bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeneReporter—sequence-based document retrieval and annotation
Authors: Bartsch Annekathrin , Bunk Boyke , Haddad Isam , Klein Johannes , Münch Richard , Johl Thorsten , Kärst Uwe , Jänsch Lothar , Jahn Dieter , Retter Ida 
Published: February 2011

Abstract
Summary: GeneReporter is a web tool that reports functional information and relevant literature on a protein-coding sequence of interest. Its purpose is to support both manual genome annotation and document retrieval. PubMed references corresponding to a sequence are detected by the extraction of query words from UniProt entries of homologous sequences. Data on protein families, domains, potential cofactors, structure, function, cellular localization, metabolic contribution and corresponding DNA binding sites complement the information on a given gene product of interest.
Availability and implementation: GeneReporter is available at http://www.genereporter.tu-bs.de. The web site integrates databases and analysis tools as SOAP-based web services from the EBI (European Bioinformatics Institute) and NCBI (National Center for Biotechnology Information).
Contact: i.retter@tu-bs.de; ida.retter@helmholtz-hzi.de
Supplementary information: Supplementary data are available at Bioinformatics online.
FISH Finder: a high-throughput tool for analyzing FISH images
Authors: Shirley James W. , Ty Sereyvathana , Takebayashi Shin-ichiro , Liu Xiuwen , Gilbert David M. 
Published: February 2011

Abstract
Motivation: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold-based segmentation algorithm for nucleus segmentation. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold-based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes.
Availability: FISH Finder is a standalone MATLAB application and platform independent software. The program is freely available from: http://code.google.com/p/fishfinder/downloads/list
Contact: gilbert@bio.fsu.edu
Entropy-accelerated exact clustering of protein decoys
Authors: Berenger Francois , Zhou Yong , Shrestha Rojan , Zhang Kam Y. J. 
Published: February 2011

Abstract
Motivation: Clustering is commonly used to identify the best decoy among many generated in protein structure prediction when using energy alone is insufficient. Calculation of the pairwise distance matrix for a large decoy set is computationally expensive. Typically, only a reduced set of decoys using energy filtering is subjected to clustering analysis. A fast clustering method for a large decoy set would be beneficial to protein structure prediction and this still poses a challenge.
Results: We propose a method using propagation of geometric constraints to accelerate exact clustering, without compromising the distance measure. Our method can be used with any metric distance. Metrics that are expensive to compute and have known cheap lower and upper bounds will benefit most from the method. We compared our method's accuracy against published results from the SPICKER clustering software on 40 large decoy sets from the I-TASSER protein folding engine. We also performed some additional speed comparisons on six targets from the ‘semfold’ decoy set. In our tests, our method chose a better decoy than the energy criterion in 25 out of 40 cases versus 20 for SPICKER. Our method also was shown to be consistently faster than another fast software performing exact clustering named Calibur. In some cases, our approach can even outperform the speed of an approximate method.
Availability: Our C++ software is released under the GNU General Public License. It can be downloaded from http://www.riken.jp/zhangiru/software/durandal_released.tgz.
Contact: kamzhang@riken.jp
SiGN-SSM: open source parallel software for estimating gene networks with state space models
Authors: Tamada Yoshinori , Yamaguchi Rui , Imoto Seiya , Hirose Osamu , Yoshida Ryo , Nagasaki Masao , Miyano Satoru 
Published: February 2011

Abstract
Summary: SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by a statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles.
Availability: SiGN-SSM is distributed under GNU Affero General Public Licence (GNU AGPL) version 3 and can be downloaded at http://sign.hgc.jp/signssm/. The pre-compiled binaries for some architectures are available in addition to the source code. The pre-installed binaries are also available on the Human Genome Center supercomputer system. The online manual and the supplementary information of SiGN-SSM is available on our web site.
Contact: tamada@ims.u-tokyo.ac.jp
Hereditary Spastic Paraplegia Associated With Axonal Neuropathy: A Novel Mutation of SPG3A in a Large Family
Authors: Al-Maawali Almundher , Rolfs Arndt , Klingenhaeger Michael , Yoon Grace 
Published: February 2011

Abstract

Spastic paraplegia Type 3A is an autosomal-dominant pure or uncomplicated hereditary spastic paraplegia. It is caused by mutations in SPG3A, the only gene associated with this condition. We identified a novel mutation, c.1040T>C (p. M347T), in a family with axonal neuropathy in addition to spastic paraplegia. This expands the spectrum of neurologic complications associated with SPG3A and highlights the importance of long-term follow-up and neurological surveillance in this patient population.
Motor Root Conduction Block in the Lewis-Sumner Syndrome
Authors: Lo Yew Long , Dan Yang-Fang , Tan Yam-Eng , Leoh Teng-Hee 
Published: February 2011

Background:
The Lewis-Sumner syndrome (LSS) is a rare immune-mediated peripheral nerve disorder presenting with asymmetric upper limb sensory complaints and motor weakness. Asian patients with LSS have not been reported in the English literature.

Methods:
Three Asian patients with features of LSS were prospectively studied.

Results:
Our patients tended to older, female, and have involvement of the upper limbs exclusively than those in the West. They have a markedly longer disease duration before a diagnosis was made, which could also be the result of difficulty in eliciting motor root conduction block as a sign of proximal demyelination as observed in every patient. Pain is a universal feature as is sensory nerve conduction abnormality. None responded to immunotherapy, but disease stabilization was observed over the chronic course.

Conclusions:
Although rare, these unique observations in Asian patients with LSS differ from those reported in Western literature. The presence of motor root conduction block demonstrated for the first time is instrumental in establishing a diagnosis.
Proline Dehydrogenase Contributes to Pathogen Defense in Arabidopsis
Authors: Cecchini Nicolás Miguel , Monteoliva Mariela Inés , Alvarez María Elena 
Published: February 2011

Abstract
l-Proline (Pro) catabolism is activated in plants recovering from abiotic stresses associated with water deprivation. In this catabolic pathway, Pro is converted to glutamate by two reactions catalyzed by proline dehydrogenase (ProDH) and Ɗ1-pyrroline-5-carboxylate dehydrogenase (P5CDH), with Ɗ1-pyrroline-5-carboxylate (P5C) as the intermediate. Alternatively, under certain conditions, the P5C derived from Pro is converted back to Pro by P5C reductase, thus stimulating the Pro-P5C cycle, which may generate reactive oxygen species (ROS) as a consequence of the ProDH activity. We previously observed that Pro biosynthesis is altered in Arabidopsis (Arabidopsis thaliana) tissues that induce the hypersensitive response (HR) in response to Pseudomonas syringae. In this work, we characterized the Pro catabolic pathway and ProDH activity in this model. Induction of ProDH expression was found to be dependent on salicylic acid, and an increase in ProDH activity was detected in cells destined to die. To evaluate the role of ProDH in the HR, ProDH-silenced plants were generated. These plants displayed reduced ROS and cell death levels as well as enhanced susceptibility in response to avirulent pathogens. Interestingly, the early activation of ProDH was accompanied by an increase in P5C reductase but not in P5CDH transcripts, with few changes occurring in the Pro and P5C levels. Therefore, our results suggest that in wild-type plants, ProDH is a defense component contributing to HR and disease resistance, which apparently potentiates the accumulation of ROS. The participation of the Pro-P5C cycle in the latter response is discussed.
LEAF TIP NECROSIS1 Plays a Pivotal Role in the Regulation of Multiple Phosphate Starvation Responses in Rice
Authors: Hu Bin , Zhu Chenguang , Li Feng , Tang Jiuyou , Wang Yiqin , Lin Aihong , Liu Linchuan , Che Ronghui , Chu Chengcai 
Published: February 2011

Abstract
Although phosphate (Pi) starvation signaling is well studied in Arabidopsis (Arabidopsis thaliana), it is still largely unknown in rice (Oryza sativa). In this work, a rice leaf tip necrosis1 (ltn1) mutant was identified and characterized. Map-based cloning identified LTN1 as LOC_Os05g48390, the putative ortholog of Arabidopsis PHO2, which plays important roles in Pi starvation signaling. Analysis of transgenic plants harboring a LTN1 promoter::β-glucuronidase construct revealed that LTN1 was preferentially expressed in vascular tissues. The ltn1 mutant exhibited increased Pi uptake and translocation, which led to Pi overaccumulation in shoots. In association with enhanced Pi uptake and transport, some Pi transporters were up-regulated in the ltn1 mutant in the presence of sufficient Pi. Furthermore, the elongation of primary and adventitious roots was enhanced in the ltn1 mutant under Pi starvation, suggesting that LTN1 is involved in Pi-dependent root architecture alteration. Under Pi-sufficient conditions, typical Pi starvation responses such as stimulation of phosphatase and RNase activities, lipid composition alteration, nitrogen assimilation repression, and increased metal uptake were also activated in ltn1. Moreover, analysis of OsmiR399-overexpressing plants showed that LTN1 was down-regulated by OsmiR399. Our results strongly indicate that LTN1 is a crucial Pi starvation signaling component downstream of miR399 involved in the regulation of multiple Pi starvation responses in rice.
Proteins of Diverse Function and Subcellular Location Are Lysine Acetylated in Arabidopsis
Authors: Finkemeier Iris , Laxa Miriam , Miguet Laurent , Howden Andrew J. M. , Sweetlove Lee J. 
Published: February 2011

Abstract
Acetylation of the ε-amino group of lysine (Lys) is a reversible posttranslational modification recently discovered to be widespread, occurring on proteins outside the nucleus, in most subcellular locations in mammalian cells. Almost nothing is known about this modification in plants beyond the well-studied acetylation of histone proteins in the nucleus. Here, we report that Lys acetylation in plants also occurs on organellar and cytosolic proteins. We identified 91 Lys-acetylated sites on 74 proteins of diverse functional classes. Furthermore, our study suggests that Lys acetylation may be an important posttranslational modification in the chloroplast, since four Calvin cycle enzymes were acetylated. The plastid-encoded large subunit of Rubisco stands out because of the large number of acetylated sites occurring at important Lys residues that are involved in Rubisco tertiary structure formation and catalytic function. Using the human recombinant deacetylase sirtuin 3, it was demonstrated that Lys deacetylation significantly affects Rubisco activity as well as the activities of other central metabolic enzymes, such as the Calvin cycle enzyme phosphoglycerate kinase, the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase, and the tricarboxylic acid cycle enzyme malate dehydrogenase. Our results demonstrate that Lys acetylation also occurs on proteins outside the nucleus in Arabidopsis (Arabidopsis thaliana) and that Lys acetylation could be important in the regulation of key metabolic enzymes.
Rapid and Reversible Light-Mediated Chromatin Modifications of Arabidopsis Phytochrome A Locus
Authors: Jang In-Cheol , Chung Pil Joong , Hemmes Hans , Jung Choonkyun , Chua Nam-Hai 
Published: February 2011

Abstract
Recent genome-wide surveys showed that acetylation of H3K9 and H3K27 is correlated with gene activation during deetiolation of Arabidopsis thaliana seedlings, but less is known regarding changes in the histone status of repressed genes. Phytochrome A (phyA) is the major photoreceptor of deetiolation, and phyA expression is reversibly repressed by light. We found that in adult Arabidopsis plants, phyA activation in darkness was accompanied by a significant enrichment in the phyA transcription and translation start sites of not only H3K9/14ac and H3K27ac but also H3K4me3, and there was also moderate enrichment of H4K5ac, H4K8ac, H4K12ac, and H4K16ac. Conversely, when phyA expression was repressed by light, H3K27me3 was enriched with a corresponding decline in H3K27ac; moreover, demethylation of H3K4me3 and deacetylation of H3K9/14 were also seen. These histone modifications, which were focused around the phyA transcription/translation start sites, were detected within 1 h of deetiolation. Mutant analysis showed that HDA19/HD1 mediated deacetylation of H3K9/14 and uncovered possible histone crosstalk between H3K9/14ac and H3K4me3. Neither small RNA pathways nor the circadian clock affected H3 modification status of the phyA locus, and DNA methylation was unchanged by light. The presence of activating and repressive histone marks suggests a mechanism for the rapid and reversible regulation of phyA by dark and light.
Farmers' involvement in value‐added produce: the case of Alabama growers
Authors: Duarte Alonso Abel 
Published: February 2011

PurposeFor many farmers across the USA the opportunity to sell their produce directly to the public in different ways allows them to avoid middle‐men and often reap higher benefits that are vital for their survival. However, to what extent do they fully maximise their produce? For instance, do farmers consider developing value‐added products when they have fruit or vegetable leftovers, or those with blemishes? The present paper aims to explore involvement in value‐added food production from the growers' standpoint.Design/methodology/approachData were collected via telephone and face‐to‐face interviews among 30 farm owners located in the state of Alabama.FindingsWhile the large majority of participating farmers (93.3 per cent) are involved in selling produce directly to the public, only 33.3 per cent are currently maximising their produce left‐overs, or unsellable produce by developing and marketing value‐added products such as jellies, jams and ice‐creams. Almost one fourth of farmers (23.3 per cent) would consider developing value‐added products. However, the lack of a commercial kitchen, a potentially considerable investment, is one significant barrier preventing the development of value‐added products.Research limitations/implicationsChoosing only farmers that are already involved in retailing their own produce, and their low number (30) are limitations that may not allow for making generalisations of the study's findings.Practical implicationsIn times where the threat of food crises is latent, the ability for food growers to maximise their harvests becomes critical. Because farm operators play a significant role in providing food for society at large, they should be accordingly supported to maximise their produce, including through the development of value‐added products.Originality/valueThe study provides a different view of value‐added produce, investigating this dimension from the farmers' viewpoint.
Climate change from the perspective of Spanish wine growers: a three‐region study
Authors: Duarte Alonso Abel , O'Neill Martin A. 
Published: February 2011

PurposeWinery operators and viticulturalists alike face many challenges in their daily and annual work cycle; not least the challenge of producing annually a consistent quality product and getting that product to the market in an ever competitive marketplace. While climate has always been a factor when it comes to meeting this challenge, it has become all the more pronounced recently due to the effects of global climatic change. Against this background, this paper aims to explore the effects of climate change from the perspective of winery operators in three prominent Spanish wine producing regions.Design/methodology/approachWineries in La Mancha, La Rioja and Penedès, totalling 570, were contacted electronically and invited to participate in an online survey. Of these businesses, 94 participated, a 16.5 per cent response rate.FindingsWhile it was found that generally climate change is not among growers' main challenges, three distinct groups emerged from this study: the “unbelievers,” the cautiously sceptical and the “believers”. This last and largest group of respondents (41.5 per cent) not only acknowledges changes due to climate change, but also strategies already in place to minimise the effects of climate change, suggesting the severity of the problem.Research limitations/implicationsComparisons among the three participating wine regions were not possible due to the low number of respondents from one of the regions. Also, the total number of respondents does not allow for making the study's findings generalisable.Practical implicationsThe wine industry, its stakeholders and government agencies need to work together to monitor any changes and find ways to address negative effects of climate change that may result in increased water usage, pesticides or changes in labour demand.Originality/valueThe study provides new insights into climate change according to winery operators' perspectives, an area that to date has received very limited attention from researchers.
Health claims regulations
Authors: Lalor Fiona , Wall Patrick G. 
Published: February 2011

PurposeThe purpose of this paper is to review and compare the scientific and regulatory environments for nutrition and health claims on foodstuffs in the USA, Japan and the European Union.Design/methodology/approachA review of the literature and the relevant legislation in the three different countries is conducted. Regulations are reviewed and scientific evidence requirements are outlined in each country.FindingsFull regulatory approval for claims across all three countries requires the support of robust scientific evidence. To obtain this, companies must submit comprehensive dossiers and detailed applications to the regulators with full descriptions of the tests and studies completed during product development. However in the USA and Japan, an alternative process exists. A health claim that is suggested but not supported by scientific evidence is known as a qualified health claim and is permitted in the USA and Japan, but not in the EU.Practical implicationsThe paper demonstrates the difference in regulatory requirements in different countries which leads to different claims being permitted in different countries. It also leads to different levels of scientific support for similar claims which causes consumer confusion and develops an uneven playing pitch for the industry. Given that the industry operates in a global market place, it is imperative that a consensus is reached as to the level of scientific evidence required to approve a health claim. In that way, consumers can be safeguarded from being misled, consumer confusion will not be a concern and products can be globally distributed in line with the increasing liberalisation of trade.Originality/valueThis paper is of value to regulators and the food industry.
Social search
Authors: McDonnell Michael , Shiri Ali 
Published: February 2011

PurposeThe purpose of this paper is to introduce the notion of social search as a new concept, drawing upon the patterns of web search behaviour. It aims to: define social search; present a taxonomy of social search; and propose a user‐centred social search method.Design/methodology/approachA mixed method approach was adopted to investigate and conceptualise the notion of social search. A review of literature on social search was carried out to identify the key trends and topics. A model of online collaboration was adopted to delineate the types and categories of social search. Four use case scenarios were developed to provide a more pragmatic approach to the understanding of social search.FindingsThe developed taxonomy of social search reveals important similarities and differences between many social search systems. This analysis reveals a gap in social search approaches. A practical method was identified that allows users to directly leverage social search without special features built into search engines.Research limitations/implicationsFor feasibility reasons, Google was used as an example of a search system that can be used for carrying out social searches.Practical implicationsThe paper provides several practical implications for web searchers as well as web designers. In particular, some recommendations are provided for the design of search engines, digital libraries and browser add‐ons.Social implicationsThe study demonstrates the value and power of “collective intelligence” in web search. It shows how general web searches can be enhanced through using socially enhanced web‐based tools such as social bookmarking systems, social tagging services and social media sites.Originality/valueThis is the first study that provides a granular analysis of the notion of social search and puts forward a taxonomy of social search. The use cases developed and reported are created based on real search topics, and show the value and validity of the approach taken.