bluuebunny/crossref_metadata_2025 huggingface dataset:
Structuring dimensions for collaborative systems evaluation
Authors: Antunes Pedro , Herskovic Valeria , Ochoa Sergio F. , Pino Jose A.
Published: March 2012

Collaborative systems evaluation is always necessary to determine the impact a solution will have on the individuals, groups, and the organization. Several methods of evaluation have been proposed. These methods comprise a variety of approaches with various goals. Thus, the need for a strategy to select the most appropriate method for a specific case is clear. This research work presents a detailed framework to evaluate collaborative systems according to given variables and performance levels. The proposal assumes that evaluation is an evolving process during the system lifecycle. Therefore, the framework, illustrated with two examples, is complemented with a collection of guidelines to evaluate collaborative systems according to product development status.
A survey of emerging approaches to spam filtering
Authors: Caruana Godwin , Li Maozhen
Published: March 2012

From just an annoying characteristic of the electronic mail epoch, spam has evolved into an expensive resource and time-consuming problem. In this survey, we focus on emerging approaches to spam filtering built on recent developments in computing technologies. These include peer-to-peer computing, grid computing, semantic Web, and social networks. We also address a number of perspectives related to personalization and privacy in spam filtering. We conclude that, while important advancements have been made in spam filtering in recent years, high performance approaches remain to be explored due to the large scale of the problem.
Handwriting Recognition in Indian Regional Scripts
Authors: Pal Umapada , Jayadevan Ramachandran , Sharma Nabin
Published: March 2012

Offline handwriting recognition in Indian regional scripts is an interesting area of research as almost 460 million people in India use regional scripts. The nine major Indian regional scripts are Bangla (for Bengali and Assamese languages), Gujarati, Kannada, Malayalam, Oriya, Gurumukhi (for Punjabi language), Tamil, Telugu, and Nastaliq (for Urdu language). A state-of-the-art survey about the techniques available in the area of offline handwriting recognition (OHR) in Indian regional scripts will be of a great aid to the researchers in the subcontinent and hence a sincere attempt is made in this article to discuss the advancements reported in this regard during the last few decades. The survey is organized into different sections. A brief introduction is given initially about automatic recognition of handwriting and official regional scripts in India. The nine regional scripts are then categorized into four subgroups based on their similarity and evolution information. The first group contains Bangla, Oriya, Gujarati and Gurumukhi scripts. The second group contains Kannada and Telugu scripts and the third group contains Tamil and Malayalam scripts. The fourth group contains only Nastaliq script (Perso-Arabic script for Urdu), which is not an Indo-Aryan script. Various feature extraction and classification techniques associated with the offline handwriting recognition of the regional scripts are discussed in this survey. As it is important to identify the script before the recognition step, a section is dedicated to handwritten script identification techniques. A benchmarking database is very important for any pattern recognition related research. The details of the datasets available in different Indian regional scripts are also mentioned in the article. A separate section is dedicated to the observations made, future scope, and existing difficulties related to handwriting recognition in Indian regional scripts. We hope that this survey will serve as a compendium not only for researchers in India, but also for policymakers and practitioners in India. It will also help to accomplish a target of bringing the researchers working on different Indian scripts together. Looking at the recent developments in OHR of Indian regional scripts, this article will provide a better platform for future research activities.
Word-based self-indexes for natural language text
Authors: Fariña Antonio , Brisaboa Nieves R. , Navarro Gonzalo , Claude Francisco , Places Ángeles S. , Rodríguez Eduardo
Published: March 2012

The inverted index supports efficient full-text searches on natural language text collections. It requires some extra space over the compressed text that can be traded for search speed. It is usually fast for single-word searches, yet phrase searches require more expensive intersections. In this article we introduce a different kind of index. It replaces the text using essentially the same space required by the compressed text alone (compression ratio around 35%). Within this space it supports not only decompression of arbitrary passages, but efficient word and phrase searches. Searches are orders of magnitude faster than those over inverted indexes when looking for phrases, and still faster on single-word searches when little space is available. Our new indexes are particularly fast at
counting
the occurrences of words or phrases. This is useful for computing relevance of words or phrases.

We adapt
self-indexes
that succeeded in indexing arbitrary strings within compressed space to deal with large alphabets. Natural language texts are then regarded as sequences of words, not characters, to achieve word-based self-indexes. We design an architecture that separates the
searchable
sequence from its
presentation
aspects. This permits applying case folding, stemming, removing stopwords, etc. as is usual on inverted indexes.
Static index pruning in web search engines
Authors: Altingovde Ismail S. , Ozcan Rifat , Ulusoy Özgür
Published: March 2012

Static index pruning techniques permanently remove a presumably redundant part of an inverted file, to reduce the file size and query processing time. These techniques differ in deciding which parts of an index can be removed safely; that is, without changing the top-ranked query results. As defined in the literature, the query view of a document is the set of query terms that access to this particular document, that is, retrieves this document among its top results. In this paper, we first propose using query views to improve the quality of the top results compared against the original results. We incorporate query views in a number of static pruning strategies, namely term-centric, document-centric, term popularity based and document access popularity based approaches, and show that the new strategies considerably outperform their counterparts especially for the higher levels of pruning and for both disjunctive and conjunctive query processing. Additionally, we combine the notions of term and document access popularity to form new pruning strategies, and further extend these strategies with the query views. The new strategies improve the result quality especially for the conjunctive query processing, which is the default and most common search mode of a search engine.
Summarizing figures, tables, and algorithms in scientific publications to augment search results
Authors: Bhatia Sumit , Mitra Prasenjit
Published: March 2012

Increasingly, special-purpose search engines are being built to enable the retrieval of document-elements like tables, figures, and algorithms [Bhatia et al. 2010; Liu et al. 2007; Hearst et al. 2007]. These search engines present a thumbnail view of document-elements, some document metadata such as the title of the papers and their authors, and the caption of the document-element. While some authors in some disciplines write carefully tailored captions, generally, the author of a document assumes that the caption will be read in the context of the text in the document. When the caption is presented out of context as in a document-element-search-engine result, it may not contain enough information to help the end-user understand what the content of the document-element is. Consequently, end-users examining document-element search results would want a short “synopsis” of this information presented along with the document-element. Having access to the synopsis allows the end-user to quickly understand the content of the document-element without having to download and read the entire document as examining the synopsis takes a shorter time than finding information about a document element by downloading, opening and reading the file. Furthermore, it may allow the end-user to examine more results than they would otherwise. In this paper, we present the first set of methods to extract this useful information (synopsis) related to document-elements automatically. We use Naïve Bayes and support vector machine classifiers to identify relevant sentences from the document text based on the similarity and the proximity of the sentences with the caption and the sentences in the document text that refer to the document-element. We compare the two classification methods and study the effects of different features used. We also investigate the problem of choosing the optimum synopsis-size that strikes a balance between the information content and the size of the generated synopses. A user study is also performed to measure how the synopses generated by our proposed method compare with other state-of-the-art approaches.
High-performance processing of text queries with tunable pruned term and term pair indexes
Authors: Broschart Andreas , Schenkel Ralf
Published: March 2012

Term proximity scoring is an established means in information retrieval for improving result quality of full-text queries. Integrating such proximity scores into efficient query processing, however, has not been equally well studied. Existing methods make use of precomputed lists of documents where tuples of terms, usually pairs, occur together, usually incurring a huge index size compared to term-only indexes. This article introduces a joint framework for trading off index size and result quality, and provides optimization techniques for tuning precomputed indexes towards either maximal result quality or maximal query processing performance under controlled result quality, given an upper bound for the index size. The framework allows to selectively materialize lists for pairs based on a query log to further reduce index size. Extensive experiments with two large text collections demonstrate runtime improvements of more than one order of magnitude over existing text-based processing techniques with reasonable index sizes.
Large-scale validation and analysis of interleaved search evaluation
Authors: Chapelle Olivier , Joachims Thorsten , Radlinski Filip , Yue Yisong
Published: March 2012

Interleaving is an increasingly popular technique for evaluating information retrieval systems based on implicit user feedback. While a number of isolated studies have analyzed how this technique agrees with conventional offline evaluation approaches and other online techniques, a complete picture of its efficiency and effectiveness is still lacking. In this paper we extend and combine the body of empirical evidence regarding interleaving, and provide a comprehensive analysis of interleaving using data from two major commercial search engines and a retrieval system for scientific literature. In particular, we analyze the agreement of interleaving with manual relevance judgments and observational implicit feedback measures, estimate the statistical efficiency of interleaving, and explore the relative performance of different interleaving variants. We also show how to learn improved credit-assignment functions for clicks that further increase the sensitivity of interleaving.
A survey of B-tree logging and recovery techniques
Authors: Graefe Goetz
Published: March 2012

B-trees have been ubiquitous in database management systems for several decades, and they serve in many other storage systems as well. Their basic structure and their basic operations are well understood including search, insertion, and deletion. However, implementation of transactional guarantees such as all-or-nothing failure atomicity and durability in spite of media and system failures seems to be difficult. High-performance techniques such as pseudo-deleted records, allocation-only logging, and transaction processing during crash recovery are widely used in commercial B-tree implementations but not widely understood. This survey collects many of these techniques as a reference for students, researchers, system architects, and software developers. Central in this discussion are physical data independence, separation of logical database contents and physical representation, and the concepts of user transactions and system transactions. Many of the techniques discussed are applicable beyond B-trees.
Attribute and object selection queries on objects with probabilistic attributes
Authors: Nuray-Turan Rabia , Kalashnikov Dmitri V. , Mehrotra Sharad , Yu Yaming
Published: March 2012

Modern data processing techniques such as entity resolution, data cleaning, information extraction, and automated tagging often produce results consisting of objects whose attributes may contain uncertainty. This uncertainty is frequently captured in the form of a set of multiple mutually exclusive value choices for each uncertain attribute along with a measure of probability for alternative values. However, the lay end-user, as well as some end-applications, might not be able to interpret the results if outputted in such a form. Thus, the question is how to present such results to the user in practice, for example, to support
attribute-value selection
and
object selection
queries the user might be interested in. Specifically, in this article we study the problem of maximizing the quality of these selection queries on top of such a probabilistic representation. The quality is measured using the standard and commonly used set-based quality metrics. We formalize the problem and then develop efficient approaches that provide high-quality answers for these queries. The comprehensive empirical evaluation over three different domains demonstrates the advantage of our approach over existing techniques.
Differentiating search results on structured data
Authors: Liu Ziyang , Chen Yi
Published: March 2012

Studies show that about 50% of Web search is for
information exploration
purposes, where a user would like to investigate, compare, evaluate, and synthesize multiple relevant results. Due to the absence of general tools that can effectively analyze and differentiate multiple results, a user has to manually read and comprehend potential large results in an exploratory search. Such a process is time consuming, labor intensive and error prone. Interestingly, we find that the metadata information embedded in structured data provides a potential for automating or semi-automating the comparison of multiple results.

In this article we present an approach for structured data search result differentiation. We define the differentiability of query results and quantify the degree of difference. Then we define the problem of identifying a limited number of valid features in a result that can maximally differentiate this result from the others, which is proved NP-hard. We propose two local optimality conditions, namely single-swap and multi-swap, and design efficient algorithms to achieve local optimality. We then present a feature type-based approach, which further improves the quality of the features identified for result differentiation. To show the usefulness of our approach, we implemented a system CompareIt, which can be used to compare structured search results as well as any objects. Our empirical evaluation verifies the effectiveness and efficiency of the proposed approach.
Shared execution strategy for neighbor-based pattern mining requests over streaming windows
Authors: Yang Di , Rundensteiner Elke A. , Ward Matthew O.
Published: March 2012

In diverse applications ranging from stock trading to traffic monitoring, data streams are continuously monitored by multiple analysts for extracting patterns of interest in real time. These analysts often submit similar pattern mining requests yet customized with different parameter settings. In this work, we present shared execution strategies for processing a large number of neighbor-based pattern mining requests of the same type yet with arbitrary parameter settings. Such neighbor-based pattern mining requests cover a broad range of popular mining query types, including detection of clusters, outliers, and nearest neighbors. Given the high algorithmic complexity of the mining process, serving multiple such queries in a single system is extremely resource intensive. The naive method of detecting and maintaining patterns for different queries independently is often infeasible in practice, as its demands on system resources increase dramatically with the cardinality of the query workload. In order to maximize the efficiency of the system resource utilization for executing multiple queries simultaneously, we analyze the commonalities of the neighbor-based pattern mining queries, and identify several general optimization principles which lead to significant system resource sharing among multiple queries. In particular, as a preliminary sharing effort, we observe that the computation needed for the range query searches (the process of searching the neighbors for each object) can be shared among multiple queries and thus saves the CPU consumption. Then we analyze the interrelations between the patterns identified by queries with different parameters settings, including both pattern-specific and window-specific parameters. For that, we first introduce an incremental pattern representation, which represents the patterns identified by queries with different pattern-specific parameters within a single compact structure. This enables integrated pattern maintenance for multiple queries. Second, by leveraging the potential overlaps among sliding windows, we propose a metaquery strategy which utilizes a single query to answer multiple queries with different window-specific parameters. By combining these three techniques, namely the range query search sharing, integrated pattern maintenance, and metaquery strategy, our framework realizes fully shared execution of multiple queries with arbitrary parameter settings. It achieves significant savings of computational and memory resources due to shared execution. Our comprehensive experimental study, using real data streams from domains of stock trades and moving object monitoring, demonstrates that our solution is significantly faster than the independent execution strategy, while using only a small portion of memory space compared to the independent execution. We also show that our solution scales in handling large numbers of queries in the order of hundreds or even thousands under high input data rates.
Understanding cardinality estimation using entropy maximization
Authors: Ré Christopher , Suciu D.
Published: March 2012

Cardinality estimation is the problem of estimating the number of tuples returned by a query; it is a fundamentally important task in data management, used in query optimization, progress estimation, and resource provisioning. We study cardinality estimation in a principled framework: given a set of statistical assertions about the number of tuples returned by a fixed set of queries, predict the number of tuples returned by a new query. We model this problem using the probability space, over possible worlds, that satisfies all provided statistical assertions and maximizes entropy. We call this the Entropy Maximization model for statistics (MaxEnt). In this article we develop the mathematical techniques needed to use the MaxEnt model for predicting the cardinality of conjunctive queries.
Exploiting Web querying for Web people search
Authors: Nuray-Turan Rabia , Kalashnikov Dmitri V. , Mehrotra Sharad
Published: March 2012

Searching for people on the Web is one of the most common query types submitted to Web search engines today. However, when a person name is queried, the returned Webpages often contain documents related to several distinct namesakes who have the queried name. The task of disambiguating and finding the Webpages related to the specific person of interest is left to the user. Many Web People Search (WePS) approaches have been developed recently that attempt to automate this disambiguation process. Nevertheless, the disambiguation quality of these techniques leaves major room for improvement. In this article, we present a new WePS approach. It is based on issuing additional auxiliary queries to the Web to gain additional knowledge about the Webpages that need to be disambiguated. Thus, the approach uses the Web as an external data source by issuing queries to collect co-occurrence statistics. These statistics are used to assess the overlap of the
contextual entities
extracted from the Webpages. The article also proposes a methodology to make this Web querying technique efficient. Further, the article proposes an approach that is capable of combining various types of disambiguating information, including other common types of similarities, by applying a correlation clustering approach with after-clustering of singleton clusters. These properties allow the framework to get an advantage in terms of result quality over other state-of-the-art WePS techniques.
Crawling Ajax-Based Web Applications through Dynamic Analysis of User Interface State Changes
Authors: Mesbah Ali , van Deursen Arie , Lenselink Stefan
Published: March 2012

Using
JavaScript
and dynamic DOM manipulation on the client side of Web applications is becoming a widespread approach for achieving rich interactivity and responsiveness in modern Web applications. At the same time, such techniques---collectively known as
Ajax
---shatter the concept of webpages with unique URLs, on which traditional Web crawlers are based. This article describes a novel technique for crawling
Ajax
-based applications through automatic dynamic analysis of user-interface-state changes in Web browsers. Our algorithm scans the DOM tree, spots candidate elements that are capable of changing the state, fires events on those candidate elements, and incrementally infers a state machine that models the various navigational paths and states within an
Ajax
application. This inferred model can be used in program comprehension and in analysis and testing of dynamic Web states, for instance, or for generating a static version of the application. In this article, we discuss our sequential and concurrent
Ajax
crawling algorithms. We present our open source tool called
Crawljax
, which implements the concepts and algorithms discussed in this article. Additionally, we report a number of empirical studies in which we apply our approach to a number of open-source and industrial Web applications and elaborate on the obtained results.
DoublePlay
Authors: Veeraraghavan Kaushik , Lee Dongyoon , Wester Benjamin , Ouyang Jessica , Chen Peter M. , Flinn Jason , Narayanasamy Satish
Published: March 2012

Deterministic replay systems record and reproduce the execution of a hardware or software system. In contrast to replaying execution on uniprocessors, deterministic replay on multiprocessors is very challenging to implement efficiently because of the need to reproduce the order of or the values read by shared memory operations performed by multiple threads. In this paper, we present DoublePlay, a new way to efficiently guarantee replay on commodity multiprocessors. Our key insight is that one can use the simpler and faster mechanisms of single-processor record and replay, yet still achieve the scalability offered by multiple cores, by using an additional execution to parallelize the record and replay of an application. DoublePlay timeslices multiple threads on a single processor, then runs multiple time intervals (
epochs
) of the program concurrently on separate processors. This strategy, which we call
uniparallelism
, makes logging much easier because each epoch runs on a single processor (so threads in an epoch never simultaneously access the same memory) and different epochs operate on different copies of the memory. Thus, rather than logging the order of shared-memory accesses, we need only log the order in which threads in an epoch are timesliced on the processor. DoublePlay runs an additional execution of the program on multiple processors to generate checkpoints so that epochs run in parallel. We evaluate DoublePlay on a variety of client, server, and scientific parallel benchmarks; with spare cores, DoublePlay reduces logging overhead to an average of 15% with two worker threads and 28% with four threads.
Improving Software Diagnosability via Log Enhancement
Authors: Yuan Ding , Zheng Jing , Park Soyeon , Zhou Yuanyuan , Savage Stefan
Published: March 2012

Diagnosing software failures in the field is notoriously difficult, in part due to the fundamental complexity of troubleshooting
any
complex software system, but further exacerbated by the paucity of information that is typically available in the production setting. Indeed, for reasons of both overhead and privacy, it is common that only the run-time log generated by a system (e.g., syslog) can be shared with the developers. Unfortunately, the ad-hoc nature of such reports are frequently insufficient for detailed failure diagnosis. This paper seeks to improve this situation within the rubric of existing practice. We describe a tool,
LogEnhancer
that automatically “enhances” existing logging code to aid in future post-failure debugging. We evaluate
LogEnhancer
on eight large, real-world applications and demonstrate that it can dramatically reduce the set of potential root failure causes that must be considered while imposing negligible overheads.
Oxidation of indolic bases by cytochrome P450 and ferrous picolinate
Authors: Jankowski K. , Delaforge M. , Jaouen M. , Virelizier H.
Published: March 2012

Oxidations performed on four indolic bases, β‐carboline 1, ibogaine 2, reserpine 3 and ajmaline 4, by hepatic cytochrome P450 (Cyt. P450) and ferrous picolinate (Fe(PA)2), lead to alicyclic hydroxylation as major reaction products.
Discrimination of structural isomers of amphetamine using carbon dioxide negative‐ion chemical ionization mass spectrometry
Authors: Thurbide Kevin B. , Elson C. M. , Sim P. G.
Published: March 2012

The negative‒ion chemical ionization mass spectra of a group of structural isomers of amphetamine have been studied using carbon dioxide as the reagent gas. Characteristic and reproducible differences are observed for each member of the set implying that this technique offers a means of distinguishing among groups of amphetamine isomers. Characteristic adducts to the molecular ion are observed in the form (M–[H]+[O]) and (M–[H]+[CO2]). Descriptions of some fragments are given based on the mass spectral behaviour of a set of analogue compounds and the results of oxygen‐18 labelled carbon dioxide reagent gas experiments. Contents of the carbon dioxide plasma and their impact on various analytes is also discussed.
Ditregra – an auxiliary program for structural determination of diterpenes
Authors: Alvarenga Sandra A. Vestri , Gastmans Jean Pierre , Rodrigues Gilberto do Vale , Emerenciano Vicente de Paulo
Published: March 2012

This work describes the creation of heuristics rules based on 13C‐NMR spectroscopy that characterize several skeletal types of diterpenes. Using a collection of 2745 spectra we built a database linked to the expert system SISTEMAT. Several programs were applied to the database in order to discover characteristic signals that identify with a good performance, a large diversity of skeletal types. The heuristic approach used was able to differentiate groups of skeletons based firstly on the number of primary, secondary, tertiary and quaternary carbons, and secondly the program searches, for each group, if there are ranges of chemical shifts that identifies specific skeletal type. The program was checked with 100 new structures recently published and was able to identify the correct skeleton in 65 of the studied cases. When the skeleton has several hundreds of compounds, for example, the labdanes, the program employs the concept of subskeletal, and does not classify in the same group labdanes with double bounds at different positions. The chemical shift ranges for each subskeletal types and the structures of all skeletal types are given. The consultation program can be obtained from the authors.
Characterisation of the covalent structure of proteins from biological material by MALDI mass spectrometry ‣ possibilities and limitations
Authors: Kussmann Martin , Roepstorff Peter
Published: March 2012

Matrix‐assisted laser desorption/ionisation mass spectrometry (MALDI‐MS) has become a primary tool for the detailed characterisation of the covalent structure of proteins isolated from biological material, mainly because of its following potentials: high sensitivity and specificity, speed of analysis, appropriateness for mixture analysis, high tolerance towards contaminants, and compatibility with separation techniques, e.g., gel electrophoresis. These characteristics enable the structural analysis of proteins even if they are only available in limited amounts and/or in mixtures, and even if the protein preparations contain large amounts of salts, buffers, detergents and denaturants. Additionally, structural data can be generated within a relatively short time.

Whereas X‐ray crystallography and multidimensional NMR techniques can provide “absolute” structural data, i.e., a three‐dimensional “picture” of the protein of interest, MALDI‐MS‐especially in combination with selective protein chemistry – yields information on particular aspects of the entire protein structure, e.g., primary structure, active site(s), binding sites, and posttranslational modifications, all of which are often of crucial interest for the understanding of the protein function. Taking into account that protein crystallography and protein NMR studies require large quantities of highly purified sample, MALDI‐MS can be even more regarded as a powerful complement in protein structure analysis.

This review aims at describing the state‐of‐the‐art of MALDI‐MS for characterisation of proteins from biological material by evaluating its potential and limitations.
Determination of 1,5‒anhydro‒glucitol–carrier protein conjugates by matrix‒assisted laser desorption/ionization tof mass spectrometry and antibody formation
Authors: Xuan Li-Jiang , Tanaka Hiroyuki , Morimoto Satoshi , Shoyama Yukihiro , Akanuma Hiroshi , Muraoka Keiji
Published: March 2012

In order to prepare the monoclonal antibody against 1,5‐anhydro‐glucitol (1), it was conjugated with bovine serum albumin (BSA), human serum albumin (HSA) or chicken lysozyme (CL) using succinate or β‐alanine succinate as a spacer to produce individual antigen conjugates. The number of hapten contained in each antigen conjugate was determined by matrix‐assisted laser desorption/ionization tof mass (MALDI‐tof‐MS) spectrometry. The formation of monoclonal antibody (MAb) was also discussed.
Spectroscopic scale protection factor (SSPF) of solar ultraviolet radiation molecular screens. II. Substituent effect on salicylideneaniline
Authors: Morales Raúl G. E. , Hidrobo Alexis , Jara Gregorio P.
Published: March 2012

Salicylideneanilines present a broad absorption band and a high molar absorption coefficient in the UV‐A and UV‐B regions. In addition, they are photostable compounds to the solar radiation exposition. Therefore, we have recently established their potential use as a solar ultraviolet radiation molecular screens.

In the present work we have determined the dependence of the Spectroscopic Scale Protection Factor (SSPF) values with the substituent effect on the aniline ring of the salicylidene, when the substituent is an electron‐acceptor group (–CN, –COCH3, –NO2) and we have compared this effect with and without an electron‐donor group (–OCH3) at para position in the salicylidene ring.

In order to determine and compare these SSPF values versus the usual Sun Protection Factor (SPF) values, a relative scale of biological nature, we have determined the electronic absorption spectra of these substituted salicylideneaniline compounds, and we have compared these spectroscopic data with homosalate, as an SPF standard compound. Our results are conclusive respect to determine the salicylideneanilines as a new family of molecular species highly efficient in the molecular screen role.
Solution and solid state (CPMAS) NMR studies of the tautomerism of six‐membered heterocyclic compounds related to 2‐pyridones
Authors: López Concepción , Claramunt Rosa María , Alkorta Ibon , Elguero José
Published: March 2012

Several 13C and 15N chemical shifts of 2‐pyridone (1), 4(3H)‐pyrimidone (2), uracil (3) and cytosine (4) have been measured in solution and in the solid state. These data have been discussed in relation with the tautomerism of the four heterocycles. GIAO ab initio calculations of absolute shieldings have been carried out to identify the predominant tautomers in the case of compounds (1) and (2).
Chemical structures of macrocyclic bis(bibenzyls) isolated from liverworts (Hepaticae)
Authors: Asakawa Yoshinori , Toyota Masao , Tori Motoo , Hashimoto Toshihiro
Published: March 2012

Liverworts (Hepaticae) produce a number of macrocyclic bis(bibenzyls) which show interesting biological activity and are of very valuable for the chemosystematic study of liverworts. The structural elucidation of these characteristic natural products are reviewed.
Electrospray‐mass spectrometric studies of selectivity of alkali metal cations extraction by calix[4]arene crowns
Authors: Allain F. , Virelizier H. , Moulin C. , Jankowski C. K. , Dozol J. F. , Tabet J. C.
Published: March 2012

Electrospray Ionization Mass Spectrometry (ESI/MS) has quickly become a versatile method of qualitative analysis of a wide variety of host–guest complexes formed in solution. However, considerable controversy exists on how ESI spectra quantitatively reflect and compare to the results obtained on these complexes. The extraction of alkali cations from acidic aqueous solutions by nine various calix[4]arenes‐crown‐6 diluted in NPOE, was studied by using ESI/MS. The stoichiometry of cesium complex and Cs+/Na+ selectivity were evaluated.
FTIR microscopy as a method for detection of retrovirally transformed cells
Authors: Huleihel Mahmoud , Talyshinsky Marina , Erukhimovitch Vitaly
Published: March 2012

Fourier transform infrared (FTIR) spectroscopy is a unique technique that has potential for the optical diagnosis of cellular variations based on the characteristic molecular vibrational spectra of the cells. In the present study, a refinement of this technique − FTIR microscopy − was used in a mouse model to investigate spectral differences between primary cells and malignant cells transformed by murine sarcoma virus (MuSV). The advantage of FTIR microscopy is that it facilitates inspection of a restricted region of cell growth on a slide. A significant decrease in the intensities of the spectra was seen in malignant cells transformed by MuSV compared to primary normal cells. Also, there was a significant shift in the PO2− symmetric stretching mode from 1082 cm−1 for normal cells to 1086 cm−1 for malignant cells. Detectable and consistent differences between normal primary and malignant cells were evident in the shapes and positions of a number of peaks in the FTIR spectra. Our results indicated that FTIR microscopy has potential as a diagnostic method for the detection of malignant cells.
The structure of linoleic acid ester of trans‐lachnophyllol isolated from Aster tataricus
Authors: Tori Motoo , Murata Junko , Nakashima Katsuyuki , Sono Masakazu
Published: March 2012

A linoleic acid ester of an alcohol possessing two triple bonds (trans‐lachnophyllol) has been isolated from the root of Aster tataricus, and its structure determined based on the spectroscopic evidence.
Vitamin D2 at high and low concentrations exert opposing effects on molecular order and dynamics of dipalmitoyl phosphatidylcholine membranes
Authors: Kazanci Nadide , Toyran Neslihan , Haris Parvez I. , Severcan Feride
Published: March 2012

Fourier Transform Infrared spectroscopic studies show that low concentrations of vitamin D2 (1 and 3 mol %) does not induce significant change in the overall shape of the thermotropic profile of dipalmitoyl phosphatidylcholine (DPPC) membrane. In contrast, at higher concentrations of vitamin D2 (9 and 12 mol %), the phase transition shifts to lower temperatures and a significant broadening in the phase transition curve is also observed. Low concentration of vitamin D2 decreases the frequency of the CH2 stretching mode, implying an ordering effect, whilst high concentration of vitamin D2 disorders the system. Furthermore, at low and high concentrations, vitamin D2 causes opposing effect on membrane dynamics. It decreases the bandwidth of the CH2 stretching modes at low concentrations while increasing it at high concentrations. We have also observed different actions of vitamin D2 at low and high concentrations in the deep interior and interfacial region of the membrane, by monitoring the frequency of the CH3 stretching band and C=O stretching bands, respectively.
Plasmon resonance spectroscopy: probing molecular interactions at surfaces and interfaces
Authors: Salamon Zdzislaw , Tollin Gordon
Published: March 2012

Surface plasmon resonance (SPR) spectroscopy can be applied to a wide variety of interfacial systems. It involves resonant excitation by polarized light of electronic oscillations (plasmons) in a thin metal film. These generate a surface‒localized evanescent electromagnetic field that can be used to probe the optical properties perpendicular to the film plane of materials immobilized at the surface. Spectra depend on three parameters: refractive index (n), absorption coefficient (k) and thickness (t). Maxwell′s equations provide an analytical relationship between these properties and SPR spectra, allowing their evaluation. An extension of this methodology, called coupled plasmon‒waveguide resonance (CPWR or PWR), is able to characterize film properties both perpendicular and parallel to the surface plane. In a PWR device, the metal film is covered with a dielectric coating that acts as an optical amplifier, provides protection for the metal layer, and possesses a surface that allows various molecular immobilization strategies. The exceptionally narrow line widths of PWR spectra yield enhanced sensitivity and resolution. The application of this technology to several biomembrane systems will be described, demonstrating its ability to observe both binding and structural events occurring during membrane protein function.
Aggregation and properties of α‒synuclein and related proteins
Authors: El-Agnaf Omar M. A. , Irvine G. Brent
Published: March 2012

α‐Synuclein has been identified as a component of intracellular fibrillar protein deposits in several neurodegenerative diseases, and two mutant forms have been associated with early onset Parkinson′s disease. A fragment of α‐synuclein has also been identified as the non‐Aβ component of Alzheimer′s disease amyloid (NAC). Ageing solutions of α‐synuclein and NAC leads to formation of β‐sheet, detectable by circular dichroism spectroscopy, and aggregation to form amyloid‐like fibrils, detectable by electron microscopy. Differences in the rates of aggregation of the fibrils formed by α‐synuclein and the two mutant proteins are presented. The toxicity of α‐synuclein and related peptides towards neurons is also discussing in relation to the aetiology of neurodegenerative diseases.

Experiments on fragments of NAC have enabled the region of NAC responsible for its aggregation and toxicity to be identified.
Fragmentation studies of tetrahydropyridocarbazole derivatives by EI, ESI‐MS/MS and FAB
Authors: Romeiro Gilberto A. , Ferreira Vitor F. , Costa Marília dos S. , Joaquim Alexandre M. , Carneiro José Walkimarde M. , Kammerer Bernd
Published: March 2012

Four tetrahydropyridocarbazole derivatives were analysed by different mass spectrometry techniques: electrospray ionization, fast atom bombardment and by low and high resolution 70 eV electron ionization. Retro Diels Alder is the main fragmentation pathway, whereas other pathways leading to [M—1]+, [M—CH3]+ and double charge ions also occur to considerable extents. Semi‐empirical calculation provided some evidence on the nature of tropylium ions [M—1]+. Calculation of ΔHf0 indicated that [M+—1] could be formed preferentially when a hydrogen atom is lost from the methyl substituent of the homoaromatic ring.
Use of MALDI‐TOF Mass Spectrometry for Specificity Studies of Biomedically Important Proteases
Authors: Siigur Jüri , Trummal Katrin , TÕnismägi Külli , Samel Mari , Siigur Ene , Vija Heikki , Tammiste Indrek , Subbi Juhan
Published: March 2012

Proteases play crucial role starting from fertilization until to cell death. Our studies of the two Viperidae venoms (Levantine viper Vipera lebetina, Common viper Vipera berus) have demonstrated the existence of biomedically important proteases, both coagulants and anticoagulants that may be useful as diagnostic tools or potential therapeutics. We showed that venoms of both snakes contain: (i) metalloproteases and serine proteases that degrade fibrinogen, but not fibrin; (ii) factor X activators (VLFXA, VBFXAE); (iii) bradykinin‐releasing serine proteases. Additionally Vipera lebetina snake venom contains thrombolytic fibrin degrading metalloenzyme (lebetase), HUVEC cell apoptosis inducing metalloprotease (VLAIP), factor V activator (VLFVA), thermostable β‐fibrinogenase and α‐fibrinogenase which has no homolog among known serine proteases. We examined the activity of snake venom proteases against bradykinin, substance P, insulin B‐chain and 6–10 amino acid residues containing peptides synthesized according to potential cleavage regions of fibrinogen, factor X, factor IX, factor V, α2‐macroglobulin bait region and pregnancy zone protein (PZP). We used MALDI TOF mass spectrometry technique for the discovery and identification of peptides released by protease hydrolysis. The sensitive and quick MALDI‐TOF mass spectrometry methodology allows us to obtain the primary information about the substrate specificity of different proteases against various peptides and proteins.
Magnetization‒transfer 31P NMR of biochemical exchange in vivo: Application to creatine kinase kinetics
Authors: Möller Harald E. , Wiedermann Dirk
Published: March 2012

Phosphorus‒31 saturation‒transfer NMR spectroscopy provides an elegant means to study fluxes through the creatine kinase reaction in human skeletal muscle. To obtain reliable quantitative kinetic information, experimental imperfections, such as incomplete saturation and radiofrequency bleed over need to be addressed appropriately. In resting muscle, creatine kinase was near equilibrium both in normal controls and in a patient with impaired oxidative phosphorylation. Oral intake of high doses of creatine monohydrate for several days resulted in significantly increased concentrations of phosphocreatine but had no measurable effect on the phosphocreatine resynthesis rate in resting muscle.
Infrared Spectroscopic Studies on the Dipalmitoyl Phosphatidylcholine Bilayer Interactions with Calcium Phosphate: Effect of Vitamin D2
Authors: Toyran Neslihan , Severcan Feride
Published: March 2012

In the present work, the interaction of calcium‐phosphate with DPPC (dipalmitoyl phosphatidylcholine) model membranes has been studied in the presence and absence of vitamin D2 by using Fourier Transform Infrared (FTIR) spectroscopy. Calcium and phosphorus are the most abundant elements in the body. They combine in the form of calcium phosphate salt, called hydroxyapatite. Hydroxyapatite is the major structural component of the bone. Calcium phosphate assists with the digestion and absorption of food and is vitally important for the building of sturdy bone and body structures and a robust constitution. Phosphorus is extracted from foods and its use is controlled by vitamin D and calcium. FTIR spectral analysis results suggested that, calcium–phosphate complex, which is the major component of the bones, decreases the phase transition temperature to lower values, causes a loss in cooperativity of the acyl chains, decreases the order of the membrane in both phases and decreases the dynamics of the membrane in the liquid crystalline phase, increases the flexibility of the chains in the center of the bilayer in both phases, and increases the mobility of the head group of DPPC in the gel phase. The effect of calcium‐phosphate on DPPC liposomes diminishes with the addition of vitamin D2 into the liposomes. Our results suggest how calcium‐phosphate and/or vitamin D2, which have indispensable role for the functioning of the bone tissue, affect the thermal behaviour of DPPC liposomes at molecular level.
Teas: Direct Test on Quality and Antioxidant Activity using Electron Paramagnetic Resonance Spectroscopy
Authors: Morsy M. A.
Published: March 2012

The manufactured teas may conveniently be divided into three classes: Green teas, Oolongs (delicate black teas), and Black Teas. Several indirect methods are employed to measure the antioxidant activity of tea extracts that is basically takes place by monitoring the inhibition of oxidation of a suitable substrate using the extracts of antioxidant materials from the studies systems. This study is concerned with the results of electron paramagnetic resonance (EPR) spectroscopy that is utilized to investigate several categories of green and black teas: Twining Green Tea (TGT) of London, Rabea Green Tea (RGT) of Saudia, Chinese Green Tea (CGT) of China, English Breakfast Tea (EBT) of Ahmed Tea‐London, and Rabea Black Tea (RBT) of Saudia. Three EPR signals from all the studied samples are observed. The assignment of these signals will discussed and correlated with the quality of leaves. Mainly, two paramagnetic species are considered to be responsible for the observed EPR signals; manganese(II)–protein system of the leaves and a stable free radical of aromatic origin. The study will provide facts on the dependency of radical signal on the oxidative degradation procedures of the studied samples. The intensity and feature of Mn(II)‐EPR‐signal is found to be related to the disintegration of tea leaves.
Noninvasive Estimation of Temperature and pH in Human Lower Leg Muscles using 1H Nuclear Magnetic Resonance Spectroscopy
Authors: Yoshioka Yoshichika , Oikawa Hiroshi , Ehara Sigeru , Inoue Takashi , Ogawa Akira , Kambara Yoshiyuki , Itazawa Shun-Ichi , Kubokawa Manabu
Published: March 2012

The temperature and pH of human lower leg muscles were estimated noninvasively using 1H‐NMR spectroscopy at 3.0 and 1.5 T on five normal volunteers (21M, 24M, 27M, 34M, 47M). The chemical shifts of water and imidazole protons relative to cholines (–N+CH3) or creatines (–CH3) could be used as the temperature and pH probes, respectively [1–4]. Using the chemical shift, estimated values of the temperature in gastrocnemius (GAS; shell region) and soleus muscles (SOL; core region) under ambient temperature (21–25°C) were 33.6±0.4 and 35.3±0.4°C (mean±SE), respectively (significantly different; P < 0.01). The values of pH in these muscles were estimated to be 6.97 ± 0.01 and 6.96 ± 0.02, respectively. Alternation of the surface temperature of the lower leg from 40 to 10°C significantly changed the temperature in GAS (P < 0.0001) from 35.8 ± 0.4 to 26.2 ± 1.2°C and the pH in GAS rose from 6.95 ± 0.01 to 7.01 ± 0.01 (P <0.01). However, the values of pH and temperature in SOL were not significantly affected by this maneuver. These results indicate that the pH in GAS was moderately changed by muscle temperature (r= –0.59, P <0.01), and its change was estimated to be –0.005 pH units/°C.