Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant cis-acting regulatory DNA elements (PLACE) database: 1999

PLACE (http://www.dna.affrc.go.jp/htdocs/PLACE/) is a database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements. Motifs were extracted from previously published reports on genes in vascular plants. In addition to the motifs originally reported, their variations in other genes or in other plant species in later reports are also compiled. Documents for each motif in the PLACE database contains, in addition to a motif sequence, a brief definition and description of each motif, and relevant literature with PubMed ID numbers and GenBank accession numbers where available. Users can search their query sequences for cis-elements using the Signal Scan program at our web site. The results will be reported in one of the three forms. Clicking the PLACE accession numbers in the result report will open the pertinent motif document. Clicking the PubMed or GenBank accession number in the document will allow users to access to these databases, and to read the of the literature or the annotation in the DNA database. This report summarizes the present status of this database and available tools.
Longitudinal Course of Physical Function in People With Symptomatic Knee Osteoarthritis: Data From the Multicenter Osteoarthritis Study and the Osteoarthritis Initiative

Pain and functional decline are hallmarks of knee osteoarthritis (OA). Nevertheless, longitudinal studies unexpectedly reveal stable or improved physical function. The aim of this study was to impute missing and pre–total knee replacement (TKR) values to describe physical function over time among people with symptomatic knee OA.
p300/CBP is required for transcriptional induction by interleukin-4 and interacts with Stat6

Interleukin-4 (IL-4) induces tyrosine phosphorylation of the latent transcription factor Stat6, which mediates the transcriptional responses of IL-4. The transactivation domain of Stat6 has recently been mapped to the C-terminal region of Stat6. We have investigated the mechanism by which Stat6, through its transactivation domain, induces transcription. Previous studies have shown that diverse regulated transcription factors interact with coactivators such as p300 and CBP. We report that Stat6 used the interaction with p300/CBP to exert its stimulatory effects. Overexpression of p300/CBP increased IL-4-induced transcription of Stat6 activated reporter genes. The requirement of p300/CBP for Stat6-mediated transactivation is shown by coexpression of the adenovirus E1A protein. E1A repressed the IL-4-induced reporter gene activity, while mutants of E1A, which do not interact with p300/CBP, failed to block the IL-4-induced response. In addition, we found that the minimal transactivation domain of Stat6, when fused to the GAL4 DNA-binding domain, was repressed by E1A, whereas the fusion protein p300-VP16 increased the transcriptional activity. In two-hybrid protein interaction assays in mammalian cells, we mapped the interaction domain of CBP to a C-terminal region between amino acids 1850 and 2176, a region distinct from the interaction domain of CBP with Stat1, Stat2 or Stat5. Finally, we show that antibodies raised against p300 coimmunoprecipitated Stat6 and p300 from transfected COS7 cells and antibodies against Stat6 coimmunprecipitated endogenous Stat6 and CBP from Ba/F3 cells. Our data suggest that the transactivation domain of Stat6 makes contact with the basal transcription machinery by binding to p300/CBP.
Association of Somatic Comorbidities and Comorbid Depression With Mortality in Patients With Rheumatoid Arthritis: A 14‐Year Prospective Cohort Study

Patients with rheumatoid arthritis (RA) have a significantly increased risk of mortality compared with the general population. One of the most important predictors for mortality is somatic comorbidity. Moreover, studies have demonstrated that comorbid depression is associated with mortality. Which specific comorbidities are associated with mortality is less investigated. The purpose of this study was to investigate the association of a wide range of comorbidities with mortality in patients with RA.
The RDP-II (Ribosomal Database Project)

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and approximately 75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.h tml). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator@cme.msu.edu to rdpstaff@msu.edu.
LIGAND: database of chemical compounds and reactions in biological pathways

LIGAND is a composite database comprising three sections: COMPOUND for the information about metabolites and other chemical compounds, REACTION for the collection of substrate-product relations representing metabolic and other reactions, and ENZYME for the information about enzyme molecules. The current release (as of September 7, 2001) includes 7298 compounds, 5166 reactions and 3829 enzymes. In addition to the keyword search provided by the DBGET/LinkDB system, a substructure search to the COMPOUND and REACTION sections is now available through the World Wide Web (http://www.genome.ad.jp/ligand/). LIGAND may be also downloaded by anonymous FTP (ftp://ftp.genome.ad.jp/pub/kegg/ligand/).
A model of the factors that influence the implementation of a telemedicine solution in Sri Lanka

In Sri Lanka, urban hospitals offer specialized healthcare services, while rural hospitals have limited services and normally offer only basic hospital facilities. Therefore people in rural areas have to travel relatively long distances to urban hospitals which offer specialized healthcare. This is expensive, while the poor transportation systems in rural areas make travel to urban hospitals time-consuming often involve an overnight stay. The aim of this research is to improve access to healthcare by adopting telemedicine in rural areas where the patient and the clinician in the rural hospital can contact the consultant in the urban hospital using audio, video and data communication methods for specialized healthcare services. The methods used were questionnaires and interviews in the exploratory study, which had small number of participants (83) covering three regions, followed by the main survey which had large number of participants (225) and ten regions. A model for adoption of a telemedicine system in Sri Lanka was developed from the analysis of the literature and the exploratory study. The exploratory study was conducted in three districts of Sri Lanka involving clinicians, hospital staff and the general public from both rural and urban areas, and Health Ministry officials, medical directors and consultants. The major study was conducted in ten districts and on two islands of Sri Lanka to identify the factors in the model which influenced the adoption of telemedicine. The findings of the main survey clearly indicate how important the telemedicine solution is to the rural population. The results also show that hospital staff and the general public were very much in favour of adopting telemedicine. The results also indicate that both clinicians and hospital staff believe that staff involvement, and introducing new policies and standards, will influence the adoption of telemedicine. Clinicians believe that Internet connectivity and the equipment used will not have an effect on introducing telemedicine. This model will be beneficial when implementing a telemedicine system into rural areas of Sri Lanka, which will provide patients with access to specialized healthcare services.
Pediatric Sports Medicine for the Practitioner: From Physiologic Principles to Clinical Applications

Physicians who care for children are often called upon to render advice on sports and exercise. Long before the physical fitness fad struck the adult sector, children used sports to have fun, work off steam, test themselves against their peers, and learn about real life. Their physicians, once called on only to tend their wounds, now must be prepared to advise on exercise appropriate to age, size, development, and any concurrent disease, and to control access to many competitive activities. This well-written, carefully documented book provides a great deal of information by which such decisions can be informed. Its extended title accurately describes the focus of the book: exercise physiology in the immature human, with special applications to children with several forms of chronic disorders. Two initial chapters clearly describe the response of children of differing age, sex, and size to exercise. Applications to children with pulmonary, cardiovascular, endocrine, nutritional,
Alkaline deoxyribonucleases released from Neurospora crassa mycelia: two activities not released by mutants with multiple sensitivities to mutagens

Three major alkaline deoxyribonuclease (DNase) activities have been identified in sorbose-containing liquid culture medium in which wild-type Neurosporacrassa were grown: DNase A, a Ca++dependent endonuclease of molecular weight 65,000 daltons which has no specificity for single- or double-stranded DNA (ss-DNA or ds-DNA) and no activity with RNA; DNase B, a Mg++-dependent single-strand specific exonuclease of molecular weight 78,000 daltons active with both ss-DNA and RNA; DNase C, a divalent metal ion-dependent endo-exonuclease of molecular weight 65,000 having single-strand specific endonuclease activity with ss-DNA and RNA and exonuclease activity with ds-DNA. Three mutants which were shown previously to have wide spectra of sensitivities to mutagens, and which exhibited reduced release of DNase activity on sorbose-containing agar test plates (the Nuh phenotype), were deficient relative to the wild-type in the release of these major alkaline DNases into the liquid culture medium. The uvs-3 mutant released only small amounts of DNase A and DNase C; nuh-4 did not release detectable DNase C and released only a very low level of DNase B; uvs-6 released only a low level of DNase A. A nuh mutant (nuh-3) which is not mutagen sensitive relative to the wild-type released low levels of DNase B. On the other hand, an ultraviolet light-sensitive mutant (nuc-2) which does not have the Nuh phenotype was normal in the release of these DNases.
A First Attempt at Modelling Roe Deer (Capreolus capreolus) Distributions Over Europe

The presence of roe deer can be an important component within ecological and epidemiological systems contributing to the risk and spread of a range of vector-borne diseases. Deer are important hosts for many vectors, and may therefore serve as a focal point or attractant for vectors or may themselves act as a reservoir for vector-borne disease. Three spatial modelling techniques were used to generate an ensemble model describing the proportion of suitable roe deer habitat within recorded distributions for Europe as identified from diverse sources. The resulting model is therefore an index of presence, which may be useful in supporting the modelling of vector-borne disease across Europe.
A Young Child With Fever, Alopecia, and Skin Nodules

The illness started as a continuous high-grade fever noted up to 103°F. Subsequently, he also developed red painful skin nodules that initially appeared over shins and later progressed to involve thighs, trunks, upper extremities, and face. The nodules also appeared over scalp and there was a was a progressive loss of scalp hair. This article is protected by copyright. All rights reserved.
Confinement and manipulation of electron plasmas in a multicell trap

Plasma dynamics and transport are studied experimentally in a multicell Penning-Malmberg trap. The goal is to develop methods for accumulation and long-term confinement of larger numbers of charged particles (e.g., positrons) than is presently possible. In this scheme, the particles constitute non-neutral plasmas which are confined separately in a parallel array of storage cells. Experiments are presented in which pure electron plasmas are transferred from a large-diameter “master cell” trapping region into four smaller, parallel “storage cells,” three of which are offset from the magnetic symmetry axis. The physics of the transfer process, as well as the confinement properties of plasmas in the storage cells, is discussed. We show that plasmas can be transferred into the storage cells and held there for up to a day or more using the rotating wall technique, provided that the plasma radius is sufficiently small compared to that of the cell wall. Experiments regarding the confinement of plasmas with kilovolt space charge are discussed. Recommendations are provided for future efforts with high-capacity multicell traps.Plasma dynamics and transport are studied experimentally in a multicell Penning-Malmberg trap. The goal is to develop methods for accumulation and long-term confinement of larger numbers of charged particles (e.g., positrons) than is presently possible. In this scheme, the particles constitute non-neutral plasmas which are confined separately in a parallel array of storage cells. Experiments are presented in which pure electron plasmas are transferred from a large-diameter “master cell” trapping region into four smaller, parallel “storage cells,” three of which are offset from the magnetic symmetry axis. The physics of the transfer process, as well as the confinement properties of plasmas in the storage cells, is discussed. We show that plasmas can be transferred into the storage cells and held there for up to a day or more using the rotating wall technique, provided that the plasma radius is sufficiently small compared to that of the cell wall. Experiments regarding the confinement of plasmas with kilovo.
Rapid and efficient cosmid cloning

We present a procedure for cosmid cloning that allows rapid and efficient cloning of individual DNA fragments of between 32kb and 45kb. By appropriate treatment of the cloning vector, pJb8, we make left-hand and right-hand vector ends that are incapable of self-ligation but which accept dephosporylated insert DNA fragments. The inserted fragments are generated by partial digestion with MboI or Sau3A and are dephosphorylated to prevent ligation and insertion of non-contiguous fragments. The method eliminates the need to size the insert DNA fragments and prevents formation of clones containing short or multiple inserts. 1 microgram of target Drosophila DNA gives about 5 x 10(5) clones, with an average insert size of 38kb. We also describe a rapid and efficient method for preparing plasmid and cosmid DNA.
Growth Diagnosis: Selected Methods for Interpreting and Predicting Physical Development from One Year to Maturity

The authors of this important book gained their unique experience and data in longitudinal studies of the growth of healthy children in California. They here present to us chosen fruits. Published data on child growth rates are so rare that when they appear in a work of this kind we are particularly anxious to learn how we may best use the benefits of such careful labors. The book does live up to our expectations by being practical and by describing a battery of measures and ratings of the size, shape and maturity of children.
Porous Polymersomes with Encapsulated Gd‐Labeled Dendrimers as Highly Efficient MRI Contrast Agents

The use of nanovesicles with encapsulated Gd as magnetic resonance (MR) contrast agents has largely been ignored due to the detrimental effects of the slow water exchange rate through the vesicle bilayer on the relaxivity of encapsulated Gd. Here, the facile synthesis of a composite MR contrast platform is described; it consists of dendrimer conjugates encapsulated in porous polymersomes. These nanoparticles exhibit improved permeability to water flux and a large capacity to store chelated Gd within the aqueous lumen, resulting in enhanced longitudinal relaxivity. The porous polymersomes, ∼130 nm in diameter, are produced through the aqueous assembly of the polymers, polyethylene oxide‐b‐polybutadiene (PBdEO), and polyethylene oxide‐b‐polycaprolactone (PEOCL). Subsequent hydrolysis of the caprolactone (CL) block resulted in a highly permeable outer membrane. To prevent the leakage of small Gd‐chelate through the pores, Gd was conjugated to polyamidoamine (PAMAM) dendrimers via diethylenetriaminepentaacetic acid dianhydride (DTPA dianhydride) prior to encapsulation. As a result of the slower rotational correlation time of Gd‐labeled dendrimers, the porous outer membrane of the nanovesicle, and the high Gd payload, these functional nanoparticles are found to exhibit a relaxivity (R1) of 292 109 mM−1 s−1 per particle. The polymersomes are also found to exhibit unique pharmacokinetics with a circulation half‐life of >3.5 h and predominantly renal clearance.
A Generalized System for Photoresponsive Membrane Rupture in Polymersomes

Polymersomes are vesicles whose membranes comprise self‐assembled block copolymers. It has recently been shown that co‐encapsulating conjugated multiporphyrin dyes in a polymersome membrane with ferritin protein in the aqueous lumen confers photolability to the polymersome. In the present study, the photolability is shown to be extendable to vesicles containing dextran, an inert and inexpensive polysaccharide, as the luminal solute. How structural features of the polymersome/porphyrin/dextran composite affect its photoresponse is explored. Increasing dextran molecular weight, decreasing block copolymer molecular weight, and altering fluorophore‐membrane interactions results in increasing the photoresponsiveness of the polymersomes. Amphiphilic interactions of the luminal encapsulant with the membrane coupled with localized heat production in the hydrophobic bilayer likely cause differential thermal expansion in the membrane and the subsequent membrane rupture. This study suggests a general approach to impart photoresponsiveness to any biomimetic vesicle system without chemical modification, as well as a simple, bio‐inert method for constructing photosensitive carriers for controlled release of encapsulants.
Structural Origins of Silk Piezoelectricity

Uniaxially oriented, piezoelectric silk films are prepared by a two‐step method that involves first air drying aqueous, regenerated silk fibroin solutions into films, and then drawing the silk films to a desired draw ratio. The utility of two different drawing techniques—zone drawing and water‐immersion drawing—is investigated for processing the silk for piezoelectric studies. Silk films zone drawn to a ratio of λ 5 2.7 display relatively high dynamic shear piezoelectric coefficients of d14 5 –1.5 pC N21, corresponding to an increase in d14 of over two orders of magnitude due to film drawing. A strong correlation is observed between the increase in silk II, β‐sheet content with increasing draw ratio as measured by FTIR spectroscopy (Cb $ \propto $ e2.5λ), the concomitant increasing degree of orientation of β‐sheet crystals detected via wide‐angle X‐ray diffraction (full width half maximum (FWHM) = 0.22° for λ = 2.7), and the improvement in silk piezoelectricity (d14 $ \propto $ e2.4λ). Water‐immersion drawing leads to a predominantly silk I structure with a low degree of orientation (FWHM 5 75°) and a much weaker piezoelectric response compared to zone drawing. Similarly, increasing the β‐sheet crystallinity without inducing crystal alignment, e.g., by methanol treatment, does not result in a significant enhancement of silk piezoelectricity. Overall, a combination of a high degree of silk II, β‐sheet crystallinity and crystalline orientation are prerequisites for a strong piezoelectric effect in silk. Further understanding of the structural origins of silk piezoelectricity provides important options for future biotechnological and biomedical applications of this protein.
SPA: simple web tool to assess statistical significance of DNA patterns

Many statistical methods and programs are available to compute the significance of a given DNA pattern in a genome sequence. In this paper, after outlining the mathematical background of this problem, we present SPA (Statistic for PAtterns), an expert system with a simple web interface designed to be applied to two of these methods (large deviation approximations and exact computations using simple recurrences). A few results are presented, leading to a comparison between the two methods and to a simple decision rule in the choice of that to be used. Finally, future developments of SPA are discussed. This tool is available at the following address: http://stat.genopole. cnrs.fr/SPA/.
Synergetic Targeted Delivery of Sleeping‐Beauty Transposon System to Mesenchymal Stem Cells Using LPD Nanoparticles Modified with a Phage‐Displayed Targeting Peptide

An important criterion for effective gene therapy is sufficient chromosomal integration activity. The Sleeping Beauty (SB) transposon system is a plasmid system allowing efficient insertion of transgenes into the host genome. However, such efficient insertion occurs only after the system is delivered to nuclei. Since transposons do not have the transducing abilities of viral vectors, efficient delivery of this system first into cells and then into cell nuclei is still a challenge. Here, a phage display technique using a major coat displayed phage library is employed to identify a peptide (VTAMEPGQ) that can home to rat mesenchymal stem cells (rMSCs). A nanoparticle, called liposome protamine/DNA lipoplex (LPD), is electrostatically assembled from cationic liposomes and an anionic complex of protamine, DNA and targeting peptides. Various peptides are enveloped inside the LPD to improve its targeting capability for rMSCs and nuclei. The rMSC‐targeting peptide and nuclear localization signal (NLS) peptide can execute the synergetic effect to promote transfection action of LPD. The homing peptide directs the LPD to target the MSCs, whereas the NLS peptide directs transposon to accumulate into nuclei once LPD is internalized inside the cells, leading to increased gene expression. This suggests that rMSC‐targeting peptide and NLS peptide within LPD can target to rMSCs and then guide transposon into nuclei. After entering the nuclei, SB transposon increase the insertion rates into cellular chromosomes. The targeting LPD does not show obvious cell toxicity and influence on the differentiation potential of rMSCs. Therefore, the integration of SB transposon and LPD system is a promising nonviral gene delivery vector in stem cell therapy.