bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cancer Systems Biology: Current Achievements in – Omics Data Analysis, Network Reconstruction and Mathematical Modelling
Authors: Vera Julio , Wolkenhauer Olaf , Schmitz Ulf 
Published: August 2014

Abstract

Systems biology is a multidisciplinary methodology in which quantitative biological experimental data are dissected using mathematical modelling and other computational and network biology tools, aiming at understanding the structure, function and dynamical regulation of biochemical networks. Systems biology will play a major role in the future molecular and clinical oncology because (a) it can be used for the analysis of cancer‐relevant high‐throughput data, (b) it provides tools for the reconstruction of the large multilevel regulatory networks that govern critical cancer phenotypes and (c) it is necessary when investigating cancer‐relevant networks holding multiple overlapping nonlinear regulatory motifs like feedback and feedforward loops. Here, the value of the systems biology approach in handling cancer genomics and transcriptomics data, the reconstruction of cancer networks and the use of mathematical modelling in the elucidation of cancer networks as well as in the design of anticancer therapies are discusses. Some recent case studies as proof of principle are highlighted.

Key Concepts:

Systems biology is a multidisciplinary approach that involves the analysis of quantitative experimental data via mathematical modelling and computational and network biology.

Modelling of cancer‐related networks is necessary because these networks display multiple nonlinear regulatory motifs like feedback loops.

Mathematical models have been used to elucidate the structure, dynamics, dysregulation and crosstalk of cancer pathways like the JAK/STAT, p53, MAPK, NFkB and intrinsinc/extrinsic apoptosis signalling pathways, as well as in microRNA cancer regulation.

Multi‐scale mathematical models can accurately describe the spatial configuration of tumours, their crosstalk with the surrounding microenvironment and their role in physiological mechanisms like angiogenesis and immune system response.

Mathematical modelling has been used to assess and personalise conventional anticancer therapies, but it is also used in the detection of new anticancer drug targets and the development of combined or immune therapies.

Cancer bioinformatics facilitates efficient analyses and integration of diverse types of biomedical high‐throughput data for the elucidation of causes of tumour initiation, progression and metastasis but also for the management, storage and exchange of experimental and clinical data.

Cancer systems biology integrates algorithms, methodologies, software tools and web resources into customised analysis workflows to explore and understand the molecular mechanisms underlying this complex disease.

Data integration and analysis is used to identify novel robust and precise biomarkers, to identify network biomarkers and to design individual patient‐tailored therapeutic interventions.
Structure–Function Relationships in the Aromatic Amino Acid Hydroxylases Enzyme Family: Evolutionary Insights
Authors: Skjærven Lars , Teigen Knut , Martinez Aurora 
Published: August 2014

Abstract

The nonheme iron and tetrahydrobiopterin dependent aromatic amino acid hydroxylases (AAAHs) comprise a family of enzymes that catalyse the hydroxylation of
l
‐Phe,
l
‐Tyr and
l
‐Trp. These reactions are of central physiological importance. Consequently, dysfunction of the AAAHs is associated with serious disorders, that is, the genetic metabolic disease phenylketonuria for phenylalanine hydroxylase (PAH), and neurological and neuropsychiatric disorders for tyrosine hydroxylase (TH) and tryptophan hydroxylase 1 and 2 (TPH1, TPH2). Mammalian AAAHs are tetrameric proteins that present a three‐domain structure with a remarkable high similarity, in particularly for the catalytic domains. Structural analyses have provided valuable insights on the effect of disease‐associated mutations, mechanism of catalysis, the determinants for substrate specificity and regulation of enzymatic activity. The best characterised AAAH is PAH, which also seems to be the precursor of the family. The AAAHs have developed sophisticated regulatory mechanisms during evolution to control substrate
l
‐Phe (PAH), catecholamine (TH), serotonin and melatonin (TPHs) levels.

Key Concepts:

The aromatic amino acid hydroxylases (AAAHs) are tetrahydrobiopterin (BH
4
) dependent enzymes that use dioxygen as additional substrate.

The AAAHs are involved in serious inborn errors of metabolism with neuronal impact.

The AAAHs are highly homologous, contain a catalytic mononuclear nonheme iron coordinated by a 2‐His‐1‐carboxylate facial triad and show similar reaction mechanism.

Metazoans have at least three AAAH genes: phenylalanine hydroxylase (
PAH
), tyrosine hydroxylase (
TH
) and tryptophan hydroxylase(s) (
TPH
(s)), where
PAH
appears as the precursor of the family.

Mammalian PAH, TH, TPH1 and TPH2 are tetrameric, with a three‐domain subunit structure; substrate specificity is provided by the catalytic domain.

The AAAHs are highly regulated by mechanisms at the transcriptional, translational, posttranslational and allosteric levels.

Evolutionary adaptation of the enzymes is most evident at the regulatory mechanisms, along the complexity of the organisms, especially of the central nervous system (CNS).
Ionic liquids as novel solvents for the synthesis of sugar fatty acid ester
Authors: Mai Ngoc Lan , Ahn Kihun , Bae Sang Woo , Shin Dong Woo , Morya Vivek Kumar , Koo Yoon‐Mo 
Published: August 2014

AbstractSugar fatty acid esters are bio‐surfactants known for their non‐toxic, non‐ionic, and high biodegradability . With great emulsifying and conditioning effects, sugar fatty acids are widely used in the food, pharmaceutical, and cosmetic industries. Biosynthesis of sugar fatty acid esters has attracted growing attention in recent decades. In this study, the enzymatic synthesis of sugar fatty acid esters in ionic liquids was developed, optimized, and scaled up. Reaction parameters affecting the conversion yield of lipase‐catalyzed synthesis of glucose laurate from glucose and vinyl laurate (i.e. temperature, vinyl laurate/glucose molar ratio, and enzyme loads) were optimized by response surface methodology (RSM). In addition, production was scaled up to 2.5 L, and recycling of enzyme and ionic liquids was investigated. The results showed that under optimal reaction conditions (66.86 °C, vinyl laurate/glucose molar ratio of 7.63, enzyme load of 73.33 g/L), an experimental conversion yield of 96.4% was obtained which is close to the optimal value predicted by RSM (97.16%). A similar conversion yield was maintained when the reaction was carried out at 2.5 L. Moreover, the enzymes and ionic liquids could be recycled and reused effectively for up to 10 cycles. The results indicate the feasibility of ionic liquids as novel solvents for the biosynthesis of sugar fatty acid esters.
High‐Throughput Screening Technology for Automotive Applications
Authors: Sundermann Andreas , Gerlach Olga 
Published: August 2014

AbstractThe development of advanced emission control systems to meet the strict regulations requires efficient and flexible material screening capabilities. Here, a high throughput test unit is described. Two case studies demonstrate the rapid screening of relevant parameter spaces and material functionalities which can be used in product development. One involves steady‐state testing of hydrocarbon oxidation in Diesel aftertreatment systems, while the other shows the evaluation of oxygen storage capacity in the optimization of three‐way catalysts for gasoline engines.
Ionic‐Liquid‐Assisted Metal‐Free Oxidative Coupling of Amines To Give Imines
Authors: Monopoli Antonio , Cotugno Pietro , Iannone Francesco , Ciminale Francesco , Dell'Anna Maria Michela , Mastrorilli Piero , Nacci Angelo 
Published: August 2014

AbstractAn oxidative coupling of amines to give imines in ionic liquids (ILs) under metal‐free aerobic conditions has been developed. The high efficiency achievable in ILs is mechanistically explained in terms of activation of the starting materials (benzylamine and molecular oxygen) by an initial electron transfer, promoted by the ionic nature of the solvent. Reactivity data of variously p‐substituted benzylamines show a general deactivating effect, which would imply a change in the rate‐determining step in the reaction mechanism.
Palladium‐Catalyzed Regioselective 5‐exo‐O‐Cyclization/Oxidative Heck Cascades from o‐Alkynylbenzamides and Electron‐Deficient Alkenes
Authors: Madich Youssef , Álvarez Rosana , Aurrecoechea José M. 
Published: August 2014

AbstractA Pd‐catalyzed 5‐exo‐selective oxycyclization/oxidative Heck coupling cascade is described, starting from readily available ortho‐alkynylbenzamides and functionalized olefins. The key to a high regioselectivity in the cyclization step is the choice of catalyst and/or additives. Thus, Pd(OAc)2 provides the desired 5‐exo products predominantly, whereas with PdCl2 or Pd(TFA)2, the corresponding 6‐endo products prevail. The subsequent oxidative Heck‐type coupling takes place stereoselectively with the very predominant formation of E isomers, leading to an effective preparation of structurally diverse carbonyl‐substituted allylideneisobenzofuranimines.
General Suzuki Coupling of Heteroaryl Bromides by Using Tri‐tert‐butylphosphine as a Supporting Ligand
Authors: Zou Yinjun , Yue Guizhou , Xu Jianwei , Zhou Jianrong (Steve) 
Published: August 2014

AbstractA general procedure for the fast Suzuki coupling of major families of heteroaryl bromides was realized by using Pd(OAc)2/PtBu3 as the catalyst. Many couplings were finished within minutes at room temperature in n‐butanol. Different from previous studies, three typical heteroaryl bromides were systematically examined in couplings of various heteroaryl and aryl boronic acids.
Modified extended BDF scheme for the discontinuous Galerkin solution of unsteady compressible flows
Authors: Nigro A. , Ghidoni A. , Rebay S. , Bassi F. 
Published: August 2014

SUMMARYIn this paper, a high‐order DG method coupled with a modified extended backward differentiation formulae (MEBDF) time integration scheme is proposed for the solution of unsteady compressible flows. The objective is to assess the performance and the potential of the temporal scheme and to investigate its advantages with respect to the second‐order BDF. Furthermore, a strategy to adapt the time step and the order of the temporal scheme based on the local truncation error is considered. The proposed DG‐MEBDF method has been evaluated for three unsteady test cases: (i) the convection of an inviscid isentropic vortex; (ii) the laminar flow around a cylinder; and (iii) the subsonic turbulent flow through a turbine cascade. Copyright © 2014 John Wiley & Sons, Ltd.
Microwave heating and hydrolysis of rubber wood biomass in ionic liquids
Authors: Darji Dazylah , Alias Yatimah , Mohd Som Fauzi , Abd Razak Nurul Hainiza 
Published: August 2014

AbstractBACKGROUNDBiomass from rubber wood has been gaining interest due to its availability and relative economic value. However it is difficult to separate the biomass using common solvents due to its complicated structure. The recent application of ionic liquids as reaction solvents has offered a new platform for its efficient utilization. The dissolution of biomass in ionic liquid via microwave has been investigated to reduce the dissolution time.RESULTSThe pretreatment involves dissolving the biomass in various ionic liquids under domestic microwave radiation. The dissolution rate is dependent on the type of ionic liquid and biomass was found to be easily dissolved in acetate based imidazolium ionic liquid. The highest (up to 85%) substantial dissolution of rubber biomass was reached in 1‐ethyl‐3‐methylimidazolium acetate [C2mim][OAc] and 1‐butyl‐3‐methylimidazolium acetate [C4mim][OAc]. Furthermore, the amount of glucose resulting from pretreatment with [C2mim] [OAc] and [C4mim][OAc] was also higher than that from pretreatment with cloride anion. This is due to changes in physico chemical properties such as decreasing crystallinity in biomass as confirmed by XRD, TGA and FTIR analyses.CONCLUSIONAnion acetate based imidazolium ionic liquid was discovered to be a good solvent for the dissolution of rubber biomass under microwave irradiation for converting cellulose to glucose. © 2014 Society of Chemical Industry
Evaluating radiographers' diagnostic accuracy in screen‐reading mammograms: what constitutes a quality study?
Authors: Debono Josephine C. , Poulos Ann E. 
Published: August 2014

AbstractIntroductionThe aim of this study was to first evaluate the quality of studies investigating the diagnostic accuracy of radiographers as mammogram screen‐readers and then to develop an adapted tool for determining the quality of screen‐reading studies.MethodsA literature search was used to identify relevant studies and a quality evaluation tool constructed by combining the criteria for quality of Whiting, Rutjes, Dinnes et al. and Brealey and Westwood. This constructed tool was then applied to the studies and subsequently adapted specifically for use in evaluating quality in studies investigating diagnostic accuracy of screen‐readers.ResultsEleven studies were identified and the constructed tool applied to evaluate quality. This evaluation resulted in the identification of quality issues with the studies such as potential for bias, applicability of results, study conduct, reporting of the study and observer characteristics. An assessment of the applicability and relevance of the tool for this area of research resulted in adaptations to the criteria and the development of a tool specifically for evaluating diagnostic accuracy in screen‐reading.ConclusionsThis tool, with further refinement and rigorous validation can make a significant contribution to promoting well‐designed studies in this important area of research and practice.
Prebiotic potential of Jerusalem artichoke (Helianthus tuberosus L.) in Wistar rats: effects of levels of supplementation on hindgut fermentation, intestinal morphology, blood metabolites and immune response
Authors: Samal Lipismita , Chaturvedi Vishwa Bandhu , Saikumar Guttula , Somvanshi Ramesh , Pattanaik Ashok Kumar 
Published: August 2014

AbstractBACKGROUNDMany studies have been conducted using purified prebiotics such as inulin or fructooligosaccharides (FOS) as nutraceuticals, but there is very little information available on the prebiotic potential of raw products rich in inulin and FOS, such as Jerusalem artichoke (JA; Helianthus tuberosus L.). The present experiment aimed to evaluate the prebiotic effects of JA tubers in rats.RESULTSSeventy‐two Wistar weanling rats divided into four groups were fed for 12 weeks on a basal diet fortified with pulverized JA tubers at 0 (control), 20, 40 and 60 g kg−1 levels. Enhanced cell‐mediated immunity in terms of skin indurations (P = 0.082) and CD4+ T‐lymphocyte population (P = 0.002) was observed in the JA‐supplemented groups compared with the control group. Blood haemoglobin (P = 0.017), glucose (P = 0.001), urea (P = 0.004) and calcium (P = 0.048) varied favourably upon inclusion of JA. An increasing trend (P = 0.059) in the length of large intestine was apparent in the JA‐fed groups. The tissue mass of caecum (P = 0.069) and colon (P = 0.003) was increased in the JA‐supplemented groups, accompanied by higher (P = 0.007) caecal crypt depth. The pH and ammonia concentrations of intestinal digesta decreased and those of lactate and total volatile fatty acids increased in the JA‐fed groups.CONCLUSIONThe results suggest that JA had beneficial effects on immunity, blood metabolites, intestinal morphometry and hindgut fermentation of rats. © 2014 Society of Chemical Industry
EFFECTS OF CRUSHED MAIZE STRAW RESIDUES ON SOIL BIOLOGICAL PROPERTIES AND SOIL RESTORATION
Authors: Tejada M. , Benítez C. 
Published: August 2014

ABSTRACTAgriculture soils in the Mediterranean need restoration and rehabilitation after 10 millenia of use and abuse. Maize straw residues crushed at three sizes [<1 (C1), 1–10 (C2) and >10 cm (C3)] at 5 Mg ha−1 y−1 and with and without urea (150 kg N ha−1) were applied during a period of 3 years for the purpose of restoration of a Typic Xerofluvent located near Córdoba (Spain). The effect on the vegetal cover and biological properties (microbial biomass, soil respiration and enzymatic activities) were determined. The size of the crushed maize residues (particle size <1 cm) and N supply influenced in the evolution of soil biological properties and vegetal cover. The stimulation of microbial biomass, soil respiration, dehydrogenase, urease, β‐glucosidase, phosphatase and arylsulphatase activities was higher in C1 + N‐amended soils for 14·9%, 16·3%, 8·8%, 24·3%, 13·5%, 7·1% and 10·3%, respectively, compared with C2 + N and for 25·8%, 26·9%, 18·3%, 38·5%, 28·2%, 19·1% and 18·3%, respectively, compared with C3 + N. Vegetal cover from the C1 + N treatment was 11·4%, 17·8%, 29·4%, 37·6%, 44·9% and 75·1% greater than that in C2 + N, C3 + N, C1, C2, C3 and control soil. These results suggested that under dry climatic conditions, the application of crushed maize straw finely crushed + N fertilizers improved the soil biological properties and also favour the appearance of spontaneous vegetation, which will protect the soil and will contribute to its restoration. Consequently, the addition of the crushed maize straw finely crushed + N fertilizers may be considered a good environmental strategy for recovery of degraded soils. Copyright © 2014 John Wiley & Sons, Ltd.
Why do fish strand? An analysis of ten years of flow reduction monitoring data from the Columbia and Kootenay rivers, Canada
Authors: Irvine R. L. , Thorley J. L. , Westcott R. , Schmidt D. , DeRosa D. 
Published: August 2014

AbstractStranding of fish due to flow reductions has been documented in the near shore of the Columbia and Kootenay Rivers, Canada, and can result in sub‐lethal or lethal effects on fish. Ten years (1999–2009) of monitoring data have been collected at sites below two hydro‐electric dams (Hugh‐L‐Keenleyside and Brilliant Dam) following flow reductions. A generalized linear mixed effects model analysed the probability of a stranding event in relation to environmental and operational variables including the rate of change in the water levels, the duration of shoreline inundation prior to a reduction (wetted history), the river stage, the magnitude of the reduction, distance downstream from the dam, time of day, day of year (season) and whether a site had been physically altered to mitigate stranding. The results demonstrated statistically significant effects on stranding risk from minimum river stage, day of the year and whether a site had been physically re‐contoured. The combination of investigated factors giving the highest probability of stranding was a large magnitude reduction completed in the afternoon in midsummer, at low water levels when the near shore had been inundated for a long period. This research is significant in its approach to assessing years of ecosystem scale monitoring data and using the modelling results to determine ways for these findings to be applied in regulated river management to minimize fish stranding. It also highlighted data gaps that require addressing and provides ecosystem scale results to compare with stranding studies carried out in mesocosms. © 2014 The Authors. River Research and Applications published by John Wiley & Sons Ltd.
Psychosexual Symptoms and Treatment of Peyronie's Disease Within a Collaborative Care Model
Authors: Hartzell Rose 
Published: August 2014

AbstractIntroductionPeyronie's disease (PD) can be emotionally and sexually debilitating for patients and may negatively impact partner relationships.AimsThis study aims to present an ongoing collaborative care model for patients with PD and to discuss the critical need for integration of patient care among sexual medicine physicians and mental health practitioners or sex therapists.MethodsPubMed searches using the terms “Peyronie's disease” and “natural history,” “treatment,” “psychosexual,” “depression,” “relationship,” and “partner” were conducted. Expert opinion based on review of the relevant published literature and clinical experience was used to identify meaningful treatment targets for patients with PD within a collaborative care model.Main Outcome MeasureCharacteristics of PD, medical treatment, and important assessment and treatment targets, including physical, emotional, psychosexual, and relationship concerns, from peer-reviewed published literature and clinical experience.ResultsPD can result in significant patient and partner distress and relationship disruption. Sex therapy interventions may be directed at acute emotional, psychosexual, and relationship problems that occur during the initial diagnosis of PD, the period following minimally invasive or surgical treatment for PD, or recurring problems over the lifelong course of the disease. Sex therapy to improve self-acceptance, learn new forms of sexual intimacy, and improve communication with partners provides comprehensive treatment targeting emotional, psychosexual, and relationship distress. Ongoing communication between the mental health practitioner and physician working with the patient with PD about key assessments, treatment targets, and treatment responses is necessary for coordinated treatment planning and patient care.ConclusionsMen with PD are more likely now than in the past to see both a sexual medicine physician and a mental health practitioner or sex therapist, and the integration of assessments and treatment planning is essential for optimal patient outcomes.
Does human predation risk affect harvest susceptibility of white‐tailed deer during hunting season?
Authors: Little Andrew R. , Demarais Stephen , Gee Kenneth L. , Webb Stephen L. , Riffell Samuel K. , Gaskamp Joshua A. , Belant Jerrold L. 
Published: August 2014

ABSTRACTLarge carnivores are considered a primary source of mortality for many ungulate populations, but harvest by hunters is the primary means of population management. However, research is needed to evaluate how human predation risk influences observability (a surrogate to harvest susceptibility) of ungulates. We determined how hunting intensity and duration influence observation rates of white‐tailed deer (Odocoileus virginianus) and how deer behavior (i.e., movement rate and resource selection) affects observation rates. We sampled 37 adult (≥2 yr) male deer at 2 levels of risk (i.e., low‐risk = 1 hunter/101 ha; and high‐risk = 1 hunter/30 ha) during 3 exposure periods (i.e., first, second, and third weekend of hunting) on a 1,861‐ha property in Oklahoma, USA, during the 2008 and 2009 rifle deer‐seasons. Observation rates (collared deer/hunter‐hr/day) were greatest during the first weekend in both the low‐ and high‐risk treatments, but declined each weekend thereafter in both treatments. Immediately prior to hunter observation, movement rate of observed collared deer was greater than that of unobserved collared deer, but only when hunting risk was high. Greater movement rates of deer in the high‐risk treatment also led to a greater probability of observation. Hunters also had a greater probability of observing collared deer at higher elevations. Overall, deer modified their behavior to avoid detection by hunters. These results can be used to explain decreased observation rates to hunters and to modify harvest rates by altering timing and intensity of human predation risk during the recreational hunting season to help achieve population management goals through harvest. © 2014 The Wildlife Society.