bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Multifaceted FISH Approach to Study Endogenous RNAs and DNAs in Native Nuclear and Cell Structures
Authors: Byron Meg , Hall Lisa L. , Lawrence Jeanne B. 
Published: January 2013

AbstractFluorescence in situ hybridization (FISH) is not a singular technique, but a battery of powerful and versatile tools for examining the distribution ofendogenousgenes and RNAs in precise context with each other and in relation to specific proteins or cell structures. This unit offers the details of highly sensitive and successful protocols that were initially developed largely in our lab and honed over a number of years. Our emphasis is on analysis of nuclear RNAs and DNA to address specific biological questions about nuclear structure, pre‐mRNA metabolism, or the role of noncoding RNAs; however, cytoplasmic RNA detection is also discussed. Multifaceted molecular cytological approaches bring precise resolution and sensitive multicolor detection to illuminate the organization and functional roles of endogenous genes and their RNAs within the native structure of fixed cells. Solutions to several common technical pitfalls are discussed, as are cautions regarding the judicious use of digital imaging and the rigors of analyzing and interpreting complex molecular cytological results.Curr. Protoc. Hum. Genet. 76:4.15.1‐4.15.21. © 2013 by John Wiley & Sons, Inc.
Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2
Authors: Adzhubei Ivan , Jordan Daniel M. , Sunyaev Shamil R. 
Published: January 2013

AbstractPolyPhen‐2 (Polymorphism Phenotyping v2), available as software and via a Web server, predicts the possible impact of amino acid substitutions on the stability and function of human proteins using structural and comparative evolutionary considerations. It performs functional annotation of single‐nucleotide polymorphisms (SNPs), maps coding SNPs to gene transcripts, extracts protein sequence annotations and structural attributes, and builds conservation profiles. It then estimates the probability of the missense mutation being damaging based on a combination of all these properties. PolyPhen‐2 features include a high‐quality multiple protein sequence alignment pipeline and a prediction method employing machine‐learning classification. The software also integrates the UCSC Genome Browser's human genome annotations and MultiZ multiple alignments of vertebrate genomes with the human genome. PolyPhen‐2 is capable of analyzing large volumes of data produced by next‐generation sequencing projects, thanks to built‐in support for high‐performance computing environments like Grid Engine and Platform LSF.Curr. Protoc. Hum. Genet. 76:7.20.1‐7.20.41. © 2013 by John Wiley & Sons, Inc.
Overview of Molecular Genetic Diagnosis
Authors: Harada Shuko , Korf Bruce R. 
Published: January 2013

AbstractThis unit describes the overview and strategies for molecular genetic diagnosis. Molecular genetic testing is typically used to detect changes in a single gene, and includes direct sequence analysis and detection of large deletion/duplication. Occasionally linkage analysis is still used when the gene is not known. Direct mutation analysis is possible if the gene responsible for a disorder has been identified. Genetic linkage analysis is used when polymorphic markers are available that are closely linked to a disease gene but the gene itself has not been cloned, or when it is difficult or impossible to detect mutations in the gene. For direct mutation analysis, the unit offers a review of the types of mutations that can be detected and the strategies that can be employed for their detection. The unit then describes the types of disorders that are best suited for linkage‐based analysis and offers guidance for interpreting the data. The unit also overviews recent progress on high‐throughput sequencing system and its possibility for its clinical application. Curr. Protoc. Hum. Genet. 76:9.1.1‐9.1.7. © 2013 by John Wiley & Sons, Inc.
Quantification of Glycosaminoglycans in Urine by Isotope‐Dilution Liquid Chromatography‐Electrospray Ionization Tandem Mass Spectrometry
Authors: Zhang Haoyue , Young Sarah P. , Millington David S. 
Published: January 2013

AbstractMucopolysaccharidoses (MPSs) are complex lysosomal storage disorders that result in the accumulation of glycosaminoglycans (GAGs) in urine, blood, and tissues. Lysosomal enzymes responsible for GAG degradation are defective in MPSs. GAGs including chondroitin sulfate (CS), dermatan sulfate (DS), heparan sulfate (HS), and keratan sulfate (KS) are disease‐specific biomarkers for MPSs. This unit describes a stable isotope dilution‐tandem mass spectrometric method for quantifying CS, DS, and HS in urine samples. The GAGs are methanolyzed to uronic or iduronic acid‐N‐acetylhexosamine or iduronic acid‐N‐sulfo‐glucosamine dimers and mixed with internal standards derived from deuteriomethanolysis of GAG standards. Specific dimers derived from HS, DS, and CS are separated by ultra‐performance liquid chromatography (UPLC) and analyzed by electrospray ionization tandem mass spectrometry (MS/MS) using selected reaction monitoring for each targeted GAG product and its corresponding internal standard. This new GAG assay is useful for identifying patients with MPS types I, II, III, VI, and VII. Curr. Protoc. Hum. Genet. 76:17.12.1‐17.12.14. © 2013 by John Wiley & Sons, Inc.
A Dramatic Odd–Even Oscillating Behavior for the Current Rectification and Negative Differential Resistance in Carbon‐Chain‐Modified Donor–Acceptor Molecular Devices
Authors: Zhang Zhenhua , Guo Chao , Kwong Denise Jeng , Li Jie , Deng Xiaoqing , Fan Zhiqiang 
Published: January 2013

AbstractThe donor–acceptor molecule is the only molecule that features a real intrinsic rectification. However, all investigations in the last decades showed that rectification behaviors of such molecules are not promising since their rectification ratio is only on the order of 10. Use of carbon chains Cn to serve as spacers is reported, along with attempts to modulate electrical behavior of the donor–acceptor molecule. Calculations using the first‐principles method show that electrical behavior is indeed altered substantively, and a particular regularity can be clearly observed, i.e., a dramatic odd–even oscillation for electronic behavior with increasing carbon‐chain length n. For models with even‐n carbon chains, the rectification ratio is small (30), and no negative differential resistance (NDR) behavior is detected, but the rectifying performance of models with odd‐n carbon chains is tremendously improved and rectification ratios on the order of 50 to 400 can be achieved, alongside a large NDR. This study thus suggests that using a suitable spacer might be an effective way to significantly boost electrical characteristics, including rectifying performance, of the donor–acceptor molecule.
Optical Nanosphere Sensor Based on Shell‐By‐Shell Fabrication for Removal of Toxic Metals from Human Blood
Authors: El‐Safty S. A. , Abdellatef S. , Ismael M. , Shahat A. 
Published: January 2013

AbstractBecause toxic heavy metals tend to bioaccumulate, they represent a substantial human health hazard. Various methods are used to identify and quantify toxic metals in biological tissues and environment fluids, but a simple, rapid, and inexpensive system has yet to be developed. To reduce the necessity for instrument‐dependent analysis, we developed a single, pH‐dependent, nanosphere (NS) sensor for naked‐eye detection and removal of toxic metal ions from drinking water and physiological systems (i.e., blood). The design platform for the optical NS sensor is composed of double mesoporous core–shell silica NSs fabricated by one‐pot, template‐guided synthesis with anionic surfactant. The dense shell‐by‐shell NS construction generated a unique hierarchical NS sensor with a hollow cage interior to enable accessibility for continuous monitoring of several different toxic metal ions and efficient multi‐ion sensing and removal capabilities with respect to reversibility, longevity, selectivity, and signal stability. Here, we examined the application of the NS sensor for the removal of toxic metals (e.g., lead ions from a physiological system, such as human blood). The findings show that this sensor design has potential for the rapid screening of blood lead levels so that the effects of lead toxicity can be avoided.
Acidic Three‐Liquid‐Phase Microemulsion Systems Based on Balanced Catalytic Surfactant for Epoxidation and Sulfide Oxidation under Mild Conditions
Authors: Fressancourt‐Collinet Marion , Hong Bing , Leclercq Loïc , Alsters Paul. L. , Aubry Jean‐Marie , Nardello‐Rataj Véronique 
Published: January 2013

AbstractDidecyldimethylammonium tungstate has been designed as a balanced catalytic surfactant to form acidic three‐liquid‐phase microemulsion systems at room temperature in the presence of water, a non‐chlorinated solvent and dimethyldioctylammonium salts (hydrogen sulfate and dihydrogen phosphate). The triphasic system is efficient for the oxidation of olefins, sulfides and thiophenes under mild conditions. Moreover, the recovery and reusability of the catalyst, the straightforward separation of products and catalysts in two distinct phases as well as the possible use of environmentally friendly solvents such as tert‐butyl acetate, make this system particularly attractive for catalytic oxidation reactions involving hydrogen peroxide as the primary oxidant under acidic or neutral conditions.
Preparation of Cationic Poly(acrylamide)/Bentonite Nanocomposites from in situ Inverse Emulsion Copolymerization and Their Performance in Papermaking
Authors: Yoon Dong Ho , Jang Jung Won , Seo Seung Suck , Jeong Soo‐Hwan , Cheong In Woo 
Published: January 2013

ABSTRACTThis study examined the effects of acryl‐grafted bentonite (AGB) in cationic poly(acrylamide) (CPAAm)/AGB nanocomposites on the flocculation and retention of micrometer‐sized talc and ground calcium carbonate (GCC) suspensions used for papermaking. The AGB was synthesized by reacting Na+‐bentonite with (3‐acryloxypropyl)trimethoxysilane. The graft yield measured by thermogravimetric analysis was ca. 24%. Different concentrations (0, 1.0, 2.9, and 4.9 wt%, designated as CPAAm/AGB‐0, ‐1, ‐3, and ‐5, respectively) of AGB were then added to the in situ inverse emulsion copolymerization of acrylamide and [2‐(acryloyloxy)ethyl]trimethylammonium chloride to produce the CPAAm/AGB nanocomposites. The nanocomposites improved the flocculation of the GCC suspension model significantly in an AGB concentration‐dependent manner. Dynamic drainage analysis revealed a decrease in dewatering time and turbidity from 11.2 s (pure CPAAm) to 8.7 s and from 349 to 33 NTU, respectively, at the same concentration (0.3 wt%) of nanocomposite. The results of the fabrication of handsheets revealed significant improvement (up to 2–8%) in the total retention yield and ash retention yield with increasing AGB concentration at the same GCC content. © 2012 Wiley Periodicals, Inc. Adv Polym Techn 2013, 32, 21335; View this article online at wileyonlinelibrary.com. DOI 10.1002/adv.21335
Nanoindentation im Kristall‐Engineering: Quantifizierung mechanischer Eigenschaften von Molekülkristallen
Authors: Varughese Sunil , Kiran M. S. R. N. , Ramamurty Upadrasta , Desiraju Gautam R. 
Published: January 2013

AbstractNanoindentation ist ein Verfahren zur Messung von Elastizitätsmodul und Härte kleiner Materialvolumina. Diese Methode, die weithin für die Charakterisierung metallischer und anorganischer Feststoffe verwendet wird, wird heute auch an organischen und metallorganischen Kristallen eingesetzt und ist damit auch für das Gebiet des Kristall‐Engineering relevant geworden, z. B. für die Entwicklung molekularer Feststoffe mit gewünschten Eigenschaften und Funktionen. Durch Nanoindentation können Eigenschaften auf der molekularen Ebene, wie z. B. Kristallpackung, Wechselwirkungseigenschaften und inhärente Anisotropie, mit Vorgängen auf der mikro/makroskopischen Ebene, wie z. B. Desolvation, Koexistenz von Domänen, Schichtwanderung, Polymorphie und Festkörper‐Reaktivität, in Beziehung gesetzt werden. Unser Kurzaufsatz behandelt aktuelle Entwicklungen und interessante Möglichkeiten auf diesem neuen Gebiet.
Ecology of southern European pearl mussels (Margaritifera margaritifera): first record of two new populations on the rivers Terva and Beça (Portugal)
Authors: Varandas Simone , Lopes‐Lima Manuel , Teixeira Amílcar , Hinzmann Mariana , Reis Joaquim , Cortes Rui , Machado Jorge , Sousa Ronaldo 
Published: January 2013

ABSTRACTSouthern European populations of Margaritifera margaritifera (L., 1758) are under‐studied. From 1986 to 2001 this species was considered extinct in Portugal but between 2001 and 2002 six northern populations were found, five of which were previously unknown.This study comprises a comparative study of the ecology and habitat requirements of two new populations in the rivers Beça and Terva (tributaries of the River Tâmega, northern Portugal) with non‐Iberian populations.Surveys were conducted in 2010/2011 to characterize ecological status and propose possible conservation measures. Both rivers were in good environmental condition, but the River Beça had higher biological, physicochemical and hydromorphological quality.Both populations are highly susceptible to extirpation – in particular the River Terva population, given the very low number of specimens found and no sign of recent recruitment. The low number of juveniles and the existence of several threats in both rivers (e.g. fragmentation and loss of habitat caused by the presence of physical obstacles, organic pollution and bank erosion due to fires) imply the need for urgent, effective, conservation measures.Southern European M. margaritifera populations have similar ecological and habitat requirements compared with those of northern and central Europe. However, functional populations may endure higher phosphate content, pH and temperature values. As expected they present faster growth rates and reduced life spans. Copyright © 2013 John Wiley & Sons, Ltd.
Design of Novel β‐Carboline Derivatives with Pendant 5‐Bromothienyl and Their Evaluation as Phosphodiesterase‐5 Inhibitors
Authors: El‐Gamil Dalia S. , Ahmed Nermin S. , Gary Bernard D. , Piazza Gary A. , Engel Matthias , Hartmann Rolf W. , Abadi Ashraf H. 
Published: January 2013

AbstractNew derivatives with the tetrahydro‐β‐carboline‐imidazolidinedione and tetrahydro‐β‐carboline‐piperazinedione scaffolds and a pendant bromothienyl moiety at C‐5/C‐6 were synthesized and tested for their ability to inhibit PDE5 in vitro. The following SAR can be concluded: The tetracyclic scaffold is essential for PDE5 inhibition; the ethyl group is the most suitable among the adopted N‐substituents on the terminal ring (hydantoin/piperazinedione); the appropriate stereochemistry of C‐5/C‐6 derived from the aldehyde rather than C‐11a/C‐12a derived from tryptophan appears crucial for inhibition of PDE5; surprisingly, derivatives with the hydantoin terminal ring are more active than their analogs with the piperazinedione ring; the selectivity versus PDE5 relative to PDE11 with cGMP as a substrate is mainly a function of the substitution and stereochemistry pattern of the external ring, in other words of the interaction with the H‐loop residues of the isozymes. Thirteen derivatives showed PDE5 inhibitory activity with IC50 values in the range of 0.16–5.4 µm. Compound 8 was the most potent PDE5 inhibitor and showed selectivity towards PDE5 versus other PDEs, with a selectivity index of 49 towards PDE5 rather than PDE11 with cGMP as the substrate.
N‐Boc‐Protected 1,2‐Diphenylethylenediamine‐Based Dendritic Organogels with Multiple‐Stimulus‐Responsive Properties
Authors: Liu Ji , Feng Yu , Liu Zhi‐Xiong , Yan Zhi‐Chao , He Yan‐Mei , Liu Chen‐Yang , Fan Qing‐Hua 
Published: January 2013

AbstractA new class of poly(benzyl ether) dendrimers, decorated in their cores with N‐Boc‐protected 1,2‐diphenylethylenediamine groups, were synthesized and fully characterized. It was found that the gelation capability of these dendrimers was highly dependent on dendrimer generation, and the second‐generation dendrimer (R,R)‐G2DPENBoc proved to be a highly efficient organogelator. A number of experiments (SEM, TEM, FTIR spectroscopy, 1H NMR spectroscopy, rheological measurements, UV/Vis absorption spectroscopy, CD, and XRD) revealed that these dendritic molecules self‐assembled into elastically interpenetrating one‐dimensional nanostructures in organogels. The hydrogen bonding, π–π, and solvophobic interactions were found to be the main driving forces for formation of the gels. Most interestingly, these dendritic organogels exhibited smart multiple‐stimulus‐responsive behavior upon exposure to environmental stimuli such as temperature, anions, and mechanical stress.
Commercial‐scale utilization of greenhouse residues
Authors: Maroušek Josef , Kondo Yoshikazu , Ueno Masami , Kawamitsu Yoshinobu 
Published: January 2013

AbstractDevelopment of techniques utilizing waste without any additional energy or rare catalysts is a starting point for becoming sustainable. In the present work, the complex utilization of greenhouse residues was studied on a commercial scale. Only the energy produced by the process (8%) was used to run the technology, thanks to multilevel heat recuperation and high methane yields (over 340 m3 volatile solid t−1). Manifestations of labile carbon in relation to available nitrogen, methane yields, and the formation of inhibitors were investigated in detail. The results sweep away many false beliefs about the ratios of carbon to nitrogen and highlight the role of the availability of carbon in phytomass utilization.
Oxygen activation and redox partner binding in cytochromes P450
Authors: Poulos Thomas L. , Madrona Yarrow 
Published: January 2013

AbstractThe structural underpinnings of O2 activation in P450s have been limited by the inability to trap unstable oxy complexes in the crystalline state for structure determination. To date there are only two known oxy P450 structures. Even so, much is known about O2 activation in P450cam and the role that redox partner binding plays in this process. Of particular importance are changes in the I helix associated with O2 binding that enable “catalytic” waters to enter the active site and establish an H‐bonding network essential for cleavage of the OO bond. The changes in the I helix are similar to differences in the substrate‐bound (closed) and substrate‐free (open) conformations. With this information in hand, we have solved the structure of the substrate‐free form of P450cin as well as the nitric oxide complex as a mimic of the oxy complex. This information provides some insight into the similarities and differences between P450cin and P450cam in O2 activation.
The teratology society 2012–2017 strategic plan: Pushing the boundaries
Authors: Curran Christine Perdan , Lau Christopher , Schellpfeffer Michael A. , Stodgell Christopher J. , Carney Edward W. 
Published: January 2013

AbstractThe Teratology Society held its fourth strategic planning session in Albuquerque, NM, April 10–12, 2012, and launched the 2012–2017 Strategic Plan in conjunction with the 2012 annual meeting in Baltimore, MD. Building on the energy of the successful implementation of prior strategic plans (San Diego, 2007; Nashville,TN 2002; Cincinnati, OH 1998), session participants worked to identify barriers to success as a scientific society, as well as impending challenges and opportunities to which the Society needs to respond. The following report provides an overview of the Strategic Planning process, objectives, activities, and conclusions. A total of 23 members were present at the session, and the group included representation from Council, various committees, and different member constituencies. This plan, Pushing the Boundaries, and its three strategic intents: Broaden Our Identity, Expand Our Membership, and Increase Our Influence, will drive the direction of the Teratology Society for the next five years., 2013. © 2013 Wiley Periodicals, Inc.
Influence of relative humidity on analyzing electric field exposure using ELF electric field measurements
Authors: Korpinen Leena H. , Kuisti Harri A. , Tarao Hiroo , Elovaara Jarmo A. 
Published: January 2013

AbstractThe objective of the study was to investigate the influence of humidity on analyzing electric field exposure using extremely low frequency (ELF) electric field measurements. The study included 322 measurements in a climate room. We used two commercial three‐axis meters, EFA‐3 and EFA‐300, and employed two measurement techniques in the climate room where we varied the temperature from 15 to 25 °C, the relative humidity from 55% to 95%, and the electric field from 1 to 25 kV/m. We calculated Pearson correlations between humidity and percentage errors for all data and for data at different levels of humidity. When the relative humidity was below 70%, the results obtained by the different measurement methods in terms of percentage errors were of the same order of magnitude for the considered temperatures and field strength, but the results were less reliable when the relative humidity was higher than 80%. In the future, it is important to take humidity into account when electric field measurement results will be compared to the values given in different exposure guidelines. Bioelectromagnetics 34:414–418, 2013. © 2012 Wiley Periodicals, Inc.
Multicellularity arose several times in the evolution of eukaryotes (Response to DOI 10.1002/bies.201100187)
Authors: Parfrey Laura Wegener , Lahr Daniel J. G. 
Published: January 2013

AbstractThe cellular slime mold Dictyostelium has cell‐cell connections similar in structure, function, and underlying molecular mechanisms to animal epithelial cells. These similarities form the basis for the proposal that multicellularity is ancestral to the clade containing animals, fungi, and Amoebozoa (including Dictyostelium): Amorphea (formerly “unikonts”). This hypothesis is intriguing and if true could precipitate a paradigm shift. However, phylogenetic analyses of two key genes reveal patterns inconsistent with a single origin of multicellularity. A single origin in Amorphea would also require loss of multicellularity in each of the many unicellular lineages within this clade. Further, there are numerous other origins of multicellularity within eukaryotes, including three within Amorphea, that are not characterized by these structural and mechanistic similarities. Instead, convergent evolution resulting from similar selective pressures for forming multicellular structures with motile and differentiated cells is the most likely explanation for the observed similarities between animal and dictyostelid cell‐cell connections.