were discharged against medical advice
Authors: Valevski A. , Zalsman G. , Tsafrir S. , Lipschitz-Elhawi R. , Weizman A. , Shohat T. 
Published: June 2011

AbstractPurposeTo compare the readmission and the mortality rates of schizophrenia patients who were discharged against medical advice (AMA) and patients who were discharged by physician recommendation.MethodsThe records (1984–2005) of all consecutive admissions (n= 12,937) of schizophrenia patients (n= 8,052) were reviewed. Out of this group, 673 (8.3%) refused to remain in the hospital and signed a hospital form for discharge AMA. Their records were analyzed for rates of re-hospitalization and mortality at study closure. The records of AMA patients were compared to those of patients with regular discharge (n= 1345).ResultsAMA patients were younger at admission (P<0.001), comprised more males (P<0.01), more were single (P<0.0001), and had a shorter duration of illness than the controls (P<0.05). A total of 49.9% of AMA events occurred within the first 2weeks of hospitalization. The readmission rate was significantly higher for AMA patients than for the controls (P<0.001). The mortality rate as a result of suicide (P<0.0001) and accidents (P<0.05) was higher for AMA patients compared to controls.ConclusionThe schizophrenia patients discharged AMA have a higher readmission rate and a higher mortality rate due to suicide and accidents compared to non-AMA discharged patients. Patients with AMA discharge warrant special community surveillance to improve outcome.
Neurocognitive functions of heavy cannabis using schizophrenia patients
Authors: Lev-Ran S. , Segev A. , Braw Y. , Levkovitz Y. 
Published: June 2011

AbstractThis current study assessed neurocognitive functioning in a carefully selected sample of schizophrenia patients with and without heavy cannabis use and healthy controls. All subjects were negative for any other substance use. Schizophrenia subjects had impaired neurocognitive functions across a wide range of tasks compared to healthy controls. Cannabis using schizophrenia patients had focused impairments on tasks of attention, and the findings suggest an impulsive pattern of response among these patients.
Role of endogenous pituitary adenylate cyclase activating polypeptide (PACAP) in myelination of the rodent brain: Lessons from PACAP‐deficient mice
Authors: Vincze András , Reglodi Dóra , Helyes Zsuzsanna , Hashimoto Hitoshi , Shintani Norihito , Ábrahám Hajnalka 
Published: June 2011

AbstractPituitary adenylate‐cyclase activator polypeptide (PACAP), as a consequence of its effect on the elevation of intracellular cAMP level, strongly influences brain development including myelination. While proliferation of oligodendroglial progenitors is stimulated by PACAP applied in vitro, their differentiation is inhibited. However, the in vivo role of PACAP on myelination has never been examined.In the present study the role of endogenous PACAP in myelination was examined in PACAP‐deficient mice, in several areas of the brain with a special attention to the cerebral cortex. In young postnatal and adult mice myelination was studied with immunohistochemistry detecting a protein present in the myelin sheath, the myelin basic protein, with Luxol Fast Blue staining and with electron microscopy. Results obtained in PACAP‐deficient mice were compared to age‐matched wild type controls.We found that the sequence of myelination in the PACAP‐deficient animals was similar to that observed in controls. According to this, in both PACAP‐deficient and wild type mice, the somatosensory cortex was myelinated before motor areas that preceded the myelination of associational cortical areas. Archicortical associational areas such as the cingulate cortex were myelinated before neocortical areas. Myelination in the corpus callosum followed the known rostro‐caudal direction in both PACAP‐deficient and wild type animals, and the ventrolateral part of the corpus callosum was myelinated earlier than the dorsomedial part in both groups. In contrast to the similarity in its sequence, striking difference was found in the onset of myelination that started earlier in PACAP‐deficient mice than in wild type controls in all of the examined brain regions, including cerebral archi‐ and neocortex. The first myelinated axons in each of the examined brain regions were observed earlier in the PACAP‐deficient mice than in controls. When age‐matched animals of the two groups were compared, density of myelinated fibers in the PACAP‐deficient mice was higher than in controls in all of the examined areas.We propose that endogenous PACAP exerts an inhibitory role on myelination in vivo. Since myelin sheath of the central nervous system contains several factors blocking neurite outgrowth, inhibition of myelination by PACAP gives time for axonal development and synapse formation, and therefore, strengthens neuronal plasticity.
Impact of placenta previa on obstetric outcome
Authors: Daskalakis George , Simou Maria , Zacharakis Dimitrios , Detorakis Stelios , Akrivos Nikolaos , Papantoniou Nikolaos , Fouskakis Dimitrios , Antsaklis Aris 
Published: June 2011

AbstractObjectiveTo determine the maternal and perinatal outcome for different types of placenta previa (PP).MethodsA retrospective review of 132 singleton pregnancies with PP. Outcome measures, including the incidence of obstetric hysterectomy, the neonatal Apgar score, and the neonatal weight, were evaluated by logistic regression analysis.ResultsThe incidence of PP was 1.0%. Of the women with PP, 51.5% had complete PP, 20.5% had incomplete PP, 5.3% had marginal PP, and 22.7% had a low‐lying placenta. Most (93.9%) women were delivered by cesarean delivery. In total, 19.7% women underwent obstetric hysterectomy; of these, 92.3% had complete PP. Mothers with 2 or more previous cesarean deliveries had an increased risk for obstetric hysterectomy (P < 0.01). The gestational age at delivery was a significant linear predictor of the 5‐minute Apgar score. Mothers with incomplete PP delivered neonates with lower Apgar scores than did mothers with complete PP.ConclusionA history of multiple cesarean deliveries increased the risk for obstetric hysterectomy in women with PP. The type of PP had no effect on maternal and neonatal outcome, with exception of the fact that neonates in the incomplete PP group had lower Apgar scores than neonates in the complete PP group.
Accuracy of Palpating the Long Head of the Biceps Tendon: An Ultrasonographic Study
Authors: Gazzillo Gregory P. , Finnoff Jonathan T. , Hall Mederic M. , Sayeed Yusef A. , Smith Jay 
Published: June 2011

ObjectiveTo determine the accuracy of palpating the long head of the biceps tendon (LHBT) within the intertubercular groove with the use of ultrasonographic localization as a gold standard.DesignProspective, single‐blinded pilot study.SettingSports medicine clinic at a tertiary care academic institution.ParticipantsTwenty‐five male and female asymptomatic volunteers ages 24‐41 years (mean, 30.9 ± 4.3 years) with body mass indices of 19.3 to 36.3 kg/m2 (23.84 ± 4.8 kg/m2).MethodsThree examiners of differing experience (a sports medicine board‐certified staff physician, a sports medicine fellow, and a physical medicine and rehabilitation resident) identified the LHBT location in the intertubercular groove via palpation on a subject in the supine position and marked its location by taping an 18‐gauge Tuohy needle to the skin overlying the groove. The examiner order was randomized. A fourth examiner who was blinded to the palpation order assessed the previous examiner's palpation accuracy by comparing the needle position to the sonographically determined tendon position.Main Outcome MeasuresNeedle placement in relation to the intertubercular groove was graded as being within the groove, medial to the groove, or lateral to the groove. In the latter 2 cases, the distance from the needle to the closest groove edge was recorded.ResultsOverall accuracy rate was 5.3% (4/75), ranging from 0% (0/25) for the resident to 12% (3/25) for the fellow (P ≤ .007 for interexaminer differences). All missed palpations were localized medial to the intertubercular groove by an average of 1.4 ± 0.5 cm (range, 0.3 for the fellow to 3.5 cm for the resident).ConclusionBased on the current methodology, clinicians have a tendency to localize the intertubercular groove medial to its actual location. Consequently, clinicians should exercise caution when relying on clinical palpation to either diagnose a biceps tendon disorder or perform a bicipital tendon sheath injection. When clinically indicated, sonographic guidance can be used to accurately identify the LBHT within the intertubercular groove.
Reduction of monocyte chemoattractant protein 1 and macrophage migration inhibitory factor by a polyphenol-rich extract in subjects with clustered cardiometabolic risk factors
Authors: Broekhuizen Lysette N. , van Wijk Diederik F. , Vink Hans , Stalmach A. , Crozier A. , Hutten B. A. , Kastelein John J. P. , Hugenholtz Paul G. , Koenig Wolfgang , Stroes Erik S. G. 
Published: June 2011

Inflammation is a hallmark of the metabolic syndrome, which also contributes to a pro-atherogenic state. NF-κB activation, a critical step in regulating inflammatory reactions, can be inhibited by polyphenol (PF) extracts, at least in vitro. In the present study, we set out to study whether a PF-rich extract could attenuate the chronic inflammatory state and/or an acute immune response in vivo in subjects with clustered metabolic risk factors. A commercially available, PF-rich extract (500 mg daily) or placebo was administered for 4 weeks to thirty-four subjects with two or more metabolic risk factors using a randomised, double-blind, cross-over design. During the final study visit, an acute inflammatory challenge (lipopolysaccharide (LPS) 1 ng/kg body weight) was administered to a random subgroup of subjects (PF-rich extract (n 12) and placebo (n 12)). The PF-rich extract modestly reduced the inflammatory chemokines monocyte chemoattractant protein 1 (MCP-1) and macrophage migration inhibitory factor (MIF) (MCP-1 − 6·5 % (PF, median 116 (interquartile range 97–136) pg/ml v. placebo, median 124 (interquartile range 105–153) pg/ml; P < 0·05); MIF − 10·8 % (PF, median 2512 (interquartile range 1898–3972) pg/ml v. placebo, median 2814·5 (interquartile range 2296–3852) pg/ml; P < 0·05); however, other measured markers of inflammation and cardiometabolic disease, such as C-reactive protein, IL-6, HDL-cholesterol, adiponectin and oxidised LDL, remained unaffected. Following the LPS challenge, we found a statistically significant 48 % reduction of MCP-1 production in the PF-rich extract group (n 12) v. placebo (n 12) over 6 h (PF 766 (sd 155) v. placebo 1466 (sd 989) ng/ml; P < 0·05, area under the curve). In conclusion, short-term oral administration of the PF-rich extract caused a modest anti-inflammatory effect in subjects with clustered metabolic risk factors. Further dose-ranging studies are needed to evaluate whether and to what extent PF-rich extracts can be used to reduce the pro-inflammatory state in subjects with metabolic diseases at increased cardiovascular risk.
On a theorem of Birch concerning sums of distinct integers taken from certain sequences
Authors: Zannier U. 
Published: June 2011

In [1] B. J. Birch, solving in the affirmative a conjecture of Erdὅs, proved the following result:Theorem 1. Let p and q be coprime integers greater than 1. Then every large natural number may be written as a sum of distinct terms of type paqb.In fact Birch pointed out that, with similar arguments, one could obtain a stronger version where the exponent b of q can be bounded in terms of p and q. The proofs were entirely elementary.
Non-commutative Noetherian Unique Factorization Domains often have stable range one
Authors: Gilchrist Martin 
Published: June 2011

Let R be a Noetherian ring. If R is commutative then (a) every non-unit is contained in a height-1 prime ideal - this is the Krull principal ideal theorem - but (b) R can have an arbitrarily large stable range. The main aim of this paper is to show that if certain non-commutative rings satisfy condition (a) then they have stable range one. We shall prove theTheorem. Let R be a Noetherian domain which is not commutative. Suppose that every non-unit of R lies in at least one height-1 prime ideal and that every height-1 prime is completely prime. Then the stable range of R is one.
Splitting ℂP∞ and Bℤ/pn into Thom spectra
Authors: Gray Brayton , Ray Nigel 
Published: June 2011

In recent years, much work in algebraic topology has been devoted to stable splitting phenomena. Often the existence of these splittings has first been detected at the cohomological level in terms of modules over the Steenrod algebra.For example, W. Richter has exhibited a decomposition of ΩSU(n) of the form(see [7]). Not only were cohomology calculations the initial evidence for this situation, but they further suggested that each summand Gk might be the Thom complex of a suitable k-plane complex vector bundle. This possibility was also verified by Mitchell.
Commutativity ofC*-algebras and associativity ofJB*-algebras
Authors: Iochum B. , Loupias G. , Rodriguez-Palacios A. 
Published: June 2011

AbstractA n.c.JB*-algebra is associative and commutative if and only if it has no non-zero nilpotent elements. This generalizes the analogous theorem of Kaplansky forC*-algebras. Different characterizations of associativity are given.
Completely positive maps which are compact from L∞ to L1
Authors: Mingo James A. 
Published: June 2011

AbstractWe define a class of completely positive maps, closed under composition, on a von Neumann algebra. We show that when the algebra has no atomic part, the correspondences associated to this class of completely positive maps are disjoint from the identity correspondence. This enables one simultaneously to generalize the statement and simplify the proof of a theorem of A. Connes and V. F. R. Jones on factors of type II1 with property T.
Bromoform concentrations in slush-layer water in Antarctic fast ice
Authors: Nomura Daiki , Ooki Atsushi , Simizu Daisuke , Fukuchi Mitsuo 
Published: June 2011

AbstractBromoform concentrations in water of the slush layer that developed at the interface between snow and sea ice were measured during the seasonal warming in Lützow-Holm Bay, East Antarctica. Mean bromoform concentration was 5.5 ± 2.4 pmol l-1, which was lower than that of the under-ice water (10.9 ± 3.5 pmol l-1). Temporal decrease in bromoform concentrations and salinity with increasing temperature of the slush water suggest that the bromoform concentrations were reduced through dilution with meltwater input from the upper surface of sea ice. In contrast, bromoform concentrations in the under-ice water increased during this period while the salinity of the under-ice water decreased. It is speculated that the sea ice meltwater input contained high bromoform concentrations from the brine channels within the sea ice and from the bottom of the ice that were contributed to the increased bromoform concentrations in the under-ice water.
What Can We Learn About the Ideology of the Newest
Supreme Court Justices?
Authors: Jessee Stephen A. , Tahk Alexander M. 
Published: June 2011

AbstractIn this article, we present a principled method for updating
estimates of the ideology of Supreme Court justices based on each
new vote they cast. We apply this method to the ideological
positions of the newly appointed members of the Court: John Roberts,
Samuel Alito, and Sonia Sotomayor. This approach allows us to gain
not only an estimate of justices' ideologies but also a greater
understanding of the level of uncertainty we should have about these
values, including how much we can learn about a new justice's views
after he or she has cast a given number of votes on the Court.