bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of potential obese-specific biomarkers and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy
Authors: Yang Yongli , Wang Xiaoyi , Li Mingli , Wang Shuyan , Wang Huiyu , Chen Qiang , Lu Shaoxiong
Published: May 2024

Abdominal subcutaneous fat deposition (ASFD) is not only related to meat quality in the pig industry but also to human health in medicine. It is of great value to elucidate the potential molecular mechanisms of ASFD. The present study aims to identify obese-specific biomarkers and key pathways correlated with ASFD in pigs. The ASF-related mRNA expression dataset GSE136754 was retrieved from the Gene Expression Omnibus (GEO) database and systematically analyzed using a comprehensive bioinformatics method. A total of 565 differentially expressed genes (DEGs) were identified between three obese and three lean pigs, and these DEGs were mainly involved in the p53 signaling pathway, MAPK signaling pathway and fatty acid metabolism. A protein-protein interaction (PPI) network, consisting of 540 nodes and 1,065 edges, was constructed, and the top ten genes with the highest degree scores—ABL1, HDAC1, CDC42, HDAC2, MRPS5, MRPS10, MDM2, JUP, RPL7L1 and UQCRFS1—were identified as hub genes in the whole PPI network. Especially HDAC1, MDM2, MRPS10 and RPL7L1 were identified as potential robust obese-specific biomarkers due to their significant differences in single gene expression levels and high ROC area; this was further verified by quantitative real-time PCR (qRT-PCR) on abdominal subcutaneous fat samples from obese-type (Saba) and lean-type (Large White) pigs. Additionally, a mRNA-miRNA-lncRNA ceRNA network consisting of four potential biomarkers, 15 miRNAs and 51 lncRNAs was established, and two targeted lncRNAs with more connections, XIST and NEAT1, were identified as potentially important regulatory factors. The findings of this study may provide novel insights into the molecular mechanism involved in ASFD.
Effectiveness of in-group versus individually administered pain neuroscience education on clinical and psychosocial outcomes in patients with chronic low back pain: randomized controlled study protocol
Authors: Salazar-Méndez Joaquín , Cuyul-Vásquez Iván , Ponce-Fuentes Felipe , Núñez-Cortés Rodrigo , Mendez-Rebolledo Guillermo , Fuentes Jorge
Published: May 2024

Objective

(1) This trial will compare the clinical and psychosocial effectiveness of in-group and individually pain neuroscience education (PNE) in patients with chronic low back pain (CLBP). In addition, (2) the influence of social determinants of health on post-treatment results will be analyzed.

Methods

A three-arm randomized controlled trial will be conducted. Sixty-nine participants with CLBP will be recruited in a 1:1:1 ratio. Participants, assessor, and statistician will be blinded to group assignment. The PNE intervention will be adapted to the context of the participants. An experimental group (n = 33) will receive PNE in an in-group modality, the other experimental group (n = 33) will receive PNE in an individually modality and the control group (n = 33) will continue with usual care. Additionally, participants will be encouraged to stay active by walking for 20–30 min 3–5 times per week and will be taught an exercise to improve transversus abdominis activation (bracing or abdominal following). The outcome measures will be fear avoidance and beliefs, pressure pain threshold, pain self-efficacy, catastrophizing, pain intensity, and treatment expectation. Outcome measures will be collected at one-week before intervention, immediately post-intervention, and four-weeks post-intervention.

Conclusion

The innovative approach of PNE oriented to fear beliefs proposed in this study could broaden the application strategies of this educational therapeutic modality. Impact. Contextualized PNE delivered by physical therapist could be essential to achieve a good cost-effectiveness ratio of this intervention to improve the clinical condition of people with CLBP.
Research Trends on Living Donors for Liver Transplantation: A Text Network Analysis and Topic Modeling
Authors: Choi Seongmi , Kim Mihui , Seo Won Jin
Published: May 2024

Purpose: This study aimed to identify research topics and trends on living liver donors over time through text network analysis and topic modeling.Methods: Five electronic databases (PubMed, CINAHL, Embase, Web of Science, and PsycINFO) were reviewed for studies published through September 2023, and 392 studies were included. Text network analysis was used to identify the basic characteristics and centrality of the network. The topics were named after extracting meaningful topics through topic modeling using latent Dirichlet allocation.Results: A total of 1,111 keywords were extracted from the abstracts of 392 selected studies, among which “length of stay,” “morbidity,” “mortality,” “pain,” and “quality of life” showed high frequency and centrality. Through topic modeling analysis, the following four topics were derived: objective health indicators (topic 1), subjective health indicators (topic 2), hepatobiliary-related indicators (topic 3), and early health indicators (topic 4). An analysis of trends in these topics over time showed that the proportion of topics 1, 3, and 4 increased or remained stable. In contrast, there was no significant change in topic 2, representing subjective health indicators.Conclusion: This study explored research trends on living liver donors using text network analysis and topic modeling. Based on the main topics derived, research on postoperative outcomes for living liver donors has focused on objective health indicators, hepatobiliary-related indicators, and early health indicators compared to subjective health indicators. We suggest that future studies utilize integrated indicators of physical and psychosocial aspects.
Trends in Changes of Cognition, Depression, Physical Performance, and Activities of Daily Living among People with Dementia Attending Dementia Specific Day Care
Authors: Kim Hwasoon , Park Miyoun , Park Min-Ji , Lee Hae Ri , Jeong Ji Hye , Heo Jiyoung
Published: May 2024

Purpose: This study aimed to identify trends in changes of cognitive function, physical function, depression, and activities of daily living (ADL) among people with dementia who had used day care centers for at least 12 months, through the analysis of data collected from day care center records.Methods: The participants in this descriptive survey were 63 older people with dementia. Data were collected from two dementia day care centers located in Incheon city. General characteristics and disease related characteristics were analyzed in terms of the frequency, percentage, mean, and standard deviation. Correlations between major variables were analyzed using Pearson correlation coefficient. Cognitive function, depression, physical performance, and ADL were analyzed using the mean, standard deviation, Wilcoxon signed-rank test, and Friedman test.Results: The mean age of the participants was 77.33±6.73 years (range, 58 to 91 years) when they began attending the centers. Cognitive function significantly increased at 3 months (18.63±5.06), 6 months (18.73±5.20), and 12 months (18.63±5.43) compared to baseline (17.41±4.77). Depression significantly decreased at 3 months(2.94±2.96), 6 months (3.13±3.14), and 12 months (2.81±3.27) compared to baseline (5.20±3.87). At 3 months, 6 months, and 12 months, the physical function score (respectively 10.19±2.90, 10.33±2.84, 10.11±2.55) increased significantly compared to baseline (9.13±3.01). ADLs decreased at 3 months (8.51±1.92), 6 months (8.67±2.12), and 12 months (8.89±2.19) compared to baseline (8.41±1.88).Conclusion: Without receiving customized day care service for dementia, cognitive function and physical function will decline and depressive feelings will increase. Therefore, delaying cognitive decline, reducing depression, and improving physical function through the use of day care services, especially at an early stage are essential to strengthen and maintain aging in place.
Mediating Effect of Academic Emotion Regulation on the Relationship Between Self-Determined Learning Motivation and Learning Flow in Nursing Students in Remote Online Classes
Authors: Jo Eunhee , Hwang Soon-Jung
Published: May 2024

Purpose: This descriptive research study explores the relationship between remote online classes, nursing students’ self-determined learning motivation and learning flow, to identify the mediating effect of academic emotion regulation.Methods: The study sample comprised 147 third- and fourth-year nursing students from two universities in Jeonbuk State, all of whom had clinical practice experience. Descriptive statistics, independent t-tests, and one-way analysis of variance were conducted using SPSS/WIN 23.0 for data analysis. Hayes’ PROCESS macro Version 3.5 was used to verify the significance of the indirect effects of the variables.Results: Self-determined learning motivation had a significant positive effect on the mediating variable, academic emotion regulation(β=.21, p=.001), and on learning flow. Additionally, academic emotion regulation significantly positively influenced learning flow. When considering the mediating effect of academic emotion regulation, the indirect effect size between self-determined learning motivation and learning flow was .07, with a bootstrapping confidence interval ranging from 0.02 to 0.13, excluding zero, which was statistically significant, indicating a mediating effect.Conclusion: The findings confirm that academic emotion regulation is a crucial variable that can enhance students’ learning flow, thereby maximizing educational effectiveness during rapid changes in online education methods. Consequently, educational programs should be developed that consider the emotional aspects of learning to improve academic emotion regulation. Furthermore, universities should establish educational policies and measures that expand various digital education platforms to reflect and respond to the online education environment.
Efectos de Bioestimulantes en la Mitigación del Estrés Hídrico y Optimización del Nitrógeno en Vitis vinifera: Un Análisis de Crecimiento y Rendimiento
Authors:   , Maluenda Electorat Gaspar
Published: May 2024

En el contexto de una crisis medioambiental global, las prácticas de fertilización nitrogenada en aumento exacerban la situación. El empleo excesivo de fertilizantes interrumpe el ciclo natural del nitrógeno, generando impactos negativos en el medio ambiente y comprometiendo la salud humana. Paralelamente, la escasez hídrica se ha consolidado como una preocupación creciente a nivel global, especialmente para los productores agrícolas. Esta investigación evaluó la eficacia de dos bioestimulantes comerciales diseñados para abordar estas problemáticas: BlueN, que utiliza Methylobacterium symbioticum para fijar nitrógeno atmosférico, y Sosdia Stress Plus, dirigido a ajustar el potencial osmótico de la planta ante condiciones adversas. El estudio se centró en su aplicación en Vitis vinífera en dos áreas dedicadas a la producción de uva vinífera y una a la uva de mesa, midiendo su influencia en el crecimiento y rendimiento.Los resultados revelaron que BlueN generó impactos positivos en ambos tipos de uvas, incrementando el peso de las bayas y el rendimiento. En algunos casos, se observaron tendencias al aumento del diámetro y ancho de los brotes. Aunque las plantas no presentaron cambios en su contenido nutricional, el incremento en el tamaño de las bayas y el rendimiento sugieren que BlueN podría estar actuando más como un promotor hormonal que como un simple fertilizante.En lo que respecta a Sosdia Stress Plus, se identificaron leves reducciones en el potencial hídrico foliar que se asociaron con un menor crecimiento de los brotes. A nivel vegetativo y productivo, este producto no mostró diferencias notables. Sin embargo, es importante considerar que las condiciones climáticas podrían haber influido significativamente en el desarrollo del ensayo, dado que las elevadas temperaturas durante esta temporada ejercieron un estrés considerable en las plantas.
Museo de la Construcción Textil: de la fibra a la arquitectura al vestuario
Authors:   , Lillo Yévenes Belén
Published: May 2024

El texto analiza la evolución de los museos a lo largo del tiempo, desde los primeros gabinetes de curiosidades hasta las modernas instituciones del siglo XXI, destacando su transformación en espacios culturales públicos que buscan educar, inspirar y entretener a una audiencia diversa. Esta evolución ha sido impulsada por cambios sociales, políticos y tecnológicos, así como por una creciente especialización temática y una arquitectura museística más innovadora que se ha convertido en un símbolo cultural en muchas ciudades.Especialmente en el ámbito de la indumentaria, se observa una tendencia hacia la especialización con la creación de museos dedicados a la moda y los textiles, que ofrecen una visión profunda y contextualizada de la historia y evolución de lo textil a lo largo del tiempo. Estos museos no solo exhiben prendas históricas, sino que también exploran la conexión entre la moda, la cultura y la sociedad, enriqueciendo nuestra comprensión de la indumentaria como fenómeno cultural en constante transformación.La propuesta para la construcción de un Museo del Textil en la exfábrica de Caffarena en el barrio Yungay de Santiago ejemplifica esta evolución y especialización, fusionando historia, arquitectura y cultura para preservar y celebrar la rica tradición textil de Chile. Este proyecto no solo busca revitalizar un importante patrimonio industrial en el barrio, sino también crear un espacio cultural dinámico que se integre con otros espacios cercanos, enriqueciendo la oferta de la ciudad.
Using image schemas to develop spaciotemporal conceptualizations in the learning of English phrasal verbs with off during reading comprehension tasks
Authors:   ,   Pontificia Universidad Católica de Chile. Facultad de Letras, Contreras Armijo Javier Andrés
Published: May 2024

The Chilean educational system, for years, has emphasized the relevance of developing a communicative approach to teach English as a Foreign Language in our classrooms. In fact, most of the curricular adjustments over the past 15 years, have turned to promoting English educational settings in the light of tasks that can consider the four language skills to engage students and facilitate learning. However, there seems to be a great distance from these goals and the actual practices and strategies developed by national academic programs. This situation has done nothing but to increase an already worrying reality regarding rote-learning strategies to teach grammatical structures, the overall preference of focusing on prescriptive methods rather than descriptive ones and classrooms centered on learning grammatical structures on a side, and communicative skills on the other. Therefore, the aim of this study is to develop a teaching strategy for phrasal verbs with off in the light of reading comprehension tasks. Also, that image schemas and Cognitive Linguistics principles facilitate the learning of structures that commonly are associated with random meanings and memory-based skills to learn them. The study, practices and instruments were designed following mixed-method principles to collect both quantitative and qualitative data to analyze results. Our research concluded that image schemas do not only facilitate the learning of phrasal verbs with off but, also, have a long-term effect on memory. Moreover, the use of reading comprehension tasks promotes learning of these structures and the understanding of non-adapted material in the EFL classrooms.
Osteopenia in HIV Positive Patients After 8 Months on Tenofovir: A Case Study
Authors: Geetha Karra , Sakshi R. , Chandana T. , Chandu Ch. Sai , Ramarao T.
Published: May 2024

Tenofovir, a nucleotide reverse transcriptase inhibitor, is a key component of highly active antiretroviral therapy (HAART) for HIV infection. While effective in suppressing viral replication, long-term use of tenofovir has been associated with adverse effects, including bone mineral density (BMD) loss and increased risk of osteopenia and osteoporosis. Tenofovir-induced osteopenia is a significant concern in the management of HIV-infected individuals, as it can lead to increased fracture risk and reduced quality of life.
We present the case of a 40-year-old female patient with HIV who was on a Tenofovir disoproxil fumarate (TDF)-containing regimen consisting ofTenofovir disoproxil fumarate, lamivudine, dolutegravir (TLD) for 8 months and developed symptoms suggestive of osteopenia. The patient presented with difficulty in walking, knee pain and swelling, hip joint pain, and limited left arm mobility, which had significantly impacted her daily activities, leading to her being bedridden for two months. Laboratory findings revealed reduced BMD in the lumbar spine and femoral neck, along with low serum vitamin D levels, supporting the diagnosis of tenofovir-induced osteopenia. The management of tenofovir-induced osteopenia involves discontinuation of TDF and initiation of alternative antiretroviral therapy, as well as supplementation with calcium and vitamin D. In this case, the patient was switched to abacavir, lamivudine, and dolutegravir, which are not associated with significant bone-related side effects. Calcium and vitamin D supplementation were also prescribed to improve bone health. This case highlights the importance of monitoring bone health in patients on TDF therapy and prompt recognition and management of osteopenia to prevent further bone loss and improve quality of life in these patients. Regular assessment of BMD and serum vitamin D levels is essential to detect osteopenia early and initiate appropriate interventions.
Effect of Growth Regulator and Anti-oxidant on Fruit Quality of Litchi (Litchi chinensis) cv. Bombai Grown in New Alluvial Zone of West Bengal
Authors: De Madhumita , Sen Ritwika , Dey Susmita , Datta Soustav , Rathour T.P. , Datta Pallab , Sinha Gayatri , Paul Mouli , Lal Deepa , Chawla Ritik
Published: May 2024

An investigation was carried out at the Horticultural Research Station, Mondouri, Bidhan Chandra Krishi Viswavidyalaya, West Bengal to evaluate the impact of growth regulators as well as anti-oxidant on the fruit quality and yield of 15 years old litchi plants cv. Bombai. The experiment was set up using a Randomized Block Design (RBD) with 7 treatments [GA3 (20 ppm), GA3 (40 ppm), Citric Acid (200 ppm), Citric Acid (400 ppm), NAA (25 ppm), NAA (50 ppm), Control (Water spray)] and 3 replications. The spray solutions of several plant growth regulators and antioxidant were applied immediately after flowering. Results showed that treatment with growth regulator NAA and antioxidant Citric acid significantly improved fruits' physical and bio-chemical quality compared to the Control group. Among the different treatments, NAA 50 ppm is considered to be the best treatment considering all the quality parameters, i.e., maximum fruit weight (24.92 g), fruit length (4.82 cm) as well as diameter (3.99 cm), fruit retention at harvest (23.77 panicle-1) and yield (94.82 kg plant-1). This treatment also showed maximum TSS (19.6°Brix), total sugar (14.11%), reducing sugar (11.12%) and TSS: acidity (81.66). Finally, it can be concluded that NAA 50 ppm applied immediately after flowering was found to be the most superior in improving the morphological characters and bio-chemical constituents of fruits that can be selected for further improvement.
Performance of Different Hybrids of Sponge Gourd (Luffa cylindrica L.) in Terms of Growth, Yield and Quality
Authors: Mohanty Deepali Mahima , Topno Samir E. , Bahadur Vijay
Published: May 2024

The present investigation was carried out at the Department of Horticulture, Naini Agricultural Institute, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, Uttar Pradesh during the year 2023-24 with a view to check the performance of different hybrids of sponge gourd in terms of growth, yield and quality. Hybrids comprised of H1 (AVT-1 2021/SPGHYB-1), H2 (AVT-1 2021/SPGHYB-2), H3 (AVT-1 2021/SPGHYB-3), H4 (AVT-1 2021/SPGHYB-4), H5 (AVT-1 2021/SPGHYB-5), H6 (AVT-1 2021/SPGHYB-6), H7 (GENNEXT Ayushi) and H8 (VNR Alok). Among the different hybrids VNR Alok performs best in terms of growth parameters like early germination, maximum vine length, flowering parameters like earliness in flowering and maturity, yield parameters like early fruit setting, maximum length of fruit, early harvesting, highest fruit yield/ha and quality parameters like Vit-C and TSS. Maximum B:C ratio was obtained in the same hybrid.
In vitro Assessment of Fungicides against Alternaria alternata Causing Leaf Spot of Okra
Authors: Choudhary Ajay , Panchouli Lokesh Kumar
Published: May 2024

The present investigation was undertaken to test the efficacy of some promising fungicides for its effective management against leaf spot of okra under in vitro. Okra is affected by several fungal, bacterial, viral and nematode induced diseases. Alternaria alternata attacked old leaves and progress upwards. In initial stage of infection small, scattered, brown colored necrotic spots with concentric rings appeared on older leaves that later enlarged in size and these spots were accompanied by narrow chlorotic margins.Diseased stem and leaves of okra, showing characteristic symptoms of Alternaria blight were collected from the vegetable field of JNKVV, Jabalpur. Based on present investigation it could be concluded that among the Nine chemical fungicides namely Tebuconazole, Hexaconazole, Mencozeb, Copper oxychloride, Carbandazim, Thiram, Propiconazole, Copper oxychloride + Carbandazim and captan + Hexaconazole showed the best result with the maximum inhibition in growth of A. alternata was recorded by Propiconazole (100 %) followed by Tebuconazole (86.02 %) at all the concentrations. This finding will be greatly helpful to okra growers by integrating with different management strategies for the purpose of control of okra leaf spot of okra in field condition which may impart positive impact.
COMPARAÇÃO ENTRE PLACAS ESTABILIZADORAS PRODUZIDAS POR IMPRESSÃO 3D E O MÉTODO CONVENCIONAL: UMA REVISÃO INTEGRATIVA DE LITERATURA
Authors: Matos Beserra Vitória , Barreto Costa Carmo Alessandra , Magalhães Ana Raquel , Santos Oliveira Thaís , Carvalho de Lima Porto Edla , Amorim Helfenstein Alexandra
Published: May 2024

Objetivo: Analisar características das placas estabilizadoras produzidas por impressão tridimensional (3D), comparando-as com as produzidas pelo método convencional. Materiais e Métodos: Uma revisão integrativa de literatura foi realizada através das bases de dados Medline/Pubmed, BVS (Biblioteca Virtual em Saúde), SciELO e Google acadêmico, seguindo diretrizes do PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses). Na seleção dos artigos, os descritores utilizados foram Bruxism, CAD/CAM, Printing Three-Dimensional, Acrylic Resins, dentro da faixa temporal 2013 a 2023. Resultados: Após um levantamento nas bases de dados e retirada das duplicatas, foram identificados 1.880 artigos. Os textos completos de 78 publicações foram examinados e, 16 incluídos ao final. Duas revisões de literatura sobre as placas CAD/CAM, cinco estudos clínicos comparando as placas impressas com as convencionais e nove estudos in vitro que comparam as características mecânicas e de biocompatibilidade das placas. Considerações finais: Neste estudo constatou-se que as placas estabilizadoras impressas são biocompatíveis, necessitam de ajustes oclusais mínimos e têm uma melhor precisão na adaptação, comparadas às convencionais. Em contrapartida, as convencionais apresentam melhor resistência à flexão, menor envelhecimento hidrotérmico e maior resistência ao desgaste, o que resulta em maior durabilidade. Essas propriedades fazem com que as placas de acrílico, produzidas de forma convencional, sejam ainda as priorizadas na terapia oclusal do bruxismo.
Rubber, 9. Chemicals and Additives
Authors: Engels Hans‐Wilhelm , Weidenhaupt Herrmann‐Josef , Pieroth Manfred , Hofmann Werner , Menting Karl‐Hans , Mergenhagen Thomas , Schmoll Ralf , Uhrlandt Stefan
Published: June 2011

The article contains sections titled:

1.Introduction2.Vulcanization Chemicals2.1.Basics of Vulcanization2.2.Sulfur‐Containing Cross‐Linking Agents2.3.Vulcanization Accelerators2.3.1.Classes of Accelerators2.3.2.Toxicology and Ecology of Organic Vulcanization Accelerators2.3.3.Delivery Forms of Vulcanization Accelerators2.4.Accelerator Activators2.5.Sulfur‐Free Cross‐Linking Agents2.5.1.Peroxides (Organic Peroxides and Peroxycarboxylic Acids)2.5.2.Quinone Dioxime2.5.3.Polymethylolphenol Resins2.5.4.Other Cross‐Linking Agents2.5.5.Radiation Cross‐Linking2.6.Vulcanization Retarders3.Antidegradants3.1.Appearance of Aging and Fatigue3.2.Classification and Types of Antidegradants3.2.1.Staining Antidegradants that Act as Anti‐Flex‐Cracking Agents and Antiozonants3.2.2.Staining Antidegradants with Protection against Fatigue, but Not against Ozone3.2.3.Staining Antidegradants with Little or No Protection against Fatigue and None against Ozone3.2.4.Nonstaining Antidegradants with Protection against Fatigue or Ozone3.2.5.Nonstaining Antidegradants without Protection against Fatigue or Ozone3.2.6.Nonstaining Antiozonants without Protection against Aging3.2.7.Other Antidegradants3.3.Choice of Antidegradants4.Fillers and Pigments4.1.Typical Properties and Types of Fillers4.1.1.Action of Fillers4.1.2.Properties of Fillers and Their Significance4.2.Carbon Blacks4.3.White Fillers4.3.1.Precipitated Silicas4.3.1.1.Production4.3.1.2.Physicochemical Properties4.3.1.3.Commercial Products4.3.1.4.Essentials of Rubber Silicas4.3.2.Inactive White Fillers4.3.3.Coating of Fillers4.4.Pigments4.4.1.White Pigments4.4.2.Inorganic Colored Pigments4.4.3.Organic Colored Pigments4.5.Organic Fillers5.Plasticizers5.1.General5.2.Mineral Oils5.3.Synthetic Plasticizers5.4.Natural Products6.Processing Additives6.1.Behavior and Classification of Processing Additives6.2.Peptizers6.3.Dispersing Agents and Lubricants6.4.Homogenizers6.5.Tackifiers6.6.Release Agents6.6.1.Batch‐Off Release Agents6.6.2.Mold Release Agents6.6.3.Release Agents for Special Applications6.6.3.1.Mandrel Release Agents6.6.3.2.Bladder Release Agents6.6.3.3.Inside Tire Paint6.6.3.4.Outside Tire Paints6.7.Other Processing Additives7.Rubber Adhesion7.1.Adhesion of Rubber to Reinforcing Materials7.2.Rubber – Metal Bond8.Chemical Blowing Agents8.1.Cellular Rubber Articles8.2.Product Types and Properties9.Latex Chemicals10.Flameresistant Rubber Articles10.1.Combustion Process in Polymeric Materials10.2.Testing of Flammability10.3.Inhibition of Combustion
Modeling the Moisture Content Distribution over a Rotating Porous Cylinder using Markov Chains
Authors: Mizonov V. , Zaitsev V. , Volynskii V. , Leznov V.
Published: June 2011

The objective of this study is to describe moisture distribution in a rotating porous cylinder. Variable orientation of the gravitational and centrifugal forces during rotation causes rather complex, unsteady distribution of the moisture content. The optimal speed of rotation which provides the minimum nonhomogeneity of the distribution can be found. A cell model for this purpose is proposed. The model is based on the theory of Markov chains. Transition probabilities in the chain of cells are conditioned by pure diffusion and convection caused by the forces. The basic features of the process are investigated and the optimal process parameters are found.
Experimental and Numerical Investigation of Pressure Swirl Atomizers
Authors: Renze P. , Heinen K. , Schönherr M.
Published: June 2011

The prediction of droplet size distributions for atomization nozzles is important for process design and improvement of industrial spraying processes. However, especially for non‐Newtonian liquids, the published research applicable for engineering purposes is rare. To derive fundamental correlations for droplet size distributions in the future, the multiphase flow inside the spray nozzle is investigated by computational fluid dynamics, and measurements of droplet size distributions are done under the same flow conditions. In the present paper, two different hollow‐cone nozzles were investigated using the volume‐of‐fluid method with large‐eddy turbulence modeling inside the open source software OpenFOAM®. An experimental test rig suitable for spraying organic solvents was built.
Impact of Storage Duration on the Gaseous Emissions during Convective Drying of Urban Residual Sludges
Authors: Fraikin L. , Salmon T. , Herbreteau B. , Levasseur J.‐P. , Nicol F. , Crine M. , Léonard A.
Published: June 2011

Drying has become an important step within the context of sludge management. Sometimes, sludges from several wastewater treatment plants are centralized in order to dry them at an acceptable cost. Depending on sludge supply, there can be a delay between delivery and feeding into the dryer. The impact of sludge storage duration on the drying kinetics and on the exhaust emissions of volatile organic compounds (VOCs), and ammonia is investigated. Results show that, after 20 days of storage, the drying time is multiplied by 1.5, and the emissions of VOCs and NH3 are multiplied by 5 and 40, respectively.
One‐pot synthesis of a new antifungal polymerisable monomer and its characterisation by coordination‐ion spray mass spectrometry
Authors: Zerbib C. , Amigoni S. , Taffin de Givenchy E. , Massi L. , Precheur I. , Guittard F.
Published: June 2011

We have investigated the synthesis of a new antifungal agent with a polymerisable moiety for the prevention of denture stomatisis. Nystatin (antifungal polyene) is modified in one step by reaction with isocyanatoethylmethacrylate to afford a new polymerisable antifungal agent in good yield (90%). In order to prove the monografting of the acrylate derivative and to localise the new group in the skeleton of the molecule, a rapid and efficient analytical method involving electrospray ionisation mass spectrometry (ESI‐MS) was developed for the study. In view of the structures of such antifungal agents, their complexation with metal cations was investigated by Coordination‐Ion Spray Mass Spectrometry (CIS‐MS). This mass spectrometry study covers two aspects: improving the MS signal to overcome the low ionisation efficiency in ESI‐MS and exploring the complexation behaviour of the induced structure to optimise the antifungal properties. Copyright © 2011 John Wiley & Sons, Ltd.
Time‐resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media
Authors: Chippendale Thomas W. E. , Španěl Patrik , Smith David
Published: June 2011

Preliminary measurements have been made of the volatile compounds emitted by the bacterium E. coli JM109 cultured in the commonly used media Dulbecco's modified Eagle's medium (DMEM) and lysogeny broth (LB) using selected ion flow tube mass spectrometry, SIFT‐MS, as a step towards the real time, non‐invasive monitoring of accidental infections of mammalian cell cultures. In one procedure, the culture medium alone and the E. coli cells/medium combination were held at 37°C in bottles sealed with septa for a given time period, usually overnight, to allow the bacterium to proliferate, after which the captured headspace was analysed directly by SIFT‐MS. Several compounds were seen to be produced by the E. coli cells that depended on the liquid medium used: when cultured in DMEM, copious amounts of ethanol, acetaldehyde and hydrogen sulphide were produced; in LB ammonia is the major volatile product. In a second procedure, to ensure aerobic conditions prevailed in the cell culture, selected volatile compounds were monitored by SIFT‐MS in real time for several hours above the open‐to‐air E. coli/DMEM culture held at close to 37°C. The temporal variations in the concentrations of some compounds, which reflect their production rates in the culture, indicate maxima. Thus, the maxima in the ethanol and acetaldehyde production are a reflection of the reduction of glucose from the DMEM by the vigorous E. coli cells and the maximum in the hydrogen sulphide level is an indication of the loss of the sulphur‐bearing amino acids from the DMEM. Serendipitously, emissions from DMEM inadvertently infected with the bacterium C. testosteroni were observed when large quantities of ammonia were seen to be produced. The results of this preliminary study suggest that monitoring volatile compounds might assist in the early detection of bacterial infection in large‐scale bioreactors. Copyright © 2011 John Wiley & Sons, Ltd.
Outstanding challenges in protein–ligand docking and structure‐based virtual screening
Authors: Waszkowycz Bohdan , Clark David E. , Gancia Emanuela
Published: June 2011

With an ever‐increasing number of protein structures being solved by X‐ray crystallography, the use of protein–ligand docking algorithms to assess candidate ligands for a binding site has become commonplace. In particular, over the last decade, high‐throughput docking has been widely applied to the virtual screening of large chemical databases for supporting hit‐finding programs in drug discovery. However, the techniques and practice of protein–ligand docking in general, and of structure‐based virtual screening in particular, are still evolving and significant limitations remain to be addressed. In this review, we seek to highlight some of the active areas of research and debate in this promising, but challenging, field. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 229–259 DOI: 10.1002/wcms.18

This article is categorized under:

Structure and Mechanism > Computational Biochemistry and Biophysics
Hydrocarbon σ‐radical cations
Authors: Shubina Tatyana E. , Fokin Andrey A.
Published: June 2011

The structure and transformations of radical cations derived from saturated hydrocarbons in the gas phase and solution may be, in most cases, predicted with high‐level computational methods. The review covers so‐called sigma‐radical cations, i.e., the species with partially broken CH and CC bonds. The radical cations formed from the small acyclic (methane, ethanes, and butanes), as well as cyclic (cyclopropane, cyclobutane, and rotanes) and polycyclic hydrocarbons were analyzed. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 661–679 DOI: 10.1002/wcms.24

This article is categorized under:

Structure and Mechanism > Molecular Structures
Diversity selection algorithms
Authors: Gillet Valerie J.
Published: June 2011

Molecular diversity has been an important topic in chemoinformatics for the last two decades following the introduction of high‐throughput screening and combinatorial chemistry techniques. This article reviews the main algorithms that have been developed for assessing the diversity of a set of compounds and for selecting a diverse subset of compounds from a larger library. Particular focus is given to recent trends including the use of scaffolds as a way of assessing molecular diversity and the importance now given to optimizing multiple properties simultaneously in an attempt to reduce late stage attrition during the drug development stage of drug discovery. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 580‐589 DOI: 10.1002/wcms.33

This article is categorized under:

Computer and Information Science > Chemoinformatics
The Cambridge Structural Database: experimental three‐dimensional information on small molecules is a vital resource for interdisciplinary research and learning
Authors: Groom Colin R. , Allen Frank H.
Published: June 2011

Crystal structure determination is the method of choice for the analysis of novel chemical compounds from monatomic metals to proteins and viruses, with some 700,000 crystal structures published so far. Of these, over 500,000 (70%) are carbon‐containing organic and metal‐organic small molecules, for which experimental three‐dimensional (3D) numerical results are stored in the Cambridge Structural Database (CSD), together with two‐dimensional chemical structure information and text and numerical fields that record chemical and physical properties. The CSD is fully searchable using an Internet search engine or specialist‐distributed software that provides advanced facilities for structure display and data analysis, including many special features for understanding molecular recognition processes such as protein–ligand interactions. Two knowledge bases derived from the CSD provide immediate access to information on intramolecular geometry and intermolecular interactions. CSD information is heavily used in academic and industrial research that relies on knowledge of 3D molecular geometry and intermolecular interactions, for example, in structural chemistry and biology, drug discovery, materials design and development, and in crystallography itself. As a teaching tool, the CSD has a fundamental role to play in illustrating the 3D chemical concepts that are essential for those who study chemistry as a principal or subsidiary subject. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 368–376 DOI: 10.1002/wcms.35

This article is categorized under:

Computer and Information Science > Chemoinformatics
First‐principles prediction of acidities in the gas and solution phase
Authors: Ho Junming , Coote Michelle L.
Published: June 2011

This paper provides an overview of contemporary computational protocols toward accurate prediction of acidities in the gas and aqueous phase. The performance of various density functional theory (DFT) methods and ab initio composite procedures, such as the G3MP2(+) method, for the prediction of gas‐phase acidities of a range of neutral and cationic acids is presented. Various methods for solution pKa predictions are also reviewed where the emphasis is on thermodynamic cycle‐based methods that combine ab initio or experimental gas‐phase energies with solvation free energies from continuum solvent models. The prediction of accurate solvation free energies, especially for ionic species, represents the bottleneck for accurate pKa prediction via the direct or absolute method. The success and limitations of alternative thermodynamic cycles are discussed and some of the difficulties and future challenges associated with the applications of these methods on more complicated molecules are also highlighted. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 649–660 DOI: 10.1002/wcms.43

This article is categorized under:

Structure and Mechanism > Molecular Structures
Cooperative dynamics of proteins unraveled by network models
Authors: Eyal Eran , Dutta Anindita , Bahar Ivet
Published: June 2011

Recent years have seen a significant increase in the number of computational studies that adopted network models for investigating biomolecular systems dynamics and interactions. In particular, elastic network models have proven useful in elucidating the dynamics and allosteric signaling mechanisms of proteins and their complexes. Here we present an overview of two most widely used elastic network models, the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM). We illustrate their use in (i) explaining the anisotropic response of proteins observed in external pulling experiments, (ii) identifying residues that possess high allosteric potentials, and demonstrating in this context the propensity of catalytic sites and metal‐binding sites for enabling efficient signal transduction, and (iii) assisting in structure refinement, molecular replacement and comparative modeling of ligand‐bound forms via efficient sampling of energetically favored conformers. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 426–439 DOI: 10.1002/wcms.44

This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
GROMACS—the road ahead
Authors: van der Spoel David , Hess Berk
Published: June 2011

Molecular dynamics (MD) simulations form a powerful tool that is complementary to experiments and theory. They allow detailed investigations of both biological and chemical systems at the atomic level at timescales ranging from femtoseconds to milliseconds. Mechanisms and processes not accessible to experimental techniques can be followed in ‘real time’, and hypotheses based on experiments or theoretical arguments can be tested. Limits on the accuracy of results are mainly due to the physical models, the ratio of the complexity of the problem and the amount of computer time. Here, we review the state of the art in MD simulations with a focus on imminent challenges for the GROMACS (GROningen MAchine for Chemical Simulation) software. New hardware puts new requirements on software, while the breadth of applications and the amount of physical models implemented are increasing rapidly, highlighting shortcomings in the architecture of the programs. We sketch a road map for a popular scientific software package and discuss some of the choices to be made. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 710–715 DOI: 10.1002/wcms.50

This article is categorized under:

Software > Molecular Modeling
Selected features of the polarizable continuum model for the representation of solvation
Authors: Tomasi Jacopo
Published: June 2011

The characteristics of a computational method addressing the description of solvent effects are here presented in a concise way, by selecting for the presentation a topic of large interest, i.e., the electronic, electric, and magnetic properties of molecules. The selection of these properties imposes a choice on the computational methods. They must be of quantum ab initio nature, and possibly treated at a high level of the quantum theory. In such a framework, continuum models are more adequate than the alternative models based on a discrete description of the solvent, because of the high computational cost associated with discrete models coupled to high quantum mechanics levels. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 855–867 DOI: 10.1002/wcms.54

This article is categorized under:

Molecular and Statistical Mechanics > Molecular Interactions
Reaction path Hamiltonian and the unified reaction valley approach
Authors: Kraka Elfi
Published: June 2011

One of the major goals of chemistry is to control chemical reactions with the purpose of generating new compounds with useful properties. Control of a chemical reaction implies a detailed understanding of its mechanism as it results from the breaking and forming of chemical bonds. In practice, it is rather difficult to get a detailed mechanistic and dynamical description of even the simplest chemical reactions. This has to do with the fact that apart from reactants, products, and possible stable intermediates, all other molecular forms encountered during a reaction have such a short lifetime that standard experimental means are not sufficient to detect and describe them. Progress in modern laser spectroscopy seems to provide an access to transient species with lifetimes in the pico‐ to femtosecond region; however, computational investigations utilizing state‐of‐the art methods of quantum chemistry, in particular ab initio methods, provide still the major source of knowledge on reaction mechanism and reaction dynamics. The reaction path Hamiltonian model has proven as a powerful tool to derive the dynamics of a chemical reaction by following the reacting species along the reaction path from reactants to products as traced out on the potential energy surface. In this article, the original reaction path Hamiltonian will be reviewed, extensions and applications over the past decades will be summarized, and a new perspective, namely to use it in form of the unified reaction valley approach to derive a deep and systematic insight into the mechanism of a chemical reaction will be introduced. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 531–556 DOI: 10.1002/wcms.65

This article is categorized under:

Electronic Structure Theory > Ab Initio Electronic Structure Methods
Two personal perspectives on a key issue in contemporary 3D QSAR
Authors: Clark Robert D. , Norinder Ulf
Published: June 2011

Chemists working with small molecules are under enormous pressure to be able to reliably predict how biological systems in particular and the environment in general will respond to the deployment of the corresponding compounds as medicines, cosmetics, or in other manufactured goods. To be specific and robust, any such prediction must be based on an implicit or explicit mathematical model of how chemical structure relates to biological activity—i.e., on some postulated quantitative structure–activity relationship (QSAR). Such models are necessarily limited in how broadly they can be applied. Their applicability domain depends on the structural diversity of the data set used, but also on the descriptors used to characterize how that structural variation relates to the activity in question. In principle, descriptors based on the molecular interaction fields produced by atoms distributed in three‐dimensional (3D) space should be the most general of all, but finding suitable conformations and alignment is a challenge. One way to obtain these is by taking the structure of the macromolecular target into account as well, as is done in scoring ligand/receptor complexes for virtual screening. Unfortunately, the available docking tools are generally not up to the task. Here, we share some personal observations and opinions on two possible ways to address this shortcoming: implicitly, by iterative rescoring of docked poses obtained using derived 3D QSARs; and explicitly, by evaluating ligand interaction fields with respect to target atoms rather than against generalized probe atoms. © 2011 John Wiley & Sons, Ltd.

This article is categorized under:

Computer and Information Science > Chemoinformatics
Fatty liver deposition and sparing: a pictorial review
Authors: Décarie Patrick-Olivier , Lepanto Luigi , Billiard Jean-Sébastien , Olivié Damien , Murphy-Lavallée Jessica , Kauffmann Claude , Tang An
Published: June 2011

Objective

Fatty liver deposition is a very common finding, but it has many atypical patterns of distribution that can represent diagnostic pitfalls. The purpose of this pictorial essay is to review different patterns of fatty liver deposition and sparing.

Methods

We searched our archive retrospectively, reviewed the literature, and identified six patterns of liver steatosis.

Results

Steatosis may be diffuse, geographic, focal, subcapsular, multifocal or perivascular.

Conclusions

Previous knowledge of atypical patterns of steatosis distribution may prevent misdiagnosis of infiltrative disease or focal liver lesions. When an unusual form of fatty liver deposition is suspected on ultrasound or computed tomography, magnetic resonance imaging may be used to confirm the diagnosis.