Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression, gene regulation, and roles of Fisp12/CTGF in developing tooth germs

Odontogenesis involves multiple events, including tissue–tissue interactions, cell proliferation, and cell differentiation, but the underlying mechanisms of regulation are far from clear. Because Fisp12/CTGF is a signaling protein involved in similar events in other systems, we asked whether it is expressed in developing tooth germs and what roles it may have. Indeed, Fisp12/CTGF transcripts were first expressed by dental laminas, invaginating epithelium, and condensing mesenchyme at the bud stage, and then became abundant in enamel knot and preameloblasts. Fisp12/CTGF was present not only in inner dental epithelium but also in stratum intermedium and underlying dental mesenchyme. Fisp12/CTGF expression decreased markedly in secreting ameloblasts. Tissue reconstitution experiments showed that Fisp12/CTGF expression in dental epithelium required interaction with mesenchyme but was maintained by treatment of epithelium with transforming growth factor‐1, a factor regulating Fisp12/CTGF expression in other systems, or with bone morphogenetic protein‐2. Loss‐of‐function studies using CTGF neutralizing antibodies revealed that interference with endogenous factor action in tooth germ explants led to a severe inhibition of proliferation in both epithelium and mesenchyme and a marked delay in cytodifferentiation of ameloblasts and odontoblasts. Treatment of dental epithelial and mesenchymal cells in culture with recombinant CTGF stimulated cell proliferation, whereas treatment with neutralizing antibodies inhibited it. The data demonstrate for the first time that Fisp12/CTGF is expressed during odontogenesis. Expression is confined to specific sites and times, is regulated by epithelial–mesenchymal interactions and critical soluble factors, and appears to be needed for proliferation and differentiation along both ameloblast and odontoblast cell lineages. © 2002 Wiley‐Liss, Inc.
Near infrared fluorophore selection for lifetime-based FRET imaging

Near-infrared fluorophore pairs were comparatively studied to perform quantitative lifetime-based FRET imaging. Comparison in terms of donor lifetime reduction, relative brightness and quantitative estimation of the FRETing donor fraction were carried out using a transferrin based assay applied to breast cancer cells in vitro experiments. The best pair, as defined as the brightest and leading to accurate estimation of FRETing component is identified as the most suitable for in vitro and in vivo pre-clinical application.
Integrated analysis of gene expression profile and genetic variations associated with ovarian cancer.

OBJECTIVE Ovarian cancer is the most lethal gynecologic cancer worldwide, since most patients are diagnosed at an advanced stage. To improve the early diagnosis and treatment of ovarian cancer, we performed a integrated analysis of transcription profile and genetic variations to study on the molecular pathogenesis in ovarian cancer. METHODS mRNA expression profiles of ovarian cancer and normal controls downloaded from ArrayExpress database were applied to identify differentially expressed genes (DEGs). The chromosomal distributions of these DEGs were established using DAVID. Then, DNASeq data from the Cancer Genome Atlas (TCGA) were extracted to analyze gene mutational information including the number of mutations (mut), the number of mutational genes (mutG) and chromosomal distributions of mutations. Statistical method was offered to carrying on correlation analysis of gene mutations and differential expression. RESULTS A total of 1732 DEGs were identified, and the chromosomal distributions of 97 genes were unknown. These DEGs were most significantly distributed on chromosome 4 with p value = 1.34E-7. Chromosome 1 enriched the most DEGs (11.56%). Statistical algorithm showed that DEGs presented significantly positive correlation with mut (p = 0.000009) and mutG (p = 0.00001). In 48.7% DEGs, gene mutations were found. CONCLUSIONS We conducted scientific analysis on integration of DEGs in expression profiles and genetic mutations in ovarian cancer, displayed the correlation of differential expression and genetic variations. The result indicated that expression profiles were significantly correlated to genotype.
Diagnostic challenges of motility disorders: optimal detection of CD117+ interstitial cells of Cajal

Aims: Several gastrointestinal motility diseases are associated with altered numbers of interstitial cells of Cajal (ICC), and testing for alterations in numbers of ICC has been proposed as one way to improve routine diagnosis in motility diseases. However, the protocols currently used to visualize ICC in formalin‐fixed paraffin‐embedded (FFPE) tissue using antibodies to CD117 have not been optimized for studying motility disorders. The aims of this study were therefore to determine the optimal protocol using FFPE tissue, determine normal values for ICC in non‐neoplastic human colon, and compare results with those obtained using immunofluorescence (IF).
Specific antibody levels at the cervix during the menstrual cycle of women vaccinated with human papillomavirus 16 virus-like particles.

BACKGROUND In early-phase trials, a human papillomavirus 16 (HPV16) virus-like particle (VLP) vaccine has been shown to be well tolerated, immunogenic, and protective against HPV16 in women, most of whom were taking oral contraceptives. Previous studies have not determined whether HPV immunization results in specific antibody levels in the human genital tract or whether these levels might vary during contraceptive or ovulatory cycles. Therefore, we determined the levels of total and specific antibodies in the cervical secretions of women who had been immunized with HPV16 VLPs and examined the influence of the menstrual cycle and oral contraceptive use on these levels. METHODS Two groups of women were immunized, seven who were taking oral contraceptives and 11 who were ovulating. After seroconversion, serum and cervical secretions were collected twice weekly for 5 weeks. Total immunoglobulins (IgG and IgA) and vaccine-specific IgGs were determined by enzyme-linked immunosorbent assay. Nonparametric statistical analyses were used to determine the statistical significance of differences in IgG levels between groups, and correlations between serum- and cervical-specific IgG levels were determined by the Spearman correlation coefficient. RESULTS All participants developed detectable titers of anti-HPV16 VLP IgGs in their cervical secretions after immunization. The cervical titers of specific IgG and total IgGs and IgAs among participants in the contraceptive group were relatively constant throughout the contraceptive cycle. In contrast, the cervical titers of specific IgG and total IgGs and IgAs among participants in the ovulatory group varied during the menstrual cycle, being highest during the proliferative phase, decreasing approximately ninefold around ovulation, and increasing approximately threefold during the luteal phase. Serum- and cervical-specific IgG levels were correlated (r =.86) in women in the contraceptive group but not in women in the ovulatory group (r =.27). CONCLUSIONS The relatively high titer of anti-HPV16 antibodies at the cervix is promising in terms of vaccine efficacy; however, the decrease in antibody titer around ovulation raises the possibility that the HPV16 VLP vaccine might be less effective during the peri-ovulatory phase.
A combined approach for noise reduction in medical images using Dual Tree Discrete Wavelet Transform and Rotated Dual Tree Discrete Wavelet Transform

Medical imaging suffers from image noise. To remove this noise spatial domain and transform domain techniques are used. But spatial domain techniques have limitation of edge blurring w.r. t transform based techniques. Therefore in this paper we have proposed a transform based denoising technique. We have used Dual tree DWT and Rotated version of Dual Tree DWT jointly to improve our denoising results. Our main focus is to get more directional information from this transform which will improve denoising results. We have compared our results with existing methods and results are very encouraging. PSNR is used as image quality measure.
Antimicrobial activity of some Australian plant species from the genus Eremophila

Plant species of the genus Eremophila (Myoporaceae) are native to Australia and are known to produce a diverse range of unusual secondary compounds. The purpose of this research was to examine the antimicrobial activity of 72 Eremophila species most of which had not been the subject of any previous pharmacological testing. Organic extracts of Eremophila species were screened for antimicrobial activity against Gram‐positive and Gram‐negative bacteria and yeasts of medical importance. Extracts of a number of Eremophila species showed selective activity against Gram‐positive bacteria with MICs for the most active species in the range of 16 to 62 μg/ml for Streptococcus species, and 62 to 250 μg/ml for standard strains of Staphylococcus aureus. Extracts with the greatest activity against standard strains were tested against 68 clinical isolates of multi‐resistant methicillin‐resistant S. aureus (mMRSA). The majority of the clinical isolates were susceptible to concentrations below 62.5 μg/ml for the extracts of E. drummondii, E. linearis, E. serrulata, E. acrida, E. neglecta, E. virens and a new undescribed species affiliated with E. prolata. The extract of E. virens inhibited growth of all 68 clinical mMRSA isolates at the minimum tested concentration of 31 μg/ml. This study has shown for the first time that a number of different Eremophila species manifest selective antibacterial activity against Gram‐positive organisms which are important causes of human disease. It shows that there are several Eremophila species possessing interesting antibacterial activity besides those that have published traditional use. These may yield novel antibacterial compounds with potential to be used in biomedical applications. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
What future role might N-acetyl-cysteine have in the treatment of Obsessive Compulsive Spectrum disorders? A systematic review

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Complementary in-vivo measurements for human body communication

The actual way of living is characterized by a large use of connected terminals and devices. This connectivity needs permanent intercommunication between terminals and requires miniaturization, power management, and intelligence. In this context, Human Body Communication (HBC) is an emerging and promising communication technique of Body Area Network (BAN) which enshrines these requirements. HBC is a non-radio frequency technique which uses the human body as a communication channel. This communication technique is in full development. However, it is controversial without consensus in terms of the propagation mechanism and characteristics even the large number of research and academic reports. This work joins the efforts to characterize the channel and for a better understanding of the communication through the human body for both galvanic and capacitive coupling. The originality in this paper is to bring up the HBC coupling, from a new point of view, by proposing in vivo measurements. In addition to the usual parameters (channel length for example), we aim to discuss the effect of the electrical contact impedance as a function of the applied force and contact gel, and the distance between the electrodes and the body.
Tempo and Mode in the Molecular Evolution of Influenza C

Abstract: Influenza C contributes to economic damage caused by working days lost through absence or inefficiency and may occasionally cause an acute respiratory illness in a paediatric setting. All Influenza C sequences from the NCBI Influenza Virus Resource were examined to determine the date of the most recent common ancestor (t-MRCA), the average nucleotide substitution rate, and the location of residues under positive selection, for each of the seven genome segments of this virus. The segment with the deepest phylogeny was found to be segment 4, encoding the haemagglutinin-esterase protein (HE) with mean t-MRCA at 1890 of the common era (AD), at a 95% highest posterior density (HPD) of 1857-1924 AD. Other genome segments have slightly more recent common ancestors, ranging from mean t-MRCAs of 1916 AD (HPD 1891-1937) for segment 7, encoding the two non-structural proteins (NS) to 1944 AD (HPD 1940-1948) for segment 2 encoding the type 1 basic polymerase (PB1). On the basis of the Bayesian analysis a reclassification of lineages within genome segments is proposed. Some evidence for positive selection was found in the receptor-binding domain of the haemagglutinin-esterase protein. However, average ω (omega) values ranged from 0.05 for polymerase basic protein 2 (PB2) to 0.38 for non-structural protein 2 (NS2), suggesting that strong to moderate purifying selection is the main trend. Characteristic combinations of segment lineages were identified (genome constellations) and shown to have a relatively short life-span before being broken up by reassortment.
A proteomic approach to evaluate the butyrophilin gene family expression in human milk fat globule membrane

Human butyrophilin (BTN) expression in milk fat globule (MFGM) was evaluated using two dimensional electrophoresis (2‐DE) as the separation technique, and peptide mass mapping by matrix‐assisted laser desorption/ionisation‐mass spectrometry (MALDI‐MS) as the identification tool. Since milk composition changes throughout lactation time, 2‐DE maps in the pH range 4–7 of colostral MFGM and mature MFGM were compared, showing only slight differences in BTN spot distribution. The BTN gene family codes for seven proteins (BTN, BTN2A1, BTN2A2, BTN2A3, BTN3A1, BTN3A2, BTN3A3), their presence in human tissues has to date been evaluated only at a transcriptional level. Among 70 spots, analyzed and identified by MALDI‐MS, 13 spots were identified as BTN spots and only one as a fragment of BTN2A1. BTN was present in multiple glycoforms, and two smaller BTN forms of about 45 kDa were also identified. We propose an array of BTNs on human MFGM, which could provide breast‐fed infants with immune molecules during the neonatal period.
Efavirenz replacement by immediate full‐dose nevirapine is safe in HIV‐1‐infected patients in Cambodia

Efavirenz is used for the antiretroviral treatment of HIV/tuberculosis‐coinfected patients in developing countries. A switch to nevirapine is regularly carried out because of the cost and side effects of efavirenz. Pharmacokinetic studies suggested that nevirapine should be initiated at full dose when used as a substitute for efavirenz.
Pharmacokinetic Profile of the Anti-Sickling Hydroxyurea in Wild-Type and Transgenic Sickle Cell Mice

The pharmacokinetic profile of hydroxyurea (HU) was investigated by measuring the rate of drug disappearance from the plasma in wild-type and transgenic (Tg) sickle cell mice. The absorption and elimination processes of HU exhibited first-order kinetics after intraperitoneal administration of HU at 10, 50, 100 or 200 mg/kg body weight (BW). The dosage had a marked effect on the pharmacokinetics of HU in the Tg sickle cell mice. Although the area under the plasma concentration curve (AUC) increased in direct proportion with the HU dose in the wild-type mice, the AUC increased to a much greater extent at higher doses in the Tg sickle cell mice. In the Tg sickle cell mice, there was a considerable increase in the mean residence time (MRT) and a significant reduction in the apparent clearance (CL/F) at HU dose ≧100 mg/kg BW, when compared to the lower doses. At an HU dose of 200 mg/kg BW, the CL/F in the Tg sickle cell mice was reduced by about 50% of the value obtained at a dose of 10 mg/kg BW. This phenomenon was not noticeable in the wild-type mice. The MRT value in the wild-type mice at all doses was relatively constant. The steady-state distribution volume of HU in both the wild-type and Tg sickle cell mice was relatively constant at all doses of the drug. The AUC, CL/F, MRT, and terminal half-life values at any given HU dose showed significant differences between the wild-type and Tg sickle cell mice. Following intraperitoneal administration of HU at a dose of 10, 50, 100, or 200 mg/kg BW, the mean percentage of HU excreted in the urine of the wild-type and Tg sickle cell mice over 120 min was 84 ± 6.4% and 50 ± 8.2%, respectively, indicating a significant difference in the amount of HU excreted in urine in the two kinds of mice. The results obtained in this study may be useful in establishing an optimal dose of HU in the treatment and management of patients with sickle cell disease and other hemoglobinopathies.
Making Stem Cell Lines Suitable for Transplantation

Human stem cells, progenitor cells, and cell lines have been derived from embryonic, fetal, and adult sources in the search for graft tissue suitable for the treatment of CNS disorders. An increasing number of experimental studies have shown that grafts from several sources survive, differentiate into distinct cell types, and exert positive functional effects in experimental animal models, but little attention has been given to developing cells under conditions of good manufacturing practice (GMP) that can be scaled up for mass treatment. The capacity for continued division of stem cells in culture offers the opportunity to expand their production to meet the widespread clinical demands posed by neurodegenerative diseases. However, maintaining stem cell division in culture long term, while ensuring differentiation after transplantation, requires genetic and/or oncogenetic manipulations, which may affect the genetic stability and in vivo survival of cells. This review outlines the stages, selection criteria, problems, and ultimately the successes arising in the development of conditionally immortal clinical grade stem cell lines, which divide in vitro, differentiate in vivo, and exert positive functional effects. These processes are specifically exemplified by the murine MHP36 cell line, conditionally immortalized by a temperature-sensitive mutant of the SV40 large T antigen, and cell lines transfected with the c-myc protein fused with a mutated estrogen receptor (c-mycERTAM), regulated by a tamoxifen metabolite, but the issues raised are common to all routes for the development of effective clinical grade cells.
Characterization and PCR-Based Replicon Typing of Resistance Plasmids in Acinetobacter baumannii

ABSTRACT Acinetobacter baumannii is an opportunistic pathogen, especially in intensive care units, and multidrug-resistant isolates have increasingly been reported during the last decade. Despite recent progress in knowledge of antibiotic resistance mechanisms in A. baumannii, little is known about the genetic factors driving isolates toward multidrug resistance. In the present study, the A. baumannii plasmids were investigated through the analysis and classification of plasmid replication systems and the identification of A. baumannii-specific mobilization and addiction systems. Twenty-two replicons were identified by in silico analysis, and five other replicons were identified and cloned from previously uncharacterized A. baumannii resistance plasmids carrying the OXA-58 carbapenem-hydrolyzing oxacillinase. Replicons were classified into homology groups on the basis of their nucleotide homology. A novel PCR-based replicon typing scheme (the A. baumannii PCR-based replicon typing [AB-PBRT] method) was devised to categorize the A. baumannii plasmids into homogeneous groups on the basis of the nucleotide homology of their respective replicase genes. The AB-PBRT technique was applied to a collection of multidrug-resistant A. baumannii clinical isolates carrying the blaOXA-58 or blaOXA-23 carbapenemase gene. A putative complete conjugative apparatus was identified on one plasmid whose self-conjugative ability was demonstrated in vitro. We showed that this conjugative plasmid type was widely diffused in our collection, likely representing the most important vehicle promoting the horizontal transmission of A. baumannii resistance plasmids.
DYNAMICS OF HYBRID INCOMPATIBILITY IN GENE NETWORKS IN A CONSTANT ENVIRONMENT

After an ancestral population splits into two allopatric populations, different mutations may fix in each. When pairs of mutations are brought together in a hybrid offspring, epistasis may cause reduced fitness. Such pairs are known as Bateson-Dobzhansky-Muller (BDM) incompatibilities. A well-known model of BDM incompatibility due to Orr suggests that the fitness load on hybrids should initially accelerate, and continue to increase as the number of potentially incompatible substitutions increases (the “snowball effect”). In the gene networks model, which violates a key assumption of Orr's model (independence of fixation probabilities), the snowball effect often does not occur. Instead, we describe three possible dynamics in a constant environment: (1) Stabilizing selection can constrain two allopatric populations to remain near-perfectly compatible. (2) Despite constancy of environment, punctuated evolution may obtain; populations may experience rare adaptations asynchronously, permitting incompatibility. (3) Despite stabilizing selection, developmental system drift may permit genetic change, allowing two populations to drift in and out of compatibility. We reinterpret Orr's model in terms of genetic distance. We extend Orr's model to the finite loci case, which can limit incompatibility. Finally, we suggest that neutral evolution of gene regulation in nature, to the point of speciation, is a distinct possibility.
The General Transcription-Repair Factor TFIIH Is Recruited to the Excision Repair Complex by the XPA Protein Independent of the TFIIE Transcription Factor (*)

Recent studies have revealed that the general transcription factor TFIIH is also a general excision repair factor which, along with several other proteins, is required for transcription-independent excision reaction. As a general transcription factor, TFIIH is recruited to RNA polymerase II-promoter complex by another general transcription factor called TFIIE. We were interested in knowing whether TFIIE is also involved in recruiting TFIIH to the excision repair complex. We found that cell-free extract depleted of TFIIE carried out excision repair at a normal rate, leading us to conclude that TFIIE is not involved in recruiting TFIIH to the damage site and has no role in general excision repair. In contrast, the human damage recognition protein XPA specifically binds to TFIIH and apparently recruits it to the damage site. The carboxyl-terminal half of XPA is responsible for specific interaction with TFIIH. The C261S/C264S mutant of XPA bound the ERCC1•XPF complex normally, but failed to bind TFIIH and failed to complement an XP-A mutant cell-free extract indicating that the XPA-TFIIH interaction is essential to effecting the excision reaction. Interestingly, XPA also binds to the p34 subunit of TFIIE specifically and in competition with the p56 subunit of TFIIE. This latter interaction has no apparent role in general excision repair but may be relevant in the transcription-coupled repair reaction.