bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial and anti-endotoxin activity of N-acetylcysteine, calcium hydroxide and their combination against Enterococcus faecalis, Escherichia coli and lipopolysaccharides
Authors: Khoury Rayana Duarte , Abu Hasna Amjad , Gagliardi Carolina Fedel , Marinho Renata Marques de Melo , Carvalho Cláudio Antonio Talge , Bresciani Eduardo , Valera Marcia Carneiro 
Published: October 2024

Background
The management of endodontic infections is a complex challenge, mainly due to the involvement of diverse microorganisms and their by-products. This study aimed to evaluate the efficacy of N-acetylcysteine (NAC), calcium hydroxide (Ca(OH)2), and their combined application as intracanal medications in combating Enterococcus faecalis, Escherichia coli, and lipopolysaccharides (LPS) from E. coli.

Methods
A total of 60 single-rooted human teeth were carefully selected and divided into six groups. These tooth canals were deliberately exposed to E. faecalis (ATCC 29212) and E. coli (ATCC 25922) to induce biofilm formation. Subsequently, the specimens were treated with NAC, Ca(OH)2, or a combination of both substances. Three samples of the root canals were collected at three moments: the first sample (S1) was to confirm the initial contamination, the second sample (S2) was immediately post-instrumentation, and the third sample (S3) was collected after the use of the intracanal medication. The antimicrobial efficacy of these intracanal medications was assessed by enumerating colony-forming units per milliliter (CFU/mL). In addition to this, the kinetic chromogenic Limulus Amebocyte Lysate (LAL) assay by Lonza was used to quantify LPS from E. coli. Data tested for normality; then, Kruskal-Wallis and Friedman tests were used, and Dunn’s for multiple comparisons.

Results
The findings of this study showed significant reductions in the microbial load of E. faecalis and E. coli by S3. Notably, there were no statistically significant differences among the treatment groups concerning these microorganisms. However, it was observed that only the combination of NAC and Ca(OH)2 led to a noteworthy decrease in the quantity of E. coli’s LPS after 7-days, demonstrating a statistically significant difference from the other treatment groups. NAC + Ca(OH)2 combination, applied for a duration of 7-days, proved to be more suitable in reducing the presence of E. faecalis, E. coli, and LPS from E. coli within the context of endodontic infections.
Trend in the Co‐Occurrence of Extreme Daily Rainfall in West Africa Since 1950
Authors: Blanchet Juliette , Aly Claire , Vischel Théo , Panthou Gérémy , Sané Youssouph , Diop Kane Mariane 
Published: January 2018

AbstractWe propose in this paper a statistical framework to study the evolution of the co‐occurrence of extreme daily rainfall in West Africa since 1950. We consider two regions subject to contrasted rainfall regimes: Senegal and the central Sahel. We study the likelihood of the 3% largest daily rainfall (considering all days) in each region to occur simultaneously and, in a 20 year moving window approach, how this likelihood has evolved with time. Our method uses an anisotropic max‐stable process allowing us to properly represent the co‐occurrence of daily extremes and including the possibility of a preferred direction of co‐occurrence. In Senegal, a change is found in the 1980s, with preferred co‐occurrence along the E‐50‐N direction (i.e., along azimuth 50°) before the 1980s and weaker isotropic co‐occurrence afterward. In central Sahel, a change is also found in the 1980s but surprisingly with contrasting results. Anisotropy along the E‐W direction is found over the whole period, with greater extension after the 1980s. The paper discusses how the co‐occurrence of extremes can provide a qualitative indicator on change in size and propagation of the strongest storms. This calls for further research to identify the atmospheric processes responsible for such contrasted changes in storm properties.
Super‐detailed FEM simulations for full‐scale steel structure with fatal rupture at joints between members—Shaking‐table test of full‐scale steel frame structure to estimate influence of cumulative damage by multiple strong motion: Part 1
Authors: Mizushima Yasunori , Mukai Yoichi , Namba Hisashi , Taga Kenzo , Saruwatari Tomoharu 
Published: January 2018

AbstractThere have been several studies on analyses using finely meshed finite‐element (FE) models to understand in detail the behaviors of buildings during severe earthquakes. The accuracy of such analyses is often validated by comparing the results to the corresponding full‐scale shaking‐table test. While this approach is highly successful in terms of accuracy, no studies have considered the effect of fractures of members. In this study, numerical analyses are conducted for a steel structure subjected to multiple series of excitations in a full‐scale shaking‐table test considering fractures. The structure is modeled with planar and solid finite elements, and the fracture is treated by the mandatory deletion of elements at the time at which the fracture is observed in the experiment. The results show that by considering the fracture of steel members with the deletion of elements, the history of input excitations, and the resulting damages, the behaviors can be simulated analytically with a much higher accuracy.
Complex Multifactorial Genetic Diseases
Authors: Howrigan Daniel J , William Nancy , Darlington Todd M 
Published: January 2018

AbstractVariation in traits can be owing to genetic factors or the environment – nature versus nurture – or more likely, a combination of both. It may be of interest, especially when a trait is detrimental, to localise the regions of the genome that contain the genes involved and beyond that, to map specific risk variants. Understanding the possible roles that genes may play in trait variation and, furthermore, estimating or modelling the genetic component are important first steps to inform subsequent genetic studies. There are many different study designs and genetic analysis techniques, each with their respective strengths and weaknesses for the identification of risk variants. Knowledge of disease susceptibility genes may help in the quest for new treatments and cures.Key ConceptsTypes of trait variation.The possible roles of genes in trait variation.The components of phenotypic variation.Study designs for the estimation of genetic effects and heritability.Genetic heterogeneity.Types of genetic study designs.Various analysis techniques used in genetic studies.
Genomic
DNA
: Purification
Authors: Tümmler Burkhard , Stanke Frauke 
Published: January 2018

Abstract

Genomic deoxyribonucleic acid (DNA) can be prepared from any source by three steps: cell lysis, deproteinisation and recovery of DNA. The basic protocol needs to be adapted to the demands of the application, the number of samples to be processed, the requested yield, purity and molecular weight of the DNA and the amount and history of the source. Traditional protocols based on the lysis with sodium dodecyl sulfate/proteinase K, extraction with phenol/chloroform/isoamyl alcohol, purification with ethanol and storage in tris/ethylenediamine tetraacetic acid buffer are recommended for the purification of long‐term stable high‐molecular weight genomic DNA from freshly obtained specimens. Intact chromosomal DNA is recovered from agarose‐embedded cells. Automated extraction methods are preferred for forensic applications and high‐throughput processing for biobanking. The technically challenging recovery of ancient DNA needs to be optimised on a case‐to‐case basis, because ancient DNA is damaged and chemically modified and contains large amounts of polymerase chain reaction inhibitors.

Key Concepts

The analysis of complex genomes requires the preparation of pure genomic deoxyribonucleic acid (DNA) of high molecular weight.

Genomic DNA can be prepared from any source by three steps: cell lysis, deproteinisation and recovery of DNA.

Intact chromosomal megabase‐sized DNA is purified in solid agarose to protect the DNA during preparation.

DNA extraction for biobanking relies on automated systems and robotics.

Automated systems have been increasingly utilised for DNA extraction by forensic laboratories to handle the growing numbers of forensic casework samples while minimising the risk of human errors and assuring high reproducibility.

The recovery of ancient DNA from palaeontological specimens is a demanding task, because ancient DNA is damaged and chemically modified and contains large amounts of PCR inhibitors that interfere with DNA amplification that are copurified with the DNA.
Restriction Mapping
Authors: Tümmler Burkhard , Stanke Frauke 
Published: January 2018

Abstract

Deoxyribonucleic acid is partially or completely digested with one or more restriction endonucleases. The generated fragments are separated by size and then ordered by combinatorial analysis to generate a physical map. The size of the fragments generated by a restriction endonuclease digest depends on the frequency of the enzyme's recognition sequence in the analysed genome. Resolution of the restriction map can thus be influenced by choosing the appropriate restriction enzyme and needs to be adapted to each species. The method has been used in the past to generate physical maps of plasmids, phages or whole genomes and is meanwhile employed to generate de novo genome assemblies by next‐generation sequencing of nonmodel organisms with polyploid genomes.

Key Concepts

Restriction enzymes generate DNA fragments at sequence‐defined genomic sites.

The average size of restriction digest‐generated DNA fragments can be controlled by choosing a restriction enzyme with rare (large fragments) or frequent (small fragments) recognition sequences.

Restriction fragment‐digested DNA can be used for next‐generation sequencing, which facilitates genomic mapping of nonmodel organisms with complex genomes.
D
rosophila

as a Model for Human Diseases
Authors: Marcogliese Paul C , Wangler Michael F 
Published: January 2018

Abstract

The fruit fly has long been a powerful organism for high‐throughput
in vivo
studies in biology and genetics. Studies in
Drosophila
offer a simple platform, modelling multiple human diseases. With an ever‐expanding genetic toolkit, the fly genome has become increasingly accessible to experimental manipulation. The ectopic expression of human disease genes involved in neurodegenerative and neurodevelopmental disorders have elucidated genetic modifiers that have been revealed to also cause human disease or to be potential drug targets for human neurological disorders. Recently, fly models are being used to study other human pathology such as cancer, infections and cardiovascular disorders. Lastly, ‘humanisation’ strategies to replace endogenous fly genes with their human homologue have begun. This has been particularly beneficial in assessing putative pathogenic variants implicated in rare Mendelian disorders, and thereby aiding diagnosis. In summary, the fly has remained a relevant platform for modelling human disease and elucidating genetic pathways and potential therapeutic targets.

Key Concepts

There is a vast, ever‐expanding genetic toolkit for manipulation of genes in the fly.

Significant advances have been made to further understanding a wide range of human diseases through studies of fly models.

Humanisation via use of the T2A‐GAL4 system along with UAS human cDNA transgenics provide a method to test variants implicated in human disease.

Flies can be used to study common neurodegenerative diseases as well as rare Mendelian disorders.

Functional testing of putative disease causing variants may still be accomplished in flies even when the phenotype may not overlap with human disease presentation.
Microarray Bioinformatics
Authors: Suratannon Narissara , van Hagen Martin , van der Spek Peter J 
Published: January 2018

Abstract

Scientists deal with massive datasets that must be interpreted in the context of other databases with biomedical knowledge. HGMD and NCBI GEO repositories accumulate vast amounts of data generated arrays and next‐generation sequencing (NGS) techniques. Although there is no universal way to analyse microarray data, best practices have been highlighted by which these data obtained from multiplex measurements using microarrays are explored.
Variant analysis, copy number aberrations and RNA and proteome expression analysis using Somalogic aptamers on microarrays involve the processing of large numeric data tables linked to literature/text, categorical sequence data and last but not least unstructured clinical data of patients. Its aim is to rank a list of variants, genes (RNA transcripts) and/or proteins that are expressed differentially (including coregulated and/or antiregulated molecules) and in a biologically relevant and statistically significant manner under many different experimental conditions or disease states. Visual data‐mining approaches are used besides advanced R statistical methods to identify unexpected relationships beyond the original hypotheses for clinical decision‐making in research or therapeutic settings. Software tools such as Instem/OmniViz Tibco/Spotfire, Partek, Biodiscovery Nexus, Qiagen/Ingenuity Pathway Analysis and/or Qiagen/Ingenuity Variant Analysis help scientists to put their scientific findings in the right context to stratify patients for targeted treatment.

Key Concepts

Bioinformatics uses computational tools for integration of the analysis of biological and medical data, which are being discussed in this article.

Bioinformatics covers software to handle, acquire, store, integrate, archive, analyse and visualise OMIC data. As the field matures, the focus shifts from single experiments towards cross‐OMIC data integration of DNA, RNA and protein array and sequencing data.

Detection of mutations, deletions and amplifications.

Patient stratification in Primary Immunodeficiencies.

Targeted therapy in AML.

DNA, RNA OMICS integrative analysis.

Web based resources for genome analysis.
Host‐Induced Gene Silencing for Pest/Pathogen Control
Authors: Nagle Michael , LeBoldus Jared M , Klocko Amy L 
Published: January 2018

Abstract

Host‐induced gene silencing (HIGS) is an approach that shows promise for the control of a variety of problematic crop‐damaging organisms, ranging from nematodes and insects, to fungi and parasitic plants. In general, HIGS utilises ribonucleic acid interference (RNAi) molecules produced by the plant, which then target key genes in pests/pathogens, ideally leading to improved resistance of the plant and a reduction in damage. As this area of research is still very much in development, the possible off‐target and nontarget effects need to be assessed, as do the long‐term stability and effectiveness. Practical implementation of HIGS to commercial crop production will rely on extensive field‐testing, as well as regulatory and marketplace acceptance of new varieties.

Key Concepts

Plants are susceptible to damage from a variety of biological agents, including insect pests, and from pathogens, such as various species of fungi, nematodes and viruses.

Damage to crops by biological sources causes significant losses to yield.

Silencing of key pest and pathogen genes is a possible strategy for reducing crop damage and can be accomplished by RNA molecules expressed by the host plant.

Genetic constructs designed to silence pest and pathogen genes can be stably inserted into the host plant genome through a variety of methods, such as particle bombardment or
Agrobacterium
‐mediated transformation.

An alternate method for silencing genes consists of the direct application of purified RNA molecules to the plant itself.
Phytochemical and Pharmacological Properties of Flavonols
Authors: Sharma Ajay , Sharma Pooja , Singh Tuli Hardeep , Sharma Anil K 
Published: January 2018

Abstract

Flavonoids are polyphenolic compounds, which are ubiquitous in nature and have been categorised into flavonols, flavones, flavanones, isoflavones, catechins, anthocyanidins and chalcones according to their chemical structure. Currently more than 4000 flavonoids have been identified, which were isolated from fruits, vegetables and beverages (tea, coffee, beer, wine and fruit drinks). The flavonoids have aroused interest recently because of their beneficial effects on human health especially reported to have antiviral, antiallergic, anti‐inflammatory, antitumour and antioxidant activities. Flavonoids may enrich the immunogenic potential against such diseases of human body. Epidemiological studies have shown that flavonoid intake is inversely proportional to mortality rate because of coronary heart disease and heart attacks. However, recent studies have demonstrated that flavonoids found in fruits and vegetables may act as antioxidants. Current article mainly focuses upon the structure–function relationship of flavonols, one of the key components of flavonoids for their potential therapeutic use.

Key Concepts

Flavonols are phytochemical compounds, which are associated with beneficial health effects.

Antioxidants are molecules that inhibit the oxidation of other molecules in living organisms.

Enzymes are macromolecules biocatalysts, which accelerate the chemical reactions.

Metastasis is a pathogenic agent's spread from an initial position or primary site to a secondary site within the host cell.

Angiogenesis is the physiological process in which new blood vessels form from preexisting vessels.

Tumour is an abnormal mass of tissue or cell that may be solid or fluid‐filled.
Tumours
can be benign (not cancerous), premalignant (precancerous) or malignant (cancerous).

Apoptosis is a process of programmed cell death, which occurs in multicellular organisms.

Astrogliosis or astrocytosis is an abnormal increase in the number of astrocytes because of the destruction of nearby neurons from CNS trauma, infection, ischaemia, stroke, autoimmune responses and neurodegenerative disease.
Targeting potassium channels to treat cerebellar ataxia
Authors: Bushart David D. , Chopra Ravi , Singh Vikrant , Murphy Geoffrey G. , Wulff Heike , Shakkottai Vikram G. 
Published: January 2018

AbstractObjectivePurkinje neuron dysfunction is associated with cerebellar ataxia. In a mouse model of spinocerebellar ataxia type 1 (SCA1), reduced potassium channel function contributes to altered membrane excitability resulting in impaired Purkinje neuron spiking. We sought to determine the relationship between altered membrane excitability and motor dysfunction inSCA1 mice.MethodsPatch‐clamp recordings in acute cerebellar slices and motor phenotype testing were used to identify pharmacologic agents which improve Purkinje neuron physiology and motor performance inSCA1 mice. Additionally, we retrospectively reviewed records of patients withSCA1 and other autosomal‐dominantSCAs with prominent Purkinje neuron involvement to determine whether currently approved potassium channel activators were tolerated.ResultsActivating calcium‐activated and subthreshold‐activated potassium channels improved Purkinje neuron spiking impairment inSCA1 mice (P< 0.05). Additionally, dendritic hyperexcitability was improved by activating subthreshold‐activated potassium channels but not calcium‐activated potassium channels (P< 0.01). Improving spiking and dendritic hyperexcitability through a combination of chlorzoxazone and baclofen produced sustained improvements in motor dysfunction inSCA1 mice (P< 0.01). Retrospective review ofSCApatient records suggests that co‐treatment with chlorzoxazone and baclofen is tolerated.InterpretationTargeting both altered spiking and dendritic membrane excitability is associated with sustained improvements in motor performance inSCA1 mice, while targeting altered spiking alone produces only short‐term improvements in motor dysfunction. Potassium channel activators currently in clinical use are well tolerated and may provide benefit inSCApatients. Future clinical trials with potassium channel activators are warranted in cerebellar ataxia.
2D Heterostructure Membranes with Sunlight‐Driven Self‐Cleaning Ability for Highly Efficient Oil–Water Separation
Authors: Liu Yanan , Su Yanlei , Guan Jingyuan , Cao Jialin , Zhang Runnan , He Mingrui , Gao Kang , Zhou Linjie , Jiang Zhongyi 
Published: January 2018

AbstractIntroducing solar energy into membrane filtration to decrease energy and chemicals consumption represents a promising direction in membrane fields. In this study, a kind of 0D/2D heterojunction is fabricated by depositing biomineralized titanium dioxide (TiO2) nanoparticles with delaminated graphitic carbon nitride (g‐C3N4) nanosheets, and subsequently a kind of 2D heterostructure membrane is fabricated via intercalating g‐C3N4@TiO2 heterojunctions into adjacent graphene oxide (GO) nanosheets by a vacuum‐assisted self‐assembly process. Due to the enlarged interlayer spacing of GO nanosheets, the initial permeation flux of GO/g‐C3N4@TiO2 membrane reaches to 4536 Lm−2 h−1 bar−1, which is more than 40‐fold of GO membranes (101 Lm−2 h−1 bar−1) when utilized for oil/water separation. To solve the sharp permeation flux decline, arising from the adsorption of oil droplets, the a sunlight‐driven self‐cleaning process is followed, maintaining a flux recovery ratio of more than 95% after ten cycles of filtration experiment. The high permeation flux and excellent sunlight‐driven flux recovery of these heterostructure membranes manifest their attractive potential application in water purification.
Hierarchical Design of Metal Micro/Nanohole Array Films Optimizes Transparency and Haze Factor
Authors: Bley Karina , Semmler Johannes , Rey Marcel , Zhao Chunjing , Martic Nemanja , Klupp Taylor Robin N. , Stingl Michael , Vogel Nicolas 
Published: January 2018

AbstractThin films containing metal nanohole arrays can be fabricated with high precision, and regular, tunable features via colloidal lithography. They are ideal model structures to study the relation between structural design and optoelectronic properties, for example as transparent, conducting electrodes, where the percolation threshold sets an upper limit on the achievable transparency. An important, but less systematically studied property of transparent conductive electrodes is the amount of scattered light, as described by the haze factor. Here, the influence of structural parameters on the resulting haze factor of metal nanohole array films is investigated. It is found that transmission, transparency, and haze factor cannot be independently controlled, and propose a new fabrication paradigm to optimize the optoelectronic properties of such films. Hierarchical metal micro/nanohole array films are designed, which combine precisely controlled and highly regular structural features at two length scales. These hierarchical structures maximize transparency while simultaneously providing low haze factors. Computer simulations based on finite elements and ray optics are in close agreement with the experimental results and reveal that the reduced haze factor results from a drastic decrease of grating diffraction efficiency in the hierarchical films.