bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network predicting drug’s anatomical therapeutic chemical code
Authors: Wang Yong-Cui , Chen Shi-Long , Deng Nai-Yang , Wang Yong 
Published: April 2013

Abstract
Motivation: Discovering drug’s Anatomical Therapeutic Chemical (ATC) classification rules at molecular level is of vital importance to understand a vast majority of drugs action. However, few studies attempt to annotate drug’s potential ATC-codes by computational approaches.
Results: Here, we introduce drug-target network to computationally predict drug’s ATC-codes and propose a novel method named NetPredATC. Starting from the assumption that drugs with similar chemical structures or target proteins share common ATC-codes, our method, NetPredATC, aims to assign drug’s potential ATC-codes by integrating chemical structures and target proteins. Specifically, we first construct a gold-standard positive dataset from drugs’ ATC-code annotation databases. Then we characterize ATC-code and drug by their similarity profiles and define kernel function to correlate them. Finally, we use a kernel method, support vector machine, to automatically predict drug’s ATC-codes. Our method was validated on four drug datasets with various target proteins, including enzymes, ion channels, G-protein couple receptors and nuclear receptors. We found that both drug’s chemical structure and target protein are predictive, and target protein information has better accuracy. Further integrating these two data sources revealed more experimentally validated ATC-codes for drugs. We extensively compared our NetPredATC with SuperPred, which is a chemical similarity-only based method. Experimental results showed that our NetPredATC outperforms SuperPred not only in predictive coverage but also in accuracy. In addition, database search and functional annotation analysis support that our novel predictions are worthy of future experimental validation.
Conclusion: In conclusion, our new method, NetPredATC, can predict drug’s ATC-codes more accurately by incorporating drug-target network and integrating data, which will promote drug mechanism understanding and drug repositioning and discovery.
Availability: NetPredATC is available at http://doc.aporc.org/wiki/NetPredATC.
Contact: ycwang@nwipb.cas.cn or ywang@amss.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Active learning-based information structure analysis of full scientific articles and two applications for biomedical literature review
Authors: Guo Yufan , Silins Ilona , Stenius Ulla , Korhonen Anna 
Published: April 2013

Abstract
Motivation: Techniques that are capable of automatically analyzing the information structure of scientific articles could be highly useful for improving information access to biomedical literature. However, most existing approaches rely on supervised machine learning (ML) and substantial labeled data that are expensive to develop and apply to different sub-fields of biomedicine. Recent research shows that minimal supervision is sufficient for fairly accurate information structure analysis of biomedical abstracts. However, is it realistic for full articles given their high linguistic and informational complexity? We introduce and release a novel corpus of 50 biomedical articles annotated according to the Argumentative Zoning (AZ) scheme, and investigate active learning with one of the most widely used ML models—Support Vector Machines (SVM)—on this corpus. Additionally, we introduce two novel applications that use AZ to support real-life literature review in biomedicine via question answering and summarization.
Results: We show that active learning with SVM trained on 500 labeled sentences (6% of the corpus) performs surprisingly well with the accuracy of 82%, just 2% lower than fully supervised learning. In our question answering task, biomedical researchers find relevant information significantly faster from AZ-annotated than unannotated articles. In the summarization task, sentences extracted from particular zones are significantly more similar to gold standard summaries than those extracted from particular sections of full articles. These results demonstrate that active learning of full articles’ information structure is indeed realistic and the accuracy is high enough to support real-life literature review in biomedicine.
Availability: The annotated corpus, our AZ classifier and the two novel applications are available at http://www.cl.cam.ac.uk/∼yg244/12bioinfo.html.
Contact: yg244@cam.ac.uk
MonaLisa—visualization and analysis of functional modules in biochemical networks
Authors: Einloft Jens , Ackermann Jörg , Nöthen Joachim , Koch Ina 
Published: April 2013

Abstract
Summary: Structural modeling of biochemical networks enables qualitative as well as quantitative analysis of those networks. Automated network decomposition into functional modules is a crucial point in network analysis. Although there exist approaches for the analysis of networks, there is no open source tool available that combines editing, visualization and the computation of steady-state functional modules. We introduce a new tool called MonaLisa, which combines computation and visualization of functional modules as well as an editor for biochemical Petri nets. The analysis techniques allow for network decomposition into functional modules, for example t-invariants (elementary modes), maximal common transition sets, minimal cut sets and t-clusters. The graphical user interface provides various functionalities to construct and modify networks as well as to visualize the results of the analysis.
Availability and implementation: MonaLisa is licensed under the Artistic License 2.0. It is freely available at http://www.bioinformatik.uni-frankfurt.de/software.html. MonaLisa requires at least Java 6 and runs under Linux, Microsoft Windows and Mac OS.
Contact: ina.koch@bioinformatik.uni-frankfurt.de
The Economic Impact of Social Ties: Evidence from German Reunification*
Authors: Burchardi Konrad B. , Hassan Tarek A. 
Published: April 2013

AbstractWe use the fall of the Berlin Wall in 1989 to show that personal relationships which individuals maintain for noneconomic reasons can be an important determinant of regional economic growth. We show that West German households who had social ties to East Germany in 1989 experienced a persistent rise in their personal incomes after the fall of the Berlin Wall. Moreover, the presence of these households significantly affects economic performance at the regional level: it increases the returns to entrepreneurial activity, the share of households who become entrepreneurs, and the likelihood that firms based within a given West German region invest in East Germany. As a result, West German regions that (for idiosyncratic reasons) have a high concentration of households with social ties to the East exhibit substantially higher growth in income per capita in the early 1990s. A one standard deviation rise in the share of households with social ties to East Germany in 1989 is associated with a 4.7 percentage point rise in income per capita over six years. We interpret our findings as evidence of a causal link between social ties and regional economic development.
The immature dentate gyrus represents a shared phenotype of mouse models of epilepsy and psychiatric disease
Authors: Shin Rick , Kobayashi Katsunori , Hagihara Hideo , Kogan Jeffrey H , Miyake Shinichi , Tajinda Katsunori , Walton Noah M , Gross Adam K , Heusner Carrie L , Chen Qian , Tamura Kouichi , Miyakawa Tsuyoshi , Matsumoto Mitsuyuki 
Published: April 2013

ObjectivesThere is accumulating evidence to suggest psychiatric disorders, such as bipolar disorder and schizophrenia, share common etiologies, pathophysiologies, genetics, and drug responses with many of the epilepsies. Here, we explored overlaps in cellular/molecular, electrophysiological, and behavioral phenotypes between putative mouse models of bipolar disorder/schizophrenia and epilepsy. We tested the hypothesis that an immature dentate gyrus (iDG), whose association with psychosis in patients has recently been reported, represents a common phenotype of both diseases.MethodsBehaviors of calcium/calmodulin‐dependent protein kinase II alpha (α‐CaMKII) heterozygous knock‐out (KO) mice, which are a representative bipolar disorder/schizophrenia model displaying iDG, and pilocarpine‐treated mice, which are a representative epilepsy model, were tested followed by quantitative polymerase chain reaction (qPCR)/immunohistochemistry for mRNA/protein expression associated with an iDG phenotype. In vitro electrophysiology of dentate gyrus granule cells (DG GCs) was examined in pilocarpine‐treated epileptic mice.ResultsThe two disease models demonstrated similar behavioral deficits, such as hyperactivity, poor working memory performance, and social withdrawal. Significant reductions in mRNA expression and immunoreactivity of the mature neuronal marker calbindin and concomitant increases in mRNA expression and immunoreactivity of the immature neuronal marker calretinin represent iDG signatures that are present in both mice models. Electrophysiologically, we have confirmed that DG GCs from pilocarpine‐treated mice represent an immature state. A significant decrease in hippocampal α‐CaMKII protein levels was also found in both models.ConclusionsOur data have shown iDG signatures from mouse models of both bipolar disorder/schizophrenia and epilepsy. The evidence suggests that the iDG may, in part, be responsible for the abnormal behavioral phenotype, and that the underlying pathophysiologies in epilepsy and bipolar disorder/schizophrenia are strikingly similar.
6q deletion detected by fluorescence in situ hybridization using bacterial artificial chromosome in chronic lymphocytic leukemia
Authors: Dalsass Alessia , Mestichelli Francesca , Ruggieri Miriana , Gaspari Paola , Pezzoni Valerio , Vagnoni Davide , Angelini Mario , Angelini Stefano , Bigazzi Catia , Falcioni Sadia , Troiani Emanuela , Alesiani Francesco , Catarini Massimo , Attolico Immacolata , Scortechini Ilaria , Discepoli Giancarlo , Galieni Piero 
Published: April 2013

AbstractDeletions of the long arm of chromosome 6 are known to occur at relatively low frequency (3–6%) in chronic lymphocytic leukemia (CLL), and they are more frequently observed in 6q21. Few data have been reported regarding other bands on 6q involved by cytogenetic alterations in CLL. The cytogenetic study was performed in nuclei and metaphases obtained after stimulation with a combination of CpG‐oligonucleotide DSP30 and interleukin‐2. Four bacterial artificial chromosome (BAC) clones mapping regions in bands 6q16, 6q23, 6q25, 6q27 were used as probes for fluorescence in situ hybridization in 107 CLL cases in order to analyze the occurrence and localization of 6q aberrations. We identified 11 cases (10.2%) with 6q deletion of 107 patients studied with CLL. The trends of survival curves and the treatment‐free intervals (TFI) of patients with deletion suggest a better outcome than the other cytogenetic risk groups. We observed two subgroups with 6q deletion as the sole anomaly: two cases with 6q16 deletion, and three cases with 6q25.2–27 deletion. There were differences of age, stage, and TFI between both subgroups. By using BAC probes, we observed that 6q deletion has a higher frequency in CLL and is linked with a good prognosis. In addition, it was observed that the deletion in 6q16 appears to be the most frequent and, if present as the only abnormality, it could be associated with a most widespread disease.
Natural mortality estimators for information‐limited fisheries
Authors: Kenchington Trevor J 
Published: April 2013

AbstractThe 29 estimators of natural mortality (M) that have been proposed for ‘information‐limited’ fisheries are reviewed, together with a new alternative presented here. Each is applied to 13 example populations for which well‐founded estimates are available of bothMand the estimators' parameters. None of the 30 can provide accurate estimates for every species, and none appears sufficiently precise for use in analytical stock assessments, while several perform so poorly as to have no practical utility. If the growth coefficientKhas been reliably estimated, eitherM = 1.5 Kor Pauly's long‐established estimator can provide useful estimates ofM,but they fail with species that have long adult lives after swift juvenile growth, with those that never reach their asymptotic lengths and with species that otherwise deviate from archetypal teleost life histories. If a pre‐exploitation maximum observed age (Tmax) can be established,Mcan be estimated for both teleosts and sharks usingM = 4.3/Tmaxbut that seriously underestimates when the effective sample size (ne) is large and overestimates with species showing pronounced senescence. The new estimator presented here addressesnebut is upset by even mild senescence. Some estimators ofM‐at‐size, particularly ones recently advanced by Gislasonet al. and Charnovet al., also show promise but require further examination. It is recommended that fisheries scientists measureMby more advanced methods whenever possible. If ‘information‐limited’ estimators must be used, their uncertainties should be acknowledged and their errors propagated into management advice.
The geological significance of 40Ar/39Ar and Rb–Sr white mica ages from Syros and Sifnos, Greece: a record of continuous (re)crystallization during exhumation?
Authors: Bröcker M. , Baldwin S. , Arkudas R. 
Published: April 2013

AbstractThe Attic‐Cycladic crystalline belt in the central Aegean region records a complex structural and metamorphic evolution that documents Cenozoic subduction zone processes and exhumation. A prerequisite to develop an improved tectono‐metamorphic understanding of this area is dating of distinct P–T–D stages. To evaluate the geological significance of phengite ages of variably overprinted rocks, 40Ar/39Ar and Rb–Sr analyses were undertaken on transitional blueschist–greenschist and greenschist facies samples from the islands of Syros and Sifnos. White mica geochronology indicates a large age variability (40Ar/39Ar: 41–27 Ma; Rb–Sr: 34–20 Ma). Petrologically similar samples have either experienced greenschist facies overprinting at different times or variations in ages record variable degrees of greenschist facies retrogression and incomplete resetting of isotopic systematics. The 40Ar/39Ar and Rb–Sr data for metamorphic rocks from both islands record only minor, localized evidence for Miocene ages (c. 21 Ma) that are well documented elsewhere in the Cyclades and interpreted to result from retrogression of high‐pressure mineral assemblages during lower pressure metamorphism. Field and textural evidence suggests that heterogeneous overprinting may be due to a lack of permeability and/or limited availability of fluids in some bulk compositions and that retrogression was more or less parallel to lithological layering and/or foliation as a result of, possibly deformation‐enhanced, channelized fluid ingress. Published and new 40Ar/39Ar and Rb–Sr data for both islands indicate apparent age variations that can be broadly linked to mineral assemblages documenting transitional blueschist‐to‐greenschist‐ and/or greenschist facies metamorphism. The data do not record the timing of peak HP metamorphism, but may accurately record continuous (partial) resetting of isotopic systematics and/or (re)crystallization of white mica during exhumation and greenschist facies retrogression. The form of 40Ar/39Ar phengite age spectra are complex with the lowest temperature steps yielding Middle to Late Miocene ages. The youngest Rb–Sr ages suggest maximum ages of 20.6 ± 0.8 Ma (Syros) and 22.5 ± 0.6 Ma (Sifnos) for the timing of greenschist facies overprinting. The results of this study further accentuate the challenges of interpreting isotopic data for white mica from polymetamorphic terranes, particularly when mixing of populations and/or incomplete resetting of isotopic systematics occurs during exhumation. These data capture the full range of isotopic age variations in retrogressed HP rocks documented in previous isotopic studies, and can be interpreted in terms of the geodynamic evolution of the Aegean.
Differential expression of transcription factors Snail, Slug, SIP1, and Twist in ameloblastoma
Authors: Huat Siar Chong , Ng Kok Han 
Published: April 2013

BackgroundEpithelial‐to‐mesenchymal transition (EMT) via the mechanism of transcription repression is a crucial process for the induction of invasiveness in many human tumors. Ameloblastoma is a benign odontogenic epithelial neoplasm with a locally infiltrative behavior. Twist, an EMT promoter, has been implicated in its invasiveness. The roles of the other transcription factors remain unclarified.Materials and methodsFour transcription factors, namely Snail, Slug, SIP1, and Twist, were examined immunohistochemically in 64 ameloblastoma [18 unicystic (UA), 20 solid/multicystic (SA), 4 desmoplastic (DA), and 22 recurrent (RA)].ResultsAll four transcription factors were differentially expressed in ameloblastoma [Snail: n = 60/64 (94%); Slug: n = 21/64 (33%); SIP: n = 18/64 (28%); Twist: n = 26/64 (41%)] (P < 0.05). Their distribution patterns were heterogeneous and were not significantly different between the tumor invasive front and central area (P > 0.05). Intracellular protein localization was predominantly nuclear for Snail, cytoplasmic>nuclear for Slug and SIP1, and cytoplasmic/nuclear for Twist. Overexpression of Snail in most subsets (UA = 18/18; SMA = 19/20; DA = 4/4; RA = 19/22) compared with the other transcription factors (P < 0.05) and selective expression for Slug, SIP1, and Twist in squamous/keratinous foci and at sites of epithelial cystic degeneration were among the main observations made. Stromal cells surrounding immunoreactive tumor cells tended to stain positive.ConclusionsPresent findings suggest that these transcription factors probably play differential roles in mediating local invasiveness in ameloblastoma. Overexpression of Snail in most subsets suggests that this molecule is most likely the prototype transcription factor involved in inducing EMT in the ameloblastoma.
Identification and Characterization of a Tetramethylpyrazine Catabolic Pathway in Rhodococcus jostii TMP1
Authors: Kutanovas Simonas , Stankeviciute Jonita , Urbelis Gintaras , Tauraite Daiva , Rutkiene Rasa , Meskys Rolandas 
Published: April 2013

ABSTRACT

At present, there are no published data on catabolic pathways of
N
-heterocyclic compounds, in which all carbon atoms carry a substituent. We identified the genetic locus and characterized key reactions in the aerobic degradation of tetramethylpyrazine in
Rhodococcus jostii
strain TMP1. By comparing protein expression profiles, we identified a tetramethylpyrazine-inducible protein of 40 kDa and determined its identity by tandem mass spectrometry (MS-MS)
de novo
sequencing. Searches against an
R. jostii
TMP1 genome database allowed the identification of the tetramethylpyrazine-inducible protein-coding gene. The tetramethylpyrazine-inducible gene was located within a 13-kb genome cluster, denominated the tetramethylpyrazine degradation (
tpd
) locus, that encoded eight proteins involved in tetramethylpyrazine catabolism. The genes from this cluster were cloned and transferred into tetramethylpyrazine-nondegrading
Rhodococcus erythropolis
strain SQ1. This allowed us to verify the function of the
tpd
locus, to isolate intermediate metabolites, and to reconstruct the catabolic pathway of tetramethylpyrazine. We report that the degradation of tetramethylpyrazine is a multistep process that includes initial oxidative aromatic-ring cleavage by tetramethylpyrazine oxygenase, TpdAB; subsequent hydrolysis by (
Z
)-
N
,
N
′-(but-2-ene-2,3-diyl)diacetamide hydrolase, TpdC; and further intermediate metabolite reduction by aminoalcohol dehydrogenase, TpdE. Thus, the genes responsible for bacterial degradation of pyrazines have been identified, and intermediate metabolites of tetramethylpyrazine degradation have been isolated for the first time.
Classification of Lytic Bacteriophages Attacking Dairy Leuconostoc Starter Strains
Authors: Ali Yahya , Kot Witold , Atamer Zeynep , Hinrichs Jï¿½rg , Vogensen Finn K. , Heller Knut J. , Neve Horst 
Published: April 2013

ABSTRACT

A set of 83 lytic dairy bacteriophages (phages) infecting flavor-producing mesophilic starter strains of the
Leuconostoc
genus was characterized, and the first in-depth taxonomic scheme was established for this phage group. Phages were obtained from different sources, i.e., from dairy samples originating from 11 German dairies (50
Leuconostoc pseudomesenteroides
[
Ln. pseudomesenteroides
] phages, 4
Ln. mesenteroides
phages) and from 3 external phage collections (17
Ln. pseudomesenteroides
phages, 12
Ln. mesenteroides
phages). All phages belonged to the
Siphoviridae
family of phages with isometric heads (diameter, 55 nm) and noncontractile tails (length, 140 nm). With the exception of one phage (i.e., phage ΦLN25), all
Ln. mesenteroides
phages lysed the same host strains and revealed characteristic globular baseplate appendages. Phage ΦLN25, with different Y-shaped appendages, had a unique host range. Apart from two phages (i.e., phages P792 and P793), all
Ln. pseudomesenteroides
phages shared the same host range and had plain baseplates without distinguishable appendages. They were further characterized by the presence or absence of a collar below the phage head or by unique tails with straight striations. Phages P792 and P793 with characteristic fluffy baseplate appendages could propagate only on other specific hosts. All
Ln. mesenteroides
and all
Ln. pseudomesenteroides
phages were members of two (host species-specific) distinct genotypes but shared a limited conserved DNA region specifying their structural genes. A PCR detection system was established and was shown to be reliable for the detection of all
Leuconostoc
phage types.
Plasmid-Borne Type E Neurotoxin Gene Clusters in Clostridium botulinum Strains
Authors: Zhang Zhen , Hintsa Hannamari , Chen Ying , Korkeala Hannu , Lindstrï¿½m Miia 
Published: April 2013

ABSTRACT

A collection of 36
Clostridium botulinum
type E strains was examined by pulsed-field gel electrophoresis (PFGE) and Southern hybridization with probes targeted to
botE
and
orfX1
in the neurotoxin gene cluster. Three strains were found to contain neurotoxin subtype E1 gene clusters in large plasmids of about 146 kb in size.