bluuebunny/crossref_metadata_2025_split huggingface dataset:
Equivalent public keys and a key substitution attack on the schemes from vector decomposition
Authors: Lim Seongan , Lee Eunjeong , Park Cheol‐Min 
Published: September 2013

ABSTRACTThe vector decomposition problem has been considered as a hard problem, which is applicable to cryptography. Okamoto and Takashima proposed various types of public key cryptographic schemes based on the VDP. In this paper, we study the cryptographic implications of Okamoto‐Takashima schemes with respect to the properties of public keys. In the public key cryptography, one public key is associated to a unique private key, and an action using the public key implicitly assumes that the corresponding private action can be done only with the corresponding private key. We formalize this security issue by introducing the notion of equivalent public keys. We show that equivalent public keys exist in the Okamoto‐Takashima basic signature scheme and the homomorphic encryption scheme. We present a strong key substitution attack to their basic signature. We suggest how to prevent equivalent public keys and strong key substitution attack in their signature scheme. We point out that there are cases with no efficient methods to prevent equivalent public keys in their encryption scheme. Copyright © 2013 John Wiley & Sons, Ltd.
Thermostabilization ofBacillus subtilislipase A by minimizing the structural deformation caused by packing enhancement
Authors: Yun Hong Seung , Park Hyun June , Joo Jeong Chan , Yoo Young Je 
Published: September 2013

AbstractEnzyme thermostabilization is a critical research topic due to potential industrial benefits. Among the various reasons to increase enzyme thermostability, enhancement of residual packing at the core of the enzyme structure has been commonly accepted as a successful strategy. However, structural changes that occur with residual packing enhancement may decrease enzyme activity. In this study, a strategy to minimize structural deformation by calculating the overlapping packing volume of a single-point mutation followed by applying a double-point mutation was suggested. Four double mutants, A38V_K23A, A75V_T83A, G80A_N106A, and G172A_V100A, were selected for the in vitro experiment; three of the four showed enhancements in both thermostability and catalytic activity. In particular, G80A_N106A showed 2.78 times higher catalytic activity compared with wild type.
Milking efficiency of swingover herringbone parlours in pasture-based dairy systems
Authors: Edwards J Paul , O'Brien Bernadette , Lopez-Villalobos Nicolas , Jago Jenny G 
Published: September 2013

The objective of this study was to collect and analyse milking data from a sample of commercial farms with swingover herringbone parlours to evaluate milking efficiency over a range of parlour sizes (12–32 milking units). Data were collected from 19 farms around the Republic of Ireland equipped with electronic milk metres and herd management software that recorded data at individual milking sessions. The herd management software on each farm was programmed to record similar data for each milking plant type. Variables recorded included cow identification, milking date, identification time, cluster-attachment time, cluster/unit number, milk yield, milking duration, and average milk flow rate. Calculations were performed to identify efficiency benchmarks such as cow throughput (cows milked per h), milk harvesting efficiency (kg of milk harvested per h) and operator efficiency (cows milked per operator per h). Additionally, the work routine was investigated and used to explain differences in the benchmark values. Data were analysed using a linear mixed model that included the fixed effects of season-session (e.g. spring-AM), parlour size and their interaction, and the random effect of farm. Additionally, a mathematical model was developed to illustrate the potential efficiency gains that could be achieved by implementing a maximum milking time (i.e. removing the clusters at a pre-set time regardless of whether the cow had finished milking or not). Cow throughput and milk harvesting efficiency increased with increasing parlour size (12 to 32 units), with throughput ranging from 42 to 129 cows/h and milk harvesting efficiency from 497 to 1430 kg/h (1–2 operators). Greater throughput in larger parlours was associated with a decrease in operator idle time. Operator efficiency was variable across farms and probably dependent on milking routines in use. Both of these require consideration when sizing parlours so high levels of operator efficiency as well as cow throughput can be achieved simultaneously. The mathematical model indicated that application of a maximum milking time within the milking process could improve cow throughput (66% increase in an 18-unit parlour when truncating the milking time of 20% of cows). This could allow current herd milking durations to be maintained as herd size increases.
Ultraviolet emission from high-quality crystalline ultra-long AlN whiskers
Authors: Zuo Sibin , Zhang Haiyun , Wang Jun , Wang Wenjun 
Published: September 2013

We report here the fabrication and characterization of ultra-long AlN whiskers by physical vapor transport method. The obtained whiskers are 1–3 µm in diameter and up to millimeters in length. The whiskers grow along the [0001] crystallographic direction and are well crystallized. They exhibit a strong ultraviolet emission at 345 nm, the shortest wavelength reported in AlN whiskers or nanowires. Our results indicate that these large scales of AlN whiskers are less contaminated by oxygen and other impurities compared with the previously reported ones, which may find wide applications in fabricating ultraviolet optoelectronic devices.
Synchrotron X-Ray Microanalysis and Imaging of Synthetic Biological Calcium Carbonate in Comparison With Archaeological Samples Originating from the Large Cave of Arcy-sur-Cure (28000-24500 BP, Yonne, France)
Authors: Chalmin Emilie , Reiche Ina 
Published: September 2013

AbstractBiosynthetic calcite samples were investigated using combined synchrotron X-ray microspectroscopy mapping. These samples were prepared with bacteria isolated from the Large cave of Arcy-sur-Cure in which prehistoric figures are masked by an opaque calcite layer. The biotic or abiotic origin of this layer is the issue of the present work. As previously known, a large community of bacteria may be involved in the CaCO3 formation in caves. A mixture of calcite/vaterite was obtained from bacteria isolated from the cave. Therefore, we can offer conclusions on their calcifying capability. The rare presence of vaterite in cave environments may be treated as a marker of biotic carbonate formations. Moreover, an amorphous calcium phosphate phase was present in the form of a calcite/vaterite mixture in the biotic model samples. This mixture of phases could be used as a tracer of the biotic process of CaCO3 formation. These biotic tracer phases were not identified using the applied analytical methods in the natural samples taken from the opaque calcite layers that covered the prehistoric figures of the Large cave. In this case, based on the obtained results, the biotic calcite formation process is likely to be considered as an undetectable effect at minimum.
APPROXIMATING THE KOHLRAUSCH FUNCTION BY SUMS OF EXPONENTIALS
Authors: ZHONG MIN , LOY R. J. , ANDERSSEN R. S. 
Published: September 2013

AbstractThe Kohlrausch functions $\exp (- {t}^{\beta } )$, with $\beta \in (0, 1)$, which are important in a wide range of physical, chemical and biological applications, correspond to specific realizations of completely monotone functions. In this paper, using nonuniform grids and midpoint estimates, constructive procedures are formulated and analysed for the Kohlrausch functions. Sharper estimates are discussed to improve the approximation results. Numerical results and representative approximations are presented to illustrate the effectiveness of the proposed method.
A EUROPEAN OPTION GENERAL FIRST-ORDER ERROR FORMULA
Authors: LEDUC GUILLAUME 
Published: September 2013

AbstractWe study the value of European security derivatives in the Black–Scholes model when the underlying asset $\xi $ is approximated by random walks ${\xi }^{(n)} $. We obtain an explicit error formula, up to a term of order $ \mathcal{O} ({n}^{- 3/ 2} )$, which is valid for general approximating schemes and general payoff functions. We show how this error formula can be used to find random walks ${\xi }^{(n)} $ for which option values converge at a speed of $ \mathcal{O} ({n}^{- 3/ 2} )$.
Octave effect in auditory attention
Authors: Borra Tobias , Versnel Huib , Kemner Chantal , van Opstal A. John , van Ee Raymond 
Published: September 2013

Significance
The human auditory system can filter sounds to select specific information. For example, when attention is “drawn” toward a tone of 1,000 Hz, the ear becomes more sensitive to that tone than to other tones. Here, we report that attention is drawn not only toward one specific frequency, as previously was assumed, but to octave-related frequencies as well. We show that this “octave effect” does not require the physical presence of the attended tone, as it persists for imagined tones: thinking of a tone increases sensitivity for the imagined tone and its octave-related frequencies. We speculate that the octave effect evolved from exposure to natural vibrations containing octave-related spectral peaks, e.g., as produced by the human vocal cords.
Priming of jasmonate-mediated antiherbivore defense responses in rice by silicon
Authors: Ye Mao , Song Yuanyuan , Long Jun , Wang Ruilong , Baerson Scott R. , Pan Zhiqiang , Zhu-Salzman Keyan , Xie Jiefen , Cai Kunzheng , Luo Shiming , Zeng Rensen 
Published: September 2013

Significance
Silicon (Si) is the second most abundant element in soil, and it can increase plant resistance against many abiotic and biotic stresses. The jasmonate (JA) signaling pathway plays a crucial role in mediating antiherbivore defense responses in plants. Our work shows that Si primes JA-mediated antiherbivore defense responses and increases rice resistance to the leaffolder caterpillar and that Si accumulation in rice leaves is mediated by the JA pathway, suggesting a strong interaction between Si and JA in rice defense against insect herbivores. This interaction may represent a widespread mechanism by which Si enhances plant resistance against biotic stresses in Si-accumulating plants.
Manipulating L-type calcium channels in cardiomyocytes using split-intein protein transsplicing
Authors: Subramanyam Prakash , Chang Donald D. , Fang Kun , Xie Wenjun , Marks Andrew R. , Colecraft Henry M. 
Published: September 2013

Significance
Manipulating expression of proteins directly in isolated heart cells is an important method to study cardiac biology and disease. However, this approach is challenging for large genes (>6 kb) because these exceed the packaging capacity of commonly used viral vectors used to deliver genes into heart cells. Here, we used a split-intein–mediated protein transsplicing strategy to reconstitute the large pore-forming subunit of L-type calcium channels from two separate fragments in heart cells. This approach provides a general method to express different large proteins in heart cells and will help advance new insights into basic mechanisms underlying cardiac function and disease.
Variance in mating success does not produce strong sexual selection in a polygynous songbird
Authors: Sousa Bridget F. , Westneat David F. 
Published: September 2013

AbstractThe sexually dimorphic ornaments and songs of birds are generally thought to be the result of sexual selection. For some time, variation in dimorphism among taxa was attributed to differences in social mating patterns. However, extrapair mating provides an alternative mechanism for sexual selection in both monogamous and polygynous birds. In monogamous systems, extrapair mating typically increases variance in mating success and hence sexual selection. However, it is less clear how extrapair mating influences sexual selection in polygynous species. We measured sexual selection acting on 6 sexually dimorphic male traits in a polygynous songbird, the dickcissel (Spiza americana). We also examined patterns of association between social and extrapair mating success, between male traits and reproductive success within each mating context, and the contribution of each type of mating to overall reproductive success. Despite high variance in both mating success and male traits, we found no evidence for current sexual selection in dickcissels. Indeed, variance among males in dimorphic traits did not significantly contribute to male success in any mating context. These results add to an array of studies uncovering relatively weak sexual selection in polygynous species. It is possible that, in contrast to monogamous systems, extrapair paternity weakens sexual selection in polygynous systems. In addition, natural selection arising from high predation and interspecific brood parasitism, stochastic processes, or annual variation in selective pressures may also weaken sexual selection in this species.
Quantifying the complexity of medical research
Authors: Rodriguez-Esteban Raul , Loging William T. 
Published: September 2013

Abstract
Motivation: A crucial phenomenon of our times is the diminishing marginal returns of investments in pharmaceutical research and development. A potential reason is that research into diseases is becoming increasingly complex, and thus more burdensome, for humans to handle. We sought to investigate whether we could measure research complexity by analyzing the published literature.
Results: Through the text mining of the publication record of multiple diseases, we have found that the complexity and novelty of disease research has been increasing over the years. Surprisingly, we have also found that research on diseases with higher publication rate does not possess greater complexity or novelty than that on less-studied diseases. We have also shown that the research produced about a disease can be seen as a differentiated area of knowledge within the wider biomedical research. For our analysis, we have conceptualized disease research as a parallel multi-agent search in which each scientific agent (a scientist) follows a search path based on a model of a disease. We have looked at trends in facts published for diseases, measured their diversity and turnover using the entropy measure and found similar patterns across disease areas.
Contact: raul.rodriguez-esteban@roche.com
M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci
Authors: Ji Renkai , Cong Qian , Li Wenlin , Grishin Nick V. 
Published: September 2013

Abstract
Summary: Online Mendelian Inheritance in Man (OMIM) is a manually curated compendium of human genetic variants and the corresponding phenotypes, mostly human diseases. Instead of directly documenting the native sequences for gene entries, OMIM links its entries to protein and DNA sequences in other databases. However, because of the existence of gene isoforms and errors in OMIM records, mapping a specific OMIM mutation to its corresponding protein sequence is not trivial. Combining computer programs and extensive manual curation of OMIM full-text descriptions and original literature, we mapped 98% of OMIM amino acid substitutions (AASs) and all SwissProt Variant (SwissVar) disease-related AASs to reference sequences and confidently mapped 99.96% of all AASs to the genomic loci. Based on the results, we developed an online database and interactive web server (M2SG) to (i) retrieve the mapped OMIM and SwissVar variants for a given protein sequence; and (ii) obtain related proteins and mutations for an input disease phenotype. This database will be useful for analyzing sequences, understanding the effect of mutations, identifying important genetic variations and designing experiments on a protein of interest.
Availability and implementation: The database and web server are freely available at http://prodata.swmed.edu/M2S/mut2seq.cgi.
Contact: grishin@chop.swmed.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization
Authors: Katayama Shintaro , Töhönen Virpi , Linnarsson Sten , Kere Juha 
Published: September 2013

Abstract
Motivation: Recent transcriptome studies have revealed that total transcript numbers vary by cell type and condition; therefore, the statistical assumptions for single-cell transcriptome studies must be revisited. SAMstrt is an extension code for SAMseq, which is a statistical method for differential expression, to enable spike-in normalization and statistical testing based on the estimated absolute number of transcripts per cell for single-cell RNA-seq methods.
Availability and Implementation: SAMstrt is implemented on R and available in github (https://github.com/shka/R-SAMstrt).
Contact: shintaro.katayama@ki.se
Supplementary Information: Supplementary data are available at Bioinformatics online.
PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data
Authors: Zeng Feng , Jiang Rui , Chen Ting 
Published: September 2013

AbstractMotivation: The identification of short insertions and deletions (indels) and single nucleotide polymorphisms (SNPs) from Ion Torrent and 454 reads is a challenging problem, essentially because these techniques are prone to sequence erroneously at homopolymers and can, therefore, raise indels in reads. Most of the existing mapping programs do not model homopolymer errors when aligning reads against the reference. The resulting alignments will then contain various kinds of mismatches and indels that confound the accurate determination of variant loci and alleles.Results: To address these challenges, we realign reads against the reference using our previously proposed hidden Markov model that models homopolymer errors and then merges these pairwise alignments into a weighted alignment graph. Based on our weighted alignment graph and hidden Markov model, we develop a method called PyroHMMvar, which can simultaneously detect short indels and SNPs, as demonstrated in human resequencing data. Specifically, by applying our methods to simulated diploid datasets, we demonstrate that PyroHMMvar produces more accurate results than state-of-the-art methods, such as Samtools and GATK, and is less sensitive to mapping parameter settings than the other methods. We also apply PyroHMMvar to analyze one human whole genome resequencing dataset, and the results confirm that PyroHMMvar predicts SNPs and indels accurately.Availability and implementation: Source code freely available at the following URL: https://code.google.com/p/pyrohmmvar/, implemented in C++ and supported on Linux.Contact: ruijiang@tsinghua.edu.cn or cengf08@mails.thu.edu.cn
Consed: a graphical editor for next-generation sequencing
Authors: Gordon David , Green Phil 
Published: September 2013

Abstract
Summary: The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads. Many batch processing capabilities have been added.
Availability: The consed package is free to academic, government and non-profit users, and licensed to others for a fee by the University of Washington. The current version (26.0) is available for linux, macosx and solaris systems or as C++ source code. It includes a user’s manual (with exercises) and example datasets. http://www.phrap.org/consed/consed.html
Contact: dgordon@uw.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Adjusting scoring matrices to correct overextended alignments
Authors: Mills Lauren J. , Pearson William R. 
Published: September 2013

Abstract
Motivation: Sequence similarity searches performed with BLAST, SSEARCH and FASTA achieve high sensitivity by using scoring matrices (e.g. BLOSUM62) that target low identity (&lt;33%) alignments. Although such scoring matrices can effectively identify distant homologs, they can also produce local alignments that extend beyond the homologous regions.
Results: We measured local alignment start/stop boundary accuracy using a set of queries where the correct alignment boundaries were known, and found that 7% of BLASTP and 8% of SSEARCH alignment boundaries were overextended. Overextended alignments include non-homologous sequences; they occur most frequently between sequences that are more closely related (&gt;33% identity). Adjusting the scoring matrix to reflect the identity of the homologous sequence can correct higher identity overextended alignment boundaries. In addition, the scoring matrix that produced a correct alignment could be reliably predicted based on the sequence identity seen in the original BLOSUM62 alignment. Realigning with the predicted scoring matrix corrected 37% of all overextended alignments, resulting in more correct alignments than using BLOSUM62 alone.
Availability: RefProtDom2 (RPD2) sequences and the FASTA software are available from http://faculty.virginia.edu/wrpearson/fasta.
Contact: wrp@virginia.edu
Phosphorylated (pT371)TRF1 is recruited to sites of DNA damage to facilitate homologous recombination and checkpoint activation
Authors: McKerlie Megan , Walker John R. , Mitchell Taylor R. H. , Wilson Florence R. , Zhu Xu-Dong 
Published: September 2013

Abstract
TRF1, a duplex telomeric DNA-binding protein, plays an important role in telomere metabolism. We have previously reported that a fraction of endogenous TRF1 can stably exist free of telomere chromatin when it is phosphorylated at T371 by Cdk1; however, the role of this telomere-free (pT371)TRF1 has yet to be fully characterized. Here we show that phosphorylated (pT371)TRF1 is recruited to sites of DNA damage, forming damage-induced foci in response to ionizing radiation (IR), etoposide and camptothecin. We find that IR-induced (pT371)TRF1 foci formation is dependent on the ATM- and Mre11/Rad50/Nbs1-mediated DNA damage response. While loss of functional BRCA1 impairs the formation of IR-induced (pT371)TRF1 foci, depletion of either 53BP1 or Rif1 stimulates IR-induced (pT371)TRF1 foci formation. In addition, we show that TRF1 depletion or the lack of its phosphorylation at T371 impairs DNA end resection and repair of nontelomeric DNA double-strand breaks by homologous recombination. The lack of TRF1 phosphorylation at T371 also hampers the activation of the G2/M checkpoint and sensitizes cells to PARP inhibition, IR and camptothecin. Collectively, these results reveal a novel but important function of phosphorylated (pT371)TRF1 in facilitating DNA double-strand break repair and the maintenance of genome integrity.