bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly efficient lentiviral-mediated human cytokine transgenesis on the NOD/scid background
Authors: Punzon Isabel , Criado Luis M. , Serrano Alfredo , Serrano Fernando , Bernad Antonio 
Published: September 2003

Abstract
Human neo-organ formation from stem cells can only be assayed by in vivo xenotransplantation. The human nonobese diabetic–severe combined immunodeficient (HuNOD/scid) CD34+ cell transplantation is a model that allows examination of hematopoietic tissue formation, although human hematopoietic cell maturation is abortive. Conventional humanization of the cytokine microenvironment has depended on generation of human cytokine-transgenic mice in strains appropriate for conventional plasmid microinjection, followed by backcrossing, a costly and time-consuming approach. Lentiviral vector infection of single-cell embryos was recently reported to produce transgenic animals. Using this approach, we have generated direct human granulocyte-macrophage colony-stimulating factor (hGM-CSF) transgenic mice from lentivirus-microinjected NOD/scid embryos, with 68% efficiency and 100% penetrance; this allowed us to obtain NOD/scid transgenic mice with considerable savings of resources. This powerful technique should assist in producing novel mouse models for the study of human blood cell lineage development and other human neo-organs from stem cell xenotransplantation for which a similar “humanization” rationale may be required.
Induction of cytotoxic T-lymphocyte responses to enhanced green and yellow fluorescent proteins after myeloablative conditioning
Authors: Morris Julia C. , Conerly Melissa , Thomasson Bobbie , Storek Jan , Riddell Stanley R. , Kiem Hans-Peter 
Published: September 2003

Abstract
Lentiviral vectors are increasingly being used for transferring genes into hematopoietic stem cells (HSCs) due to their ability to transduce nondividing cells. Whereas results in in vitro studies and the nonobese diabetic/severe combined immunodeficiency (NOD/SCID) model have been highly encourgaging, studies in large animals have not confirmed the superior transduction of HSCs using lentiviral vectors versus oncoretroviral vectors. In contrast to the stable gene marking we have consistently achieved with oncoretroviral vectors in animals that received myeloablative conditioning, we observed the complete disappearance of genetically modified enhanced green or yellow fluorescent protein–expressing cells in 5 baboons that received transplants of HSCs transduced with lentiviral vectors alone or in combination with oncoretroviral vectors. Immune responses to transgene products have been found to be involved in the disappearance of gene-modified cells after nonmyeloablative conditioning. Thus, we examined whether the disappearance of genemodified cells after ablative conditioning may be due to an immune response. In 4 of 5 animals, cytotoxic T lymphocytes specific for the transgene protein were readily detected, demonstrating that immune reactions were responsible for the disappearance of the gene-marked cells in the animals. In summary, we report the induction of transgene-specific immune responses after transplantation of lentivirally transduced repopulating cells in a myeloablative setting.
VWF73, a region from D1596 to R1668 of von Willebrand factor, provides a minimal substrate for ADAMTS-13
Authors: Kokame Koichi , Matsumoto Masanori , Fujimura Yoshihiro , Miyata Toshiyuki 
Published: September 2003

Abstract
ADAMTS-13 was recently identified as a new hemostatic factor, von Willebrand factor (VWF)–cleaving protease. Either congenital or acquired defects of the enzymatic activity lead to thrombotic thrombocytopenic purpura (TTP). ADAMTS-13 specifically cleaves a peptidyl bond between Y1605 and M1606 in the A2 domain of VWF. Here, we determined the minimal region recognized as a specific substrate by ADAMTS-13. A series of partial deletions in the A2 domain flanked with N- and C-terminal tags were expressed in Escherichia coli and affinity-purified. These purified proteins were incubated with human plasma, subjected to sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE), and analyzed by Western blot. Judging from mobility shifts, all constructs except one were cleaved at the expected site. Data suggested that a minimal region as a functional substrate consisted of 73 amino acid residues from D1596 to R1668 of VWF, designated VWF73, and that further deletion of the E1660-R1668 region led to the loss of cleavage by ADAMTS-13. VWF73 was not cleaved by plasma from patients with congenital or acquired TTP, but cleaved by plasma from patients with hemolytic uremic syndrome, suggesting that VWF73 is a specific substrate forADAMTS-13. Thus, VWF73 will be a useful seed to develop a new rapid assay to determine ADAMTS-13 activity.
A Convenient Method for the Preparation of Symmetrical or Unsymmetrical Ethers by The Coupling of Two Alcohols via A New Type of Oxidation–reduction Condensation Using Tetrafluoro-1,4-benzoquinone
Authors: Shintou Taichi , Mukaiyama Teruaki 
Published: September 2003

Abstract
A new type of oxidation–reduction condensation by using tetrafluoro-1,4-benzoquinone (fluoranil), alcohols and alkoxydiphenylphosphines, in situ formed from nBuLi-treated alcohols and chlorodiphenylphosphine, proceeded smoothly to afford the corresponding symmetrical or unsymmetrical ethers in good to high yields.
Temperature-dependent Regulation of Antisense Activity Using a DNA/poly(N-isopropylacrylamide) Conjugate
Authors: Murata Masaharu , Kaku Wataru , Anada Takahisa , Sato Yoshikuni , Maeda Mizuo , Katayama Yoshiki 
Published: September 2003

Abstract
We prepared a novel antisense reagent comprising of oligodeoxynucleotides (ODNs) and a thermo-responsive polymer, poly(N-isopropylacrylamide) (PNIPAAm). The conjugate demonstrated stimuli-responsive regulation of gene expression via conformational change of the polymer chain.
Aza-Michael Reactions in Ionic Liquids. A Facile Synthesis of β-Amino Compounds
Authors: Yadav J S , Reddy B V S , Basak A K , Narsaiah A V 
Published: September 2003

Abstract
Electron-deficient olefins undergo smoothly aza-Michael reactions with a wide range of amines in ionic liquids in the absence of any acid catalyst to produce the corresponding β-amino compounds in excellent yields with high 1,4-selectivity. The recovered ionic liquids can be reused in subsequent reactions without loss of activity. Owing to the high polarity of ionic liquids, the enones show enhanced reactivity thereby reducing reaction times and improving the yields significantly.
Quantitative analysis of peroxisome proliferator‐activated receptor gamma (PPARγ) expression in arteries and hearts of patients with ischaemic or dilated cardiomyopathy
Authors: Mehrabi Mohammad R. , Haslmayer Petra , Humpeler Susanne , Strauss‐Blasche Gerhard , Marktl Wolfgang , Tamaddon Forouzan , Serbecic Nermin , Wieselthaler Georg , Thalhammer Theresia , Glogar Helmut D. , Ekmekcioglu Cem 
Published: October 2003

AbstractPPARγ, a nuclear transcription factor, is expressed in various cells within the vasculature and in cardiomyocytes. It has been suggested that PPARγ is involved in atherogenesis and in cardiac hypertrophy. Therefore, we sought to quantify PPARγ mRNA in coronary arteries, the aorta and left ventricular specimens from patients with ischaemic (CHD) and dilated cardiomyopathy (CMP). Using real‐time PCR, we were able to demonstrate the expression of PPARγ in all of the human specimens. The lowest expression of PPARγ was detected in the aorta specimens of both groups (this was set to one). In comparison, the expression in coronary arteries was 2.32‐fold in CHD‐ and 3.78‐fold in CMP specimens and in the left ventricle specimens, 2.12‐fold in CHD‐ and 3.51‐fold in CMP. Samples from CHD patients showed a higher expression of PPARγ in all of the samples compared to those from CMP patients (aorta: 1.99‐fold; coronary arteries: 1.35; left ventricles: 1.23). PPARγ levels were not significantly correlated to CD 36 expression values in any group, suggesting that higher levels of PPARγ are not principally due to increased PPARγ expression in macrophages. This was confirmed by immunohistochemical analysis, which showed that PPARγ is also located in the smooth muscle layer and in cardiomyocytes. In conclusion, our observations of increased PPAR mRNA expression in the coronary arteries and left ventricles from CHD and CMP patients suggest an important function of this nuclear receptor in the pathogenesis of heart disease.
Computational detection of cis -regulatory modules
Authors: Aerts Stein , Van Loo Peter , Thijs Gert , Moreau Yves , De Moor Bart 
Published: October 2003

Abstract
Motivation: The transcriptional regulation of a metazoan gene depends on the cooperative action of multiple transcription factors that bind to cis-regulatory modules (CRMs) located in the neighborhood of the gene. By integrating multiple signals, CRMs confer an organism specific spatial and temporal rate of transcription.
Results: Based on the hypothesis that genes that are needed in exactly the same conditions might share similar regulatory switches, we have developed a novel methodology to find CRMs in a set of coexpressed or coregulated genes. The ModuleSearcher algorithm finds for a given gene set the best scoring combination of transcription factor binding sites within a sequence window using an A*procedure for tree searching. To keep the level of noise low, we use DNA sequences that are most likely to contain functional cis-regulatory information, namely conserved regions between human and mouse orthologous genes. The ModuleScanner performs genomic searches with a predicted CRM or with a user-defined CRM known from the literature to find possible target genes. The validity of a set of putative targets is checked using Gene Ontology annotations. We demonstrate the use and effectiveness of the ModuleSearcher and ModuleScanner algorithms and test their specificity and sensitivity on semi-artificial data. Next, we search for a module in a cluster of gene expression profiles of human cell cycle genes.
Availability: The ModuleSearcher is available as a web service within the TOUCAN workbench for regulatory sequence analysis, which can be downloaded from http://www.esat.kuleuven.ac.be/~dna/BioI.
Contact: stein.aerts@esat.kuleuven.ac.be
*To whom correspondence should be addressed.
Inferring strengths of protein-protein interactions from
experimental data using linear programming
Authors: Hayashida Morihiro , Ueda Nobuhisa , Akutsu Tatsuya 
Published: October 2003

Abstract
Motivation: Several computational methods have been proposed for inference of protein-protein interactions. Most of the existing methods assume that protein-protein interaction data are given as binary data (i.e. whether or not each protein pair interacts). However, multiple biological experiments are performed for the same protein pairs and thus the ratio (strength) of the number of observed interactions to the number of experiments is available for each protein pair.
Results: We propose a new method for inference of protein-protein interactions from such experimental data. This method tries to minimize the errors between the ratios of observed interactions and the predicted probabilities in training data, where this problem is formalized as a linear program based on a probabilistic model. We compared the proposed method with the association method, the EM method and the SVM-based method using real interaction data. It is shown that a variant of the method is comparable to existing methods for binary data. It is also shown that the method outperforms existing methods for numerical data.
Availability: Programs transforming input data into LP format files are available upon request.
Supplementary information: http://sunflower.kuicr.kyoto-u.ac.jp/~morihiro/protint/supplement.html
Contact: akutsu@kuicr.kyoto-u.ac.jp
*To whom correspondence should be addressed.
Gene networks inference using dynamic Bayesian networks
Authors: Perrin Bruno-Edouard , Ralaivola Liva , Mazurie Aurélien , Bottani Samuele , Mallet Jacques , d’Alché–Buc Florence 
Published: October 2003

Abstract
This article deals with the identification of gene regulatory networks from experimental data using a statistical machine learning approach. A stochastic model of gene interactions capable of handling missing variables is proposed. It can be described as a dynamic Bayesian network particularly well suited to tackle the stochastic nature of gene regulation and gene expression measurement. Parameters of the model are learned through a penalized likelihood maximization implemented through an extended version of EM algorithm. Our approach is tested against experimental data relative to the S.O.S. DNA Repair network of the Escherichia coli bacterium. It appears to be able to extract the main regulations between the genes involved in this network. An added missing variable is found to model the main protein of the network. Good prediction abilities on unlearned data are observed. These first results are very promising: they show the power of the learning algorithm and the ability of the model to capture gene interactions.
Keywords: gene regulatory networks, structure extraction, expression profiles, dynamic Bayesian networks, Kalman filter, penalized likelihood, EM algorithm.
Contact: perrin@poleia.lip6.fr
*To whom correspondence should be addressed.
Breaking the Bonds of Precedent: The 1905–6 Government Reform Commission and the Remaking of the Qing Central State
Authors: Horowitz Richard S. 
Published: October 2003

On January 29, 1901, in the grim aftermath of the Boxer Uprising and the humiliating foreign invasion of north China that followed, the Empress Dowager Cixi issued a famous edict that initiated the New Policy (xinzheng) reforms.The weakness of China is caused by the strength of convention and the rigid network of regulations. We have many mediocre officials but few men of talent and courage. The regulations are used by mediocre men as the means of their self-protection, and taken advantage of by government clerks as sources of profit. The government officials exchange numerous documents but they never touch reality. The appointment of capable men is restricted by regulations so rigid that even men of exceptional talent are missed. What misleads the country can be expressed in one word, selfishness, and what suffocates all under heaven is precedent.
Metabolic economics and microbial proteome evolution
Authors: Akashi Hiroshi 
Published: October 2003

Abstract
Natural selection is thought to act upon protein structures to optimize biochemical properties related to their specific cellular function. Selection pressures related to efficient synthesis, rather than proper function, of proteins may act globally on the amino acid composition of the proteome, but are less firmly established. A substantial fraction of bacterial energy budgets are devoted to biosynthesis of amino acids, the building blocks of proteins. The fueling reactions of central metabolism provide precursor metabolites for synthesis of amino acids. Thus, synthesis of an amino acid entails a dual cost; energy is lost by diverting chemical intermediates from fueling reactions and additional energy is required to convert precursor metabolites to amino acids. Selection to reduce the energetic costs predicts increases in the abundance of less energetically costly amino acids in highly expressed proteins. Using synonymous codon usage bias as a measure of translation rates, we show that amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis reflects the action of natural selection to enhance metabolic efficiency. The primary structures of proteins may also reflect natural selection to enhance the rate and accuracy of their synthesis. Differences in cellular concentrations of tRNAs could lead to translation selection both within and among synonymous families. In yeast, usage of several amino acids show striking associations with gene expression. These changes in amino acid composition result in stronger correlations between amino acid usage and tRNA abundances in highly expressed genes than in less expressed loci. Proteome-wide patterns of amino acid composition in microbes appears to reflect natural selection to enhance the overall physiology of cells as well as the specific functions of proteins.
Contact: akashi@psu.edu&#x2028; http://www.bio.psu.edu/people/faculty/akashi/
Fast feature selection using a simple estimation of
distribution algorithm: a case study on splice site prediction
Authors: Saeys Yvan , Degroeve Sven , Aeyels Dirk , Van de Peer Yves , Rouzé Pierre 
Published: October 2003

Abstract
Motivation: Feature subset selection is an important preprocessing step for classification. In biology, where structures or processes are described by a large number of features, the elimination of irrelevant and redundant information in a reasonable amount of time has a number of advantages. It enables the classification system to achieve good or even better solutions with a restricted subset of features, allows for a faster classification, and it helps the human expert focus on a relevant subset of features, hence providing useful biological knowledge.
Results: We present a heuristic method based on Estimation of Distribution Algorithms to select relevant subsets of features for splice site prediction in Arabidopsis thaliana. We show that this method performs a fast detection of relevant feature subsets using the technique of constrained feature subsets. Compared to the traditional greedy methods the gain in speed can be up to one order of magnitude, with results being comparable or even better than the greedy methods. This makes it a very practical solution for classification tasks that can be solved using a relatively small amount of discriminative features (or feature dependencies), but where the initial set of potential discriminative features is rather large.
Keywords: Machine Learning, Feature Subset Selection, Estimation of Distribution Algorithms, Splice Site Prediction.
Contact: yvsae@gengenp.rug.ac.be
*To whom correspondence should be addressed.
Stakeholder engagement in participatory research in French marine and freshwater social‐ecological systems: A systematic map protocol
Authors: Chevallier Adrien , Balti Heikel , Gourguet Sophie , Macher Claire , Shin Yunne‐Jai , Moullec Fabien 
Published: January 2024

Abstract

Stakeholder engagement (SkE) in research is currently experiencing significant growth within the fields of environmental and sustainability sciences. Stakeholder engagement ensures the relevance of research questions to societal expectations and the uptake and salience of the co‐produced knowledge and results for their use in the decision‐making process.

In a context of societal challenges regarding biodiversity conservation and the sustainability of marine and freshwater social‐ecological systems (SESs), participatory approaches constitute key methods in applied research involving actions and decision‐making. There are, however, many gaps in the practical, conceptual and ethical ways stakeholders have been involved in research.

We propose here a systematic map of the literature on SkE in research on marine and aquatic SESs carried out on French European and overseas territories, in order to draw up the first comprehensive overview of how SkE has developed and changed since 1945.

This systematic map will identify a representative list of scientific articles on SkE in French marine and freshwater social‐ecological research. The literature search will include both academic literature (e.g. peer‐reviewed articles, reviews, meta‐analyses) and grey literature (e.g. reports, working papers) using the most relevant search engines for the scientific literature published between 1945 and 2023. Retrieved publications will be reviewed for relevance according to a predefined set of eligibility/ineligibility criteria by a group of trained reviewers. The eligibility check will be done in two successive screening steps: (1) title and abstract and (2) full text, each independently performed by two reviewers. All retained literature will be subjected to coding and metadata extraction using the Sysrev platform. No validity assessment will be undertaken. A database of the metadata extracted will be provided, along with a narrative description of the evidence base, and a set of figures and tables summarizing the relevant characteristics of the studies.

This systematic map will provide a reliable overview of SkE conducted in research projects on French aquatic social‐ecological systems to strengthen the science–society relationship and help future research projects implement efficient and sustainable SkE processes in France and elsewhere.
Flow‐Induced Microfluidic Assembly for Advanced Biocatalysis Materials
Authors: Lemke Phillip , Schneider Leonie , Kunz Willfried , Rieck Anna L. , Jäger Paula S. , Bruckmann Alexander , Nestler Britta , Rabe Kersten S. , Niemeyer Christof M. 
Published: January 2024

AbstractExploring the potential of microfluidic systems, this study presents a groundbreaking approach harnessing energy in microfluidic flows within a purpose‐built microreactor, enabling precise deposition of functional biomaterials. Upon optimizing reactor dimensions and integrating it into a microfluidic system, sequentially flow‐induced deposition of DNA hydrogels and transformation into DNA‐protein hybrid materials with SpyTag/SpyCatcher technology is investigated. However, limited functionalization rates restrict its viability for targeted biocatalytic processes. Therefore, the direct deposition of a phenolic acid decarboxylase is investigated, which is efficiently deposited but shows limited biocatalytic performance due to shear‐induced denaturation. This challenge is overcome by a two‐step immobilization process, resulting in microfluidic bioreactors demonstrating initial high space‐time yields of up to 7000 g L−1 d−1, but whose process stability proves unsatisfactory. However, by exploiting the principle of flow‐induced deposition to immobilize recombinant E. coli cells as functional living materials overexpressing biocatalytically relevant enzymes, bioreactors are produced that show equally high space‐time yields in continuous whole‐cell catalysis which remain constant over periods of up to 10 days. The insights gained offer optimization strategies for advanced functional materials and innovative reactor systems holding promise for applications in fundamental materials science, biosensing, and scalable production of microreactors for biocatalysis and bioremediation.