bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatic Blood Flow Plays an Important Role in Ischemia-Reperfusion Injury†
Authors: Kelly Dympna M. , Shiba Hiroaki , Nakagawa Shunichi , Irefin Samuel , Eghtesad Bijan , Quintini Cristiano , Aucejo Federico , Hashimoto Koji , Fung John J. , Miller Charles 
Published: August 2011

Abstract
Severe ischemia/reperfusion (IR) injury is associated with poor hepatic microperfusion. The aim of this study was to investigate the role of hepatic artery flow (HAF) and portal vein flow (PVF) in IR injury. From January 2004 to June 2008, 566 patients underwent orthotopic liver transplantation (OLT). The data were retrospectively reviewed via the transplant database. Patients with hepatic artery (HA) or portal vein (PV) thrombosis and retransplant patients were excluded. Intraoperative PVF and HAF values and graft weights were measured routinely, and the central venous pressure, mean arterial pressure, cardiac output, and cardiac index were recorded with hepatic blood flow measurements. Complete data were available for 312 primary OLT recipients (215 males and 97 females; mean age = 54 ± 10 years). The patients' follow-up ranged from 215 to 1746 days (705 ± 408 days). IR injury was defined by the aspartate aminotransferase (AST) level on postoperative day (POD) 2, and the patients were divided into 3 groups: (1) mild IR injury [AST < 500 U/L; n = 160 (51%)], (2) moderate IR injury [AST = 500-1000 U/L; n = 85 (27%)], and (3) severe IR injury [AST > 1000 U/L; n = 67 (21%)]. The demographics and pre-OLT variables (the Model for End-Stage Liver Disease score (MELD), platelet counts, PV thrombosis, transjugular intrahepatic portosystemic shunts, and shunts on computed tomography scans) were similar in all groups. The graft survival rate was 99% in group 1, 95.2% in group 2 (P = 0.02), and 92.3% in group 3 (P = 0.016). The patient survival rates were similar in the 3 groups. The cold ischemia time (CIT) was significantly higher in group 3 versus group 1 (P < 0.007). In the statistical analysis, low HAF, PVF, total liver blood flow (TLBF), and augmented HAF values were associated with a greater likelihood of elevated AST levels on POD 2. The strongest univariate predictors of AST were reduced augmented HAF (mL/minute/100 g) values (P < 0.001) and reduced TLBF (mL/minute/100 g) values (P < 0.001). In a covariate analysis with adjustments for CIT and donor variables, the blood flow parameters remained important predictors of graft function. In conclusion, this report demonstrates for the first time that reduced hepatic blood flow is a significant finding in patients with severe hepatic IR injury. Liver Transpl, 2011. © 2011 AASLD.
Discrepancies between the electronic medical record, the prescriptions in the Swedish national prescription repository and the current medication reported by patients
Authors: Ekedahl Anders , Brosius Helen , Jönsson Julia , Karlsson Hanna , Yngvesson Maria 
Published: August 2011

ABSTRACTPurposeTo study discrepancies between (i) the prescribed current treatment stated by patients with congestive heart failure (CHF) compared with patients with other chronic diseases, (ii) the data in the medication list (ML) in the electronic medical record and (iii) the data in the prescription list (PL) on the prescriptions stored in the national prescription repository in Sweden, to determine current, noncurrent, duplicate and missing prescriptions.MethodsAt one healthcare centre, a random sample of patients 18 years and older with a diagnosis of CHF, diabetes mellitus (DM) or osteoarthritis (OA) provided written informed consent to participate. Participants were interviewed by telephone on the prescribed current treatment.ResultsOf 161 invited patients (61 CHF, 50 DM and 50 OA), 66 patients were included. More than 80% of the patients had at least one discrepancy, a noncurrent, a duplicate or a missing prescription, in the ML and PL. The overall congruence for unique prescriptions on current treatment between the ML and the PL was only 55%. Patients with CHF had overall more discrepancies and patients with DM fewer discrepancies in the ML.ConclusionsPrescriptions for noncurrent treatment, duplicates and missing prescriptions are common in both the ML in the electronic medical record and the list on prescriptions stored in the Swedish National Prescription Repository. Patients with CHF had more discrepancies in the ML. The risk for medication errors in primary care due to incorrect information on prescribed treatment may be substantial. Copyright © 2011 John Wiley & Sons, Ltd.
Direct evidence that the carboxyl‐terminal sequence of a bacterial chemoreceptor is an unstructured linker and enzyme tether
Authors: Bartelli Nicholas L. , Hazelbauer Gerald L. 
Published: August 2011

AbstractSensory adaptation in bacterial chemotaxis involves reversible methylation of specific glutamyl residues on chemoreceptors. The reactions are catalyzed by a dedicated methyltransferase and dedicated methylesterase. In Escherichia coli and related organisms, control of these enzymes includes an evolutionarily recent addition of interaction with a pentapeptide activator located at the carboxyl terminus of the receptor polypeptide chain. Effective enzyme activation requires not only the pentapeptide but also a segment of the receptor polypeptide chain between that sequence and the coiled‐coil body of the chemoreceptor. This segment has features consistent with a role as a flexible and presumably unstructured linker and enzyme tether, but there has been no direct information about its structure. We used site‐directed spin labeling and electron paramagnetic resonance spectroscopy to characterize structural features of the carboxyl‐terminal 40 residues of E. coli chemoreceptor Tar. Beginning ∼ 35 residues from the carboxyl terminus and continuing to the end of the protein, spectra of spin‐labeled Tar embedded in native membranes or in reconstituted proteoliposomes, exhibited mobilities characteristic of unstructured, disordered segments. Binding of methyltransferase substantially reduced mobility for positions in or near the pentapeptide but mobility for the linker sequence remained high, being only modestly reduced in a gradient of decreasing effects for 10–15 residues, a pattern consistent with the linker providing a flexible arm that would allow enzyme diffusion within defined limits. Thus, our data identify that the carboxyl‐terminal linker between the receptor body and the pentapeptide is an unstructured, disordered segment that can serve as a flexible arm and enzyme tether.
Mitochondria‐Targeting Single‐Walled Carbon Nanotubes for Cancer Photothermal Therapy
Authors: Zhou Feifan , Wu Shengnan , Wu Baoyan , Chen Wei R. , Xing Da 
Published: August 2011

AbstractNanomaterials have recently attracted much attention as efficient transducers for cancer photothermal therapy, based on their intrinsic absorption properties in the near‐infrared region. This study explores a novel therapy model with mitochondria‐targeting single‐walled carbon nanotubes (SWNTs), which act efficiently to convert 980‐nm laser energy into heat and selectively destroy the target mitochondria, thereby inducing mitochondrial depolarization, cytochrome c release, and caspase 3 activation. The laser+SWNTs process affords remarkable efficacy in suppressing tumor growth in a breast cancer model, and results in complete tumor regression in some cases. Laser+SWNTs could prove to be a promising selective local treatment modality, while minimizing adverse side effects.
Acetylcholine α7 nicotinic and dopamine D2 receptors are targeted to many of the same postsynaptic dendrites and astrocytes in the rodent prefrontal cortex
Authors: Duffy Aine M. , Fitzgerald Megan L. , Chan June , Robinson Danielle C. , Milner Teresa A. , Mackie Kenneth , Pickel Virginia M. 
Published: August 2011

AbstractThe alpha‐7 nicotinic acetylcholine receptor (α7nAChR) and the dopamine D2 receptor (D2R) are both implicated in attentional processes and cognition, mediated in part through the prefrontal cortex (PFC). We examined the dual electron microscopic immunolabeling of α7nAChR and either D2R or the vesicular acetylcholine transporter (VAChT) in rodent PFC to assess convergent functional activation sites. Immunoreactivity (ir) for α7nAChR and/or D2R was seen in the same as well as separate neuronal and glial profiles. At least half of the dually labeled profiles were somata and dendrites, while most labeled axon terminals expressed only D2R‐ir. The D2R‐labeled terminals were without synaptic specializations or formed inhibitory or excitatory‐type synapses with somatodendritic profiles, some of which expressed the α7nAChR and/or D2R. Astrocytic glial processes comprised the majority of nonsomatodendritic α7nAChR or α7nAChR and D2R‐labeled profiles. Glial processes containing α7nAChR‐ir were frequently located near VAChT‐labeled terminals and also showed perisynaptic and perivascular associations. We conclude that in rodent PFC α7nACh and D2R activation can dually modulate (1) postsynaptic dendritic responses within the same or separate but synaptically linked neurons in which the D2R has the predominately presynaptic distribution, and (2) astrocytic signaling that may be crucial for synaptic transmission and functional hyperemia. Synapse, 2011. © 2011 Wiley‐Liss, Inc.
Mining flexible‐receptor molecular docking data
Authors: Machado Karina S. , Winck Ana T. , Ruiz Duncan D. , Norberto de Souza Osmar 
Published: August 2011

AbstractKnowledge discovery in databases has become an integral part of practically every aspect of bioinformatics research, which usually produces, and has to process, very large amounts of data. Rational drug design is one of the current scientific areas that has greatly benefited from bioinformatics, particularly a step, which analyzes receptor–ligand interactions via molecular docking simulations. An important challenge is the inclusion of the receptor flexibility since they can become computationally very demanding. We have represented this explicit flexibility as a series of different conformations derived from a molecular dynamics simulation trajectory of the receptor. This model has been termed as the fully flexible receptor (FFR) model. In our studies, the receptor is the enzyme InhA from Mycobacterium tuberculosis, which is the major drug target for the treatment of tuberculosis. The FFR model of InhA (named FFR_InhA) was docked to four ligands, namely, nicotinamide adenine dinucleotide, pentacyano(isoniazid)ferrate II, triclosan, and ethionamide, thus, generating very large amounts of data, which needs to be mined to produce useful knowledge to help accelerate drug discovery and development. Very little work has been done in this area. In this article, we review our work on the application of classification decision trees, regression model tree, and association rules using properly preprocessed data of the FFR molecular docking results, and show how they can provide an improved understanding of the FFR_InhA‐ligand behavior. Furthermore, we explain how data mining techniques can support the acceleration of molecular docking simulations of FFR models. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 532–541 DOI: 10.1002/widm.46This article is categorized under:

Algorithmic Development > Biological Data Mining
Technologies > Data Preprocessing
Invariant diagrams with data refinement
Authors: Preoteasa Viorel , Back Ralph-Johan 
Published: August 2011

Abstract

Invariant based programming
is an approach where we start to construct a program by first identifying the basic situations (pre- and post-conditions as well as invariants) that could arise during the execution of the algorithm. These situations are identified before any code is written. After that, we identify the transitions between the situations, which will give us the flow of control in the program. Data refinement is a technique of building correct programs working on concrete data structures as refinements of more abstract programs working on abstract data types. We study in this paper data refinement for invariant based programs and we apply it to the construction of the classical Deutsch–Schorr–Waite graph marking algorithm. Our results are formalized and mechanically proved in the Isabelle/HOL theorem prover.
Comparison of microbial hosts and expression systems for mammalian CYP1A1 catalysis
Authors: Cornelissen Sjef , Julsing Mattijs K , Schmid Andreas , Bühler Bruno 
Published: August 2011

Abstract
Mammalian cytochrome P450 enzymes are of special interest as biocatalysts for fine chemical and drug metabolite synthesis. In this study, the potential of different recombinant microorganisms expressing rat and human cyp1a1 genes is evaluated for such applications. The maximum specific activity for 7-ethoxyresorufin O-deethylation and gene expression levels were used as parameters to judge biocatalyst performance. Under comparable conditions, E. coli is shown to be superior over the use of S. cerevisiae and P. putida as hosts for biocatalysis. Of all tested E. coli strains, E. coli DH5α and E. coli JM101 harboring rat CYP1A1 showed the highest activities (0.43 and 0.42 U gCDW −1, respectively). Detection of active CYP1A1 in cell-free E. coli extracts was found to be difficult and only for E. coli DH5α, expression levels could be determined (41 nmol gCDW −1). The presented results show that efficient expression of mammalian cyp1a1 genes in recombinant microorganisms is troublesome and host-dependent and that enhancing expression levels is crucial in order to obtain more efficient biocatalysts. Specific activities currently obtained are not sufficient yet for fine chemical production, but are sufficient for preparative-scale drug metabolite synthesis.
Clonal integration in Fragaria vesca growing in metal‐polluted soils: parents face penalties for establishing their offspring in unsuitable environments
Authors: Roiloa Sergio R. , Retuerto Rubén 
Published: August 2011

AbstractClonal plants often establish descendent ramets in sites with contrasting presence of favourable and unfavourable factors. Connections between ramets allow translocation of essential resources from established ramets to developing ramets and, as consequence, integration confers net benefits to ramets growing under unfavourable conditions. Therefore, integrated ramets may survive in habitat patches that would be lethal to independent ramets or non‐clonal plants. This experiment aimed to investigate the physiological and morphological responses of the clonal plant Fragaria vesca growing in heterogeneous substrate with patches of contrasting quality (i.e. uncontaminated or heavy‐metal‐contaminated). We observed that parents reduced their photosynthetic efficiencies and growth as consequence of maintaining their offspring. This cost did not affect survival of the parents. Physiological integration brings about benefits to offspring ramets growing both at uncontaminated and heavy‐metal‐contaminated soils. The benefits of integration were detected in both physiological and morphological traits, enhancing the survivorship of offspring ramets in the Cu‐polluted soils. We conclude that integration improves the performance of developing ramets of F. vesca growing in heavy‐metal‐contaminated habitats, allowing clone systems to overcome the establishment risks and maintain their presence in these less favourable sites.
Lipoic Acid Attenuates Innate Immune Infiltration and Activation in the Visceral Adipose Tissue of Obese Insulin Resistant Mice
Authors: Deiuliis J. A. , Kampfrath T. , Ying Z. , Maiseyeu A. , Rajagopalan S. 
Published: August 2011

AbstractVisceral adipose inflammation mediated by innate and adaptive immune alterations plays a critical role in diet‐induced obesity and insulin resistance (IR). The dietary supplement α‐lipoic acid (αLA) has been shown to ameliorate inflammatory processes in macrophages, however the relative significance of these effects in the context of visceral adipose inflammation and IR remain unknown. In this study we investigated its effects via both intraperitoneal and oral administration in lean and obese transgenic mice expressing yellow fluorescent protein (YFP) under control of a monocyte specific promoter (c‐fmsYFP+). αLA significantly improved indices of insulin‐resistance concomitant with a decrease in total (YFP+CD11b+) and activated (YFP+CD11b+CD11c+) visceral adipose tissue macrophages. Histologically, the visceral adipose tissue of obese mice receiving αLA had fewer “crown‐like structures,” a hallmark of adipose inflammation in murine obesity. Monocyte adhesion assessed by intravital microscopy of cremasteric venules was attenuated by αLA. In cultured WT and toll‐like receptor 4 (TLR4) null primary mouse macrophages, αLA significantly decreased basal CCR‐2, MCP‐1 and TNF‐α expression levels. LPS treatment resulted in increased TNFα, MCP‐1, and IL‐6 expression while αLA partially abrogated the LPS effect on MCP‐1 and TNFα; Interestingly, CCR‐2 was not coordinately regulated. AαLA prevented LPS‐induced nuclear factor kappa B (NFκB) activation in the same cultured macrophages. These data suggest that αLA may modulate visceral adipose inflammation, a critical determinant of IR via TLR4 and NF‐κB pathways.
Ethnic Enclaves and the Earnings of Immigrants
Authors: Xie Yu , Gough Margaret 
Published: August 2011

AbstractA large literature in sociology concerns the implications of immigrants’ participation in ethnic enclaves for their economic and social well-being. The “enclave thesis” speculates that immigrants benefit from working in ethnic enclaves. Previous research concerning the effects of enclave participation on immigrants’ economic outcomes has come to mixed conclusions as to whether enclave effects are positive or negative. In this article, we seek to extend and improve upon past work by formulating testable hypotheses based on the enclave thesis and testing them with data from the 2003 New Immigrant Survey (NIS), employing both residence-based and workplace-based measures of the ethnic enclave. We compare the economic outcomes of immigrants working in ethnic enclaves with those of immigrants working in the mainstream economy. Our research yields minimal support for the enclave thesis. Our results further indicate that for some immigrant groups, ethnic enclave participation actually has a negative effect on economic outcomes.
Metropolitan Structure and Neighborhood Attainment: Exploring Intermetropolitan Variation in Racial Residential Segregation
Authors: South Scott J. , Crowder Kyle , Pais Jeremy 
Published: August 2011

AbstractUsing data from the 1981, 1991, and 2001 waves of the Panel Study of Income Dynamics and several decennial censuses, we examine how characteristics of metropolitan areas are associated with black and white households’ neighborhood racial composition. Results from hierarchical linear models show that about 20% to 40% of the variation in the percentage of households’ tract population that is non-Hispanic white or non-Hispanic black exists across metropolitan areas. Over time, white households’ exposure to non-Hispanic white neighbors has declined, and their exposure to non-Hispanic black neighbors has increased; the reverse trends are observed for blacks. These trends cannot be attributed to changes in the ecological structure of metropolitan areas. Blacks have fewer white neighbors in large metropolitan areas containing sizable minority populations, and blacks have more white neighbors in metropolitan areas with high government employment. Whites have more black neighbors in metropolitan areas with high levels of government employment and ample new housing; whites have fewer black neighbors in metropolitan areas with a high level of municipal fragmentation. The association between metropolitan-area percentage black and tract percentage black is weaker among whites than among blacks, suggesting that whites are especially motivated to self-segregate in metropolitan areas with large black populations.
Commutability of homogenization and linearization at identity in finite elasticity and applications
Authors: Gloria Antoine , Neukamm Stefan 
Published: August 2011

We prove under some general assumptions on elastic energy densities (namely, frame indifference, minimality at identity, non-degeneracy and existence of a quadratic expansion at identity) that homogenization and linearization commute at identity. This generalizes a recent result by S. Müller and the second author by dropping their assumption of periodicity. As a first application, we extend their

Γ

-convergence commutation diagram for linearization and homogenization to the stochastic setting under standard growth conditions. As a second application, we prove that the

Γ

-closure is local at identity for this class of energy densities.

Résumé

Nous démontrons que linéarisation et homogénéisation commutent à lʼidentité sous des hypothèses générales sur la densité dʼénergie élastique (à savoir indifférence matérielle, minimalité à lʼidentité, non-dégénérescence et existence dʼun développement quadratique à lʼidentité). Ceci généralise un résultat récent de S. Müller et du second auteur au cas non-périodique. En particulier, nous étendons au cas de lʼhomogénéisation stochastique leur diagramme de commutation de la linéarisation et de lʼhomogénéisation au sens de la

Γ

-convergence. Par ailleurs, nous démontrons que la

Γ

-fermeture est locale à lʼidentité pour la classe de densités dʼénergie non convexes considérée.
Does selection or genetic drift explain geographic differentiation of morphological characters in house sparrowsPasser domesticus?
Authors: HOLAND ANNA M. , JENSEN HENRIK , TUFTO JARLE , MOE RUNE 
Published: August 2011

SummaryUnderstanding the relative influence of genetic drift and selection is fundamental in evolutionary biology. The theory of neutrality predicts that the genetic differentiation of a quantitative trait (QST) equals the genetic differentiation at neutral molecular markers (FST) if the quantitative trait has not been under selection. Thus, the relative magnitude of observedQSTand expectedQSTunder neutral expectations suggests the importance of selection and genetic drift for any observed phenotypic divergence. BecauseQSTis based on additive genetic variance, estimatingQSTbased on phenotypic measurements is problematic due to unknown environmental effects. To account for this, we used a model where the environmental component was allowed to vary when estimatingQST. The model was used on data from 14 house sparrow (Passer domesticus) populations in Norway. In accordance with the significant phenotypic inter-population differences our analyses suggested that directional selection may have favoured different optimal phenotypes for some morphological traits across populations. In particular, different body mass and male ornamental phenotypes seemed to have been favoured. The conclusions are, however, dependent on assumptions regarding the proportion of the observed inter-population variation that is due to additive genetic differences, showing the importance of collecting such information in natural populations. By estimatingQST, allowing the additive genetic proportion of phenotypic inter-population variation to vary, and by making use of recent statistical methods to compare observedQSTwith neutral expectations, we can use data that are relatively easy to collect to identify adaptive variation in natural populations.