bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytosolic DNA-Activated Human Dendritic Cells Are Potent Activators of the Adaptive Immune Response
Authors: Kis-Toth Katalin , Szanto Attila , Thai To-Ha , Tsokos George C. 
Published: June 2011

Abstract
Recent studies in cell lines and genetically engineered mice have demonstrated that cytosolic dsDNA could activate dendritic cells (DCs) to become effector APCs. Recognition of DNA might be a major factor in antimicrobial immune responses against cytosolic pathogens and also in human autoimmune diseases such as systemic lupus erythematosus. However, the role of cytosolic dsDNA in human DC activation and its effects on effector T and B cells are still elusive. In this study, we demonstrate that intracellular dsDNA is a potent activator of human monocyte-derived DCs as well as primary DCs. Activation by dsDNA depends on NF-κB activation, partially on the adaptor molecule IFN-promoter stimulator-1 and the novel cytosolic dsDNA receptor IFI16, but not on the previously recognized dsDNA sentinels absent in melanoma 2, DNA-dependent activator of IFN regulatory factor 3, RNA polymerase III, or high-mobility group boxes. More importantly, we report for the first time, to our knowledge, that human dsDNA-activated DCs, rather than LPS- or inflammatory cytokine mixture-activated DCs, represent the most potent inducers of naive CD4+ T cells to promote Th1-type cytokine production and generate CD4+ and CD8+ cytotoxic T cells. dsDNA-DCs, but not LPS- or mixture-activated DCs, induce B cells to produce complement-fixing IgG1 and IgG3 Abs. We propose that cytosolic dsDNA represents a novel, more effective approach to generate DCs to enhance vaccine effectiveness in reprogramming the adaptive immune system to eradicate infectious agents, autoimmunity, allergy, and cancer.
TpF1 fromTreponema pallidumActivates Inflammasome and Promotes the Development of Regulatory T Cells
Authors: Babolin Chiara , Amedei Amedeo , Ozoliņš Dzintars , Žileviča Aija , D’Elios Mario Milco , de Bernard Marina 
Published: June 2011

AbstractHuman syphilis is a multistage disease, with diverse and wide-ranging manifestations caused by Treponema pallidum. Despite the fact that a cell-mediated immune response takes part in the course of syphilis, T. pallidum often manages to evade host immunity and, in untreated individuals, may trigger chronic infection. With this study, we demonstrate for the first time, to our knowledge, that Treponema pallidum induces a regulatory T (Treg) response in patients with secondary syphilis and we found that the miniferritin TpF1, produced by the bacterium, is able to expand this response and promote the production of TGF-β. Accordingly, TpF1 stimulates monocytes to release IL-10 and TGF-β, the key cytokines in driving Treg cell differentiation. Interestingly, we also found that TpF1 stimulates monocytes to synthesize and release several proinflammatory cytokines, such as TNF-α, IL-6, and IL-1β, the latter following the activation of the multiprotein complex inflammasome. Collectively, these data strongly support a central role for TpF1 both in the inflammation process, which occurs in particular during the early stage of syphilis, and in the long-term persistence of the spirochete within the host by promoting Treg response and TGF-β production.
The Income-Based Human Capital Valuation Methods in Public Health Economics Used by Forensic Economics
Authors: Grosse Scott D. , Krueger Kurt V. 
Published: June 2011

AbstractThis paper surveys the development of income-based human capital methods in public health economics which, with the exception of worklife expectancy, forms the methodological core of forensic economics. The main differences in the application of human capital valuation between the two disciplines are the use of statistical population averages and gross costs in public health economics and individual-specific estimates and net costs in forensic economics. The paper provides examples of the public health economics application of the human capital approach in cost-of-illness (COI) analyses of disease or injury, disability, and premature mortality with specific discussion of cerebral palsy.
Information Technology Systems for Critical Care Triage and Medical Response During an Influenza Pandemic: A Review of Current Systems
Authors: Bandayrel Kristofer , Lapinsky Stephen , Christian Michael 
Published: June 2011

AbstractObjectivesTo assess local, state, federal, and global pandemic influenza preparedness by identifying pandemic plans at the local, state, federal, and global levels, and to identify any information technology (IT) systems in these plans to support critical care triage during an influenza pandemic in the Canadian province of Ontario.MethodsThe authors used advanced MEDLINE and Google search strategies and conducted a comprehensive review of key pandemic influenza Web sites. Descriptive data extraction and analysis for IT systems were conducted on all of the included pandemic plans.ResultsA total of 155 pandemic influenza plans were reviewed: 29 local, 62 state, 63 federal, and 1 global. We found 70 plans that examined IT systems (10 local, 33 state, 26 federal, 1 global), and 85 that did not (19 local, 29 state, 37 federal). Of the 70 plans, 64 described surveillance systems (10 local, 32 state, 21 federal, 1 global), 2 described patient data collection systems (1 state, 1 federal); 4 described other types of IT systems (4 federal), and none were intended for triage.ConclusionsAlthough several pandemic plans have been drafted, the majority are high-level general documents that do not describe IT systems. The plans that discuss IT systems focus strongly on surveillance, which fails to recognize the needs of a health care system responding to an influenza pandemic. The best examples of the types of IT systems to guide decision making during a pandemic were found in the Kansas and the Czech Republic pandemic plans, because these systems were designed to collect both patient and surveillance data. Although Ontario has yet to develop such an IT system, several IT systems are in place that could be leveraged to support critical care triage and medical response during an influenza pandemic. (Disaster Med Public Health Preparedness. 2013;7:287-291)
Effects of Drying and Agglomeration on the Dissolution of Multi‐Component Food Powders
Authors: Chávez Montes E. , Dogan N. , Nelissen R. , Marabi A. , Ducasse L. , Ricard G. 
Published: June 2011

AbstractThis work proposes routes to produce dairy‐based multi‐component powders that meet nutritional and dissolution performance requirements. The effects of processing and composition on the physical properties of dairy powders were investigated and the relationship between such powder properties and dissolution performance was established. A spray‐dried milk‐based formulation was used as base powder, into which a carbohydrate, either starch or maltodextrin, was incorporated in varying proportions by dry mixing or fluid‐bed agglomeration. Physical properties such as particle size, density and flowability of the resulting powders were analyzed and particular attention was given to their dissolution behavior. Incorporation of either maltodextrin or starch in the final powder composition, without compromising the dissolution performance, was achieved by fluid‐bed agglomeration, provided that the amount of maltodextrin was less than 25 % or the amount of starch did not exceed 15 % and that the final agglomerate size was in the range of 250–300 μm.
Cation–π and anion–π interactions
Authors: Frontera Antonio , Quiñonero David , Deyà Pere M. 
Published: June 2011

AbstractIn this review, we analyze the interaction of ions with aromatic rings from several points of view. We start with a short history of cation–π and anion–π interactions and continue with a description of the main forces involved in these interactions. The comprehension of these forces allows us to rationalize the requirement that both the ion and the aromatic compound should have improved the interaction. Some physical properties of both the aromatic rings and the interacting ion are directly related with the strength of the interaction. An interesting part of this review is the study of the interplay of the ion–π interactions with other noncovalent forces. The strength of the ion–π interaction is considerably influenced by the presence of hydrogen bonding or other weaker interactions. These influences can be used to tune the interaction, either weakening or strengthening it. We give some experimental examples that illustrate this point. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 440–459 DOI: 10.1002/wcms.14This article is categorized under:

Molecular and Statistical Mechanics > Molecular Interactions
Low‐resolution structural approaches to study biomolecular assemblies
Authors: Bernadó Pau 
Published: June 2011

AbstractThe delineation of the intricate network of biomolecular interactions is currently the focus of intense scientific effort. However, a complete understanding of these processes can be achieved only from three‐dimensional structures of these interactions. High‐resolution structural biology techniques, X‐ray crystallography, and nuclear magnetic resonance (NMR) are still far from being of general application, thus highlighting the need for alternative methodologies that incorporate low‐resolution structural information to model biomolecular assemblies. This overview describes the main sources of low‐resolution data, i.e., NMR, cryo‐electron microscopy, small angle X‐ray scattering, and mass spectrometry, and examples are provided on how these data have been integrated into computational procedures. Special emphasis is given to the exploitation of the synergy of several low‐resolution data obtained from different methods. Despite low‐affinity complexes are a highly relevant family of biomolecular assemblies, their study is complicated by the presence of multiple species in solution. Examples are presented of how data measured for these complexes have been analyzed to obtain structurally valuable information. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 283‐297 DOI: 10.1002/wcms.15This article is categorized under:

Structure and Mechanism > Computational Biochemistry and Biophysics
The COSMO and COSMO‐RS solvation models
Authors: Klamt Andreas 
Published: June 2011

AbstractThe conductor‐like screening model COSMO, a variant of the dielectric continuum solvation models, has become very popular due to its algorithmic simplicity, numerical stability, and its great insensitivity with respect to outlying charge errors. The advanced model COSMO‐RS, i.e., COSMO for realistic solvation, is a statistical thermodynamics theory based on COSMO polarization charge densities, which overcomes many of the limitations and theoretical shortcomings of dielectric continuum models. Due to its ability to treat mixtures at variable temperatures, it has become very popular in chemical engineering and in wide areas of physical and medicinal chemistry. COSMO‐RS currently may be considered as the most accurate model for the prediction of solvation energies. This article provides a short description of the basic concepts of both the models, of the differences with other solvation models and of their application areas. Finally, direct COSMO‐RS, a recent direct integration of the COSMO‐RS concept into quantum chemical calculations, is briefly described. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 699–709 DOI: 10.1002/wcms.56This article is categorized under:

Molecular and Statistical Mechanics > Free Energy Methods
Møller–Plesset perturbation theory: from small molecule methods to methods for thousands of atoms
Authors: Cremer Dieter 
Published: June 2011

AbstractThe development of Møller–Plesset perturbation theory (MPPT) has seen four different periods in almost 80 years. In the first 40 years (period 1), MPPT was largely ignored because the focus of quantum chemists was on variational methods. After the development of many‐body perturbation theory by theoretical physicists in the 1950s and 1960s, a second 20‐year long period started, during which MPn methods up to order n = 6 were developed and computer‐programed. In the late 1980s and in the 1990s (period 3), shortcomings of MPPT became obvious, especially the sometimes erratic or even divergent behavior of the MPn series. The physical usefulness of MPPT was questioned and it was suggested to abandon the theory. Since the 1990s (period 4), the focus of method development work has been almost exclusively on MP2. A wealth of techniques and approaches has been put forward to convert MP2 from a O(M5) computational problem into a low‐order or linear‐scaling task that can handle molecules with thousands of atoms. In addition, the accuracy of MP2 has been systematically improved by introducing spin scaling, dispersion corrections, orbital optimization, or explicit correlation. The coming years will see a continuously strong development in MPPT that will have an essential impact on other quantum chemical methods. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 509–530 DOI: 10.1002/wcms.58This article is categorized under:

Electronic Structure Theory > Ab Initio Electronic Structure Methods
Computer‐aided synthesis design: 40 years on
Authors: Cook Anthony , Johnson A. Peter , Law James , Mirzazadeh Mahdi , Ravitz Orr , Simon Aniko 
Published: June 2011

AbstractThe discipline of retrosynthetic analysis is now just over 40 years old. From the earliest day, attempts were made to incorporate this approach into computer programs to test the extent in which chemical perception and synthetic thinking could be formalized. Despite pioneering research efforts, computer‐aided synthetic analysis failed to achieve widespread routine use by chemists, which can be attributed in part to the difficulty of building the required high‐quality retrosynthetic transform databases required for credible analyses. However, with the advent over the past 25 years of large comprehensive reaction databases, work on successfully automating the construction of reliable and comprehensive reaction rule databases is promising to revitalize research in this field. This review compares and contrasts the diverse approaches taken by selected programs in both the design and implementation of molecule feature perception and reaction rule representation, and we review the concepts of synthetic strategy selection, representation, and execution. In particular, we discuss the current work on automating the construction of reliable and comprehensive synthetic rule sets from available reaction databases in newer programs such as ARChem. We argue that the progress achieved in this aspect paves the way to a deeper exploration of computer approaches to applying strategy and control in the synthesis problem. © 2011 John Wiley & Sons, Ltd.This article is categorized under:

Computer and Information Science > Chemoinformatics
Umbrella sampling
Authors: Kästner Johannes 
Published: June 2011

AbstractThe calculation of free‐energy differences is one of the main challenges in computational biology and biochemistry. Umbrella sampling, biased molecular dynamics (MD), is one of the methods that provide free energy along a reaction coordinate. Here, the method is derived in a historic overview and is compared with related methods like thermodynamic integration, slow growth, steered MD, or the Jarzynski‐based fast‐growth technique. In umbrella sampling, bias potentials along a (one‐ or more‐dimensional) reaction coordinate drive a system from one thermodynamic state to another (e.g., reactant and product). The intermediate steps are covered by a series of windows, at each of which an MD simulation is performed. The bias potentials can have any functional form. Often, harmonic potentials are used for their simplicity. From the sampled distribution of the system along the reaction coordinate, the change in free energy in each window can be calculated. The windows are then combined by methods like the weighted histogram analysis method or umbrella integration. If the bias potential is adapted to result in an even distribution between the end states, then this whole range can be spanned by one window (adaptive‐bias umbrella sampling). In this case, the free‐energy change is directly obtained from the bias. The sampling in each window can be improved by replica exchange methods; either by exchange between successive windows or by running additional simulations at higher temperatures. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 932–942 DOI: 10.1002/wcms.66This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Vascular Constraints in Laparoscopic Renal Allograft: Comparative Analysis of Multiple and Single Renal Arteries in 976 Laparoscopic Donor Nephrectomies
Authors: Paragi Prakash R. , Klaassen Zachary , Stephen Fletcher H. , Tichauer Matthew , Chamberlain Ronald S. , Wellen Jason R. , Sun Harry , Geffner Stuart 
Published: June 2011

AbstractBackgroundSince the initial description of laparoscopic donor nephrectomy (LDN) in 1995, the field of renal transplantation has continued to evolve. Although the identification of donor kidneys with multiple renal arteries (MRA) was considered a contraindication to LDN, improvement in the surgical technique to surmount the technical challenges of LDN with MRA have been established as the skill and laparoscopic experience of transplant surgeons evolves with time. Consensus regarding LDN with MRA and recipient outcomes is not uniformly documented amongst the transplant community.MethodsA retrospective analysis of 976 patients who underwent LDN at our institution from January 1999 to August 2009 was performed. Patients were grouped based on the number of arteries and the data were compared with respect to patient demographics, operative characteristics, postoperative course and complications.ResultsThe two donor groups had comparable outcomes except for operative time, which was significantly prolonged in patients with MRA kidneys when compared to a single renal artery (SRA) kidney (P < 0.01). 1‐, 3‐year and estimated overall graft survival for the MRA recipient kidneys was significantly inferior when compared to SRA recipient kidneys.ConclusionsOur decade long experience with LDN demonstrates that operative times for MRA kidneys are longer than for SRA kidneys, however complication rates are similar. Laparoscopic donor nephrectomy with MRA is a safe and effective procedure for living kidney donation; however, the recipient graft outcomes with MRA kidneys warrant appropriate preoperative counseling of recipients.
Enclaves in Granitoids of North of Jonnagiri Schist Belt, Kurnool District, Andhra Pradesh: Evidence of Magma Mixing and Mingling
Authors: Ahmad Mansoor 
Published: June 2011

Abstract:
Calc-alkaline, metaluminous granitoids in the north of Jonnagiri schist belt (JSB) are associated with abundant mafic rocks as enclave. The enclaves represent xenoliths of the basement, mafic magmatic enclaves (MME) and synplutonic mafic dykes. The MME are mostly ellipsoidal and cuspate shape having lobate margin and diffuse contact with the host granitoids. Sharp and crenulated contacts between isolated MME and host granitoids are infrequent. The MME are fine-grained, slightly dark and enriched in mafic minerals compare to the host granitoids. MME exhibits evidences of physical interaction (mingling) at outcrop scale and restricted hybridization at crystal scale of mafic and felsic magmas. The textures like quartz ocelli, sphene (titanite) ocelli, acicular apatite inclusion zone in feldspars and K-feldspar megacrysts in MME, megacrysts across the contact of MME and host and mafic clots constitute textural assemblages suggestive of magma mingling and mixing recorded in the granitoids of the study area. The quartz ocelli are most likely xenocrysts introduced from the felsic magma. Fast cooling of mafic magma resulted in the growth of prismatic apatite and heterogeneous nucleation of titanite over hornblende in MME. Chemical transfer from felsic magma to MME forming magma envisage enrichment of silica, alkalis and P in MME. The MME show low positive Eu anomalies whereas hybrid and host granitoids display moderate negative Eu-anomalies. Synplutonic mafic dyke injected at late stage of crystallising host felsic magma, display back veining and necking along its length. The variable shape, dimensions, texture and composition of MME, probably are controlled by the evolving nature and kinematics of interacting magmas.
Environmental Impact on Groundwater of Maheshwaram Watershed, Ranga Reddy District, Andhra Pradesh
Authors: Purushotham D. , Narsing Rao A. , Prakash M. Ravi , Ahmed Shakeel , Babu G. Ashok 
Published: June 2011

Abstract:
Maheshwaram watershed is situated in Ranga Reddy district of at a distance of about 30 km south of Hyderabad. The watershed has an area of 53 km2 and has hard rock aquifers with semi-arid climate. The study area has been expanding at a fast pace and now has the distinction of being one of the fastest growing urban centers, facing the problem of groundwater depletion and quality deterioration due to the absence of perennial source of surface water and also due to over exploitation. Human activities involving industrial and agricultural development and the inadequate management of land and water resources have, directly or indirectly resulted in the degradation of environment viz. water and soil.
In the present study chemical analysis of groundwater samples of the study area, collected in pre- and post-monsoon has been carried out. The analysed data is utilized to characterize the hydro chemical process dominant in the area. Various classification methods such as Piper, Back and Hanshaw, Wilcox, U.S. Salinity Laboratory are employed to critically study the geochemical characteristics of groundwater.
Morphostratigraphy and Palaeoclimate Appraisal of the Leh Valley, Ladakh Himalayas, India
Authors: Sant Dhananjay A. , Wadhawan Sudesh K. , Ganjoo Rajinder K. , Basavaiah Nathani , Sukumaran Prabhin , Bhattacharya Sourabh 
Published: June 2011

Abstract:
In the present paper we study morphology, occurrence and mutual interrelationship of erosional (amphitheaters) and depositional landforms belonging to glacial (moraines), fluvio-glacial (glacial out wash), mass wasting (alluvial fans), aeolian (obstacle dune and sand sheets) and lacustrine (palaeo-lake sediments) processes within the Leh valley. These landforms are the geomorphic expression of past deglaciation grouped into five Formative Stages of Landform (FSL 1 to FSL 5) development in the Leh valley. The broad age bracket for the formative stages are based on the empirical relationship of the landforms, available chronology and their correlation with comparable climate phases. The retreat of glaciers in the Leh valley, along the southern slopes of Ladakh hill range and their retention over the northern slopes and Karakoram is further explained.