Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleotide sequences of 18S ribosomal RNA genes from the red algae Gracilaria tikvahiae McLachlan, Gracilaria verrucosa (Hudson) Papenfuss and Gracilariopsis sp

Owing especially to intensive aquaculture in recent years, marine red algae of the family Gracilariaceae have become the major source of agar in the international market. However, because of a high degree of morphological similarity among gracilariacean algae, and morphological plasticity within populations, identification and classification of these algae are often problematic. These difficulties greatly complicate assessment of natural agarophyte stocks, and may raise problems for regulatory approval of agars. Gracilaria tikvahiae McLachlan is the most thoroughly characterized of the hundred-odd described species of Gracilaria, and belongs to the subgenus Textoriella. Gracilaria verrucosa (Hudson) Papenfuss is a widely distributed, economically important species, and is the type of the other (nominate) subgenus. The verrucosa species concept has, however, recently been shown to comprise a number of similar taxa (1). Using organellar DNA restriction profiles, we have identified an assemblage of chiefly European strains conforming to the current concept of G. verrucosa (2); the G. verrucosa nuclear smallsubunit (18S) rDNA sequence below represents one of these strains, from Oslo, Norway. Species recognition has been further complicated by the discovery in the G. verrucosa type locality of an as yet unidentified species of the related genus Gracilariopsis (3) which has frequently been mistaken for G. verrucosa, therefore may be included in the original species concept (2). To assist in characterizing this Gracilariopsis sp. , we have determined the sequence of its 18S rDNA for comparison with that recently
What makes children feel safe in school? : an evaluation of the preventative model for behaviour in a local authority with a focus on childrens and adults perspectives of safety

This small scale study explores pupil and staff perspectives about what makes pupils feel safe in school. This is from the perspectives of children and staff who have been part of a project to reduce exclusion and improve attendance. The present study explored perceptions of Head Teachers and senior management about the impact of the project on children's feelings of safety. The study also explored the relationship between the implementation of the project from the perspectives of children and staff, and the initiatives put in place in relation to feeling safe. The participants were 24 children and 15 members of participating schools' senior management teams, who were interviewed using semi-structured interviews. The study also tracked exclusion and attendance figures. Thematic analysis was used to analyse interviews and descriptive statistics and nonparametric tests used to analyse exclusion and attendance data. Key findings were that children associated feeling safe with being protected and having their emotional needs met. Adults and children determined children's feelings of safety. The behaviour of peers and school behaviour management had an impact on children's feelings of safety. Children reported that specific places in school such as the playground had a role in maintaining feelings of safety, as did the school curriculum, the local community and the security of the school. The necessity for targeted work on learning and the emotional development of children to keep children safe was also a key finding. Project funding was used by schools to develop the curriculum and to employ and train additional staff. Schools reported that the playground was a key factor in maximising pupils' feelings of safety. Effective school systems which monitored and supported pupils' needs facilitated implementation of the project. Interventions that made children feel safe were significant in reducing levels of exclusion and unauthorised absence.
Isolation of two cDNAs encoding zinc finger proteins which bind to the alpha 1-antitrypsin promoter and to the major histocompatibility complex class I enhancer

Two partial cDNAs coding for DNA-binding proteins (AT-BP1 and AT-BP2) have been isolated. Both proteins, when prepared from lambda gt11 lysogens, bind to the B-domain of the alpha 1-antitrypsin promoter, an element which is important for the liver-specific expression of alpha 1-antitrypsin. Analysis of the cDNA sequences encoding these proteins reveals that both contain two zinc fingers of the Cys2-His2 type followed by a highly acidic stretch of 20 amino acids. AT-BP1 contains a second putative DNA-binding domain consisting of an 8-fold repeat of a SPKK (Ser-Pro-Lys/Arg-Lys/Arg) motif. Both proteins bind to the NF-kappa B recognition site in the MHC gene enhancer with significantly higher affinity than to the kappa immunoglobulin gene enhancer, or to the B-domain of the alpha 1-antitrypsin gene promoter. Analysis of mRNA expression shows that AT-BP1 and AT-BP2 are expressed in all the tissues examined. While the physiological roles of AT-BP1 and AT-BP2 remain to be elucidated, their predicted amino acid sequence and their DNA-binding characteristics suggest a role as transcriptional regulators.
From peripheral to full participation in a blended trade bargaining simulation

This article considers the extent and nature of student participation in a trade bargaining simulation from a community of practice perspective. This third-year economics module included a blend of online communication (through email, online chats and online discussions) and face-to-face meetings, both in smaller bargaining groups and in whole class plenary meetings. Our method of analysis includes the use of Exchange Structure Analysis of text chats and face-to-face learning conversations, triangulated by observation, survey and interview data. The focus on community of practice enables us to offer a nuanced interpretation of differences in crude participation data derived from the online chats. Superficially, the data may suggest marginalisation of participants, but Wenger's (1988) notion of peripheral participation with a trajectory towards full participation reframes the disparities in terms of an active community of practice. Some members are fully engaged with the practices of trade bargaining from the early stages of the simulation, while others move towards full participation over the duration of the simulation. Our results suggest that the laboratory-based online text chats did provide opportunities for student participation in the simulation, and that male and female students exhibited different patterns of participation in the chats.
Nucleotide sequence of the lsp-dapB interval in Escherichia coli

The Escherichia coli chromosomal region extending from the end of the Isp gene to the beginning of the dapB gene was sequenced. The Isp gene is followed by two inverted repeats (shown as arrows) which belong to the REP/PU family (1) and by two open reading fames, orfl49 and orf316, which are part of the same operon as Isp (2). A putative transcription termination signal is immediately followed by a third open reading fame, orf304, encoding a potentially membrane-bound protein. These three open reading frames are preceded by good ribosome binding sites (underlined twice) and could encode proteins of 17K, 36K and 32k that have been previously described (3). Transcription of the dapB gene (single arrow) starts 136 bp downstream of orf304 (4). REFERENCES 1Gilson.E. , ClemenU.M. , Brutlag.D. and Hofnung.M. (1984) EMBOJ. 3, 1417-1421. 2. Miller.K. W. , BouvierJ. , Stragier.P. and Wu.H. C. (1987) J. Biol. Chem. 2 6 2 . 7391-7397. \ Mackk.G. A^ (1980) y. mot Chem. 255, 8928-8935. 4. BouvierJ. , Richaud.C, Richaud.F. , Patte,J.C. and Stragier.P. (1984) J. Biol Chenu 259 14829-14834
Two dimensional single-strand conformation polymorphism analysis: a useful tool for the detection of mutations in long DNA fragments

A new two-dimensional gel system for the analysis of single strand conformational polymorphisms has been developed to identify point mutations, deletions and insertions in long DNA fragments (e.g. 2.7 kb) generated by the polymerase chain reaction. In this procedure, such DNA fragments are first restricted with frequent-cutter enzymes. The resulting small fragments are then separated in the first dimension according to their size by electrophoresis under denaturing conditions; these single stranded DNA fragments are subsequently fractionated in the second dimension by electrophoresis on a non denaturing slab gel based on their fold-back conformation which is completely sequence-dependent. The method was tested on three previously characterized pH 4.5 resistant mutants of HRV14 and was then used to determine changes in three further mutants.
A strategy for efficient in vitro translation of cDNAs using the rabbit beta-globin leader sequence

Analysis of in vitro synthesized proteins is frequently hampered by inefficient translation especially of large proteins. It had been shown that replacement of the GC-rich leader of human SRF by an in frame fusion to the human /3-globin leader sequence including the AUG initiation codon strongly stimulated translation in a reticulocyte lysate (1). We expanded on this observation and show that the /3-globin leader alone can enhance translation efficiencies both in rabbit reticulocyte lysates and in wheat germ extracts. The region homologous to the 5' end of rabbit /3-globin RNA but lacking the AUG initiation codon was inserted into the pBluescript KS vector (Stratatene) to generate plasmid pBAT (Figure 1A). The cRNAs tested lack most of their natural leader but retain the authentic initiation codon. Upon translation in a reticulocyte lysate the correct translation product of a cRNA encoding human TF-IID (A.A. & T.W., unpublished) is only detectable in the presence of the /3-globin leader (Figure IB, lanes 3 and 4) and translation of mouse Oct2.2 (2) is stimulated 25 fold (Figure IB, lanes 5 and 6). For a variety of applications in vitro translation in wheat germ extracts is preferred. Again translation of TF-IID is strongly enhanced by the leader insertion (Figure 1C, lanes 3 and 4) but even the level of Oct2.2 translation can be increased (Figure 1C, lanes 7 and 8). Full length human retinoblastoma Rbl05 (3) translation product is only detectable when the natural leader is replaced by the j3-globin leader (Figure 1C, lanes 5 and 6). The identical result is obtained upon translation in reticulocyte lysates (data not shown). Our results demonstrate that the /3-globin leader sequence alone increases in vitro translation efficiencies with various cDNAs/RNAs in both reticulocyte lysates and wheat germ extracts. This strategy is thus extremely useful for a variety of applications, e.g. when high levels of full length protein synthesis are required or when functional analyses of cDNAs lacking a leader sequence are performed.
Differentiation and function of mouse monocyte‐derived dendritic cells in steady state and inflammation

Summary: Although monocytes were originally described as precursors to all the different subpopulations of macrophages found in the steady state and formed under inflammatory and infectious conditions, recent data have demonstrated conclusively that monocytes can also differentiate into dendritic cells (DCs). Monocytes are the precursors to different subsets of DCs, such as Langerhans cells and DCs found in the lamina propria of the gastrointestinal, respiratory, and urogenital tracts. In addition, monocyte‐derived DCs (moDCs), newly formed during inflammatory reactions, appear to fulfill an essential role in defense mechanisms against pathogens by participating in the induction of both adaptive and innate immune responses. In this regard, moDCs have the capacity to activate antigen‐specific CD4+ T‐cell responses and to cross‐prime CD8+ T cells, during viral, bacterial, and parasitic infections. In addition, monocytes have been recently described as the precursors to a subset of DCs specialized in innate immunity against pathogens, named TipDCs [for TNF‐α (tumor necrosis factor‐α)‐iNOS (inducible nitric oxide synthase)‐producing DCs] that display a remarkable microbicidal activity and also provide iNOS‐dependent help for antibody production by B cells. Importantly, in contrast to DCs developing in the steady state, moDCs formed during inflammatory and infectious processes are subjected to diverse soluble mediators that determine the multiple functional specificities displayed by moDCs, as a result of the remarkable developmental plasticity of monocytes. In this review, we discuss recent findings dealing with the differentiation and functional relevance of moDCs that have widened the frontiers of DC immunobiology in relation to innate and adaptive immunity and the etiology of chronic inflammatory diseases.
Alcohol-dependent patients attempting and not attempting suicide: a comparison

Background: Alcohol dependence is a psychiatric disorder associated with an increased risk of suicidal behaviour. This is also associated with an increased number of suicide risk factors. Objective: The current study examined the sociodemographic and clinical characteristics of a number of alcohol-dependent patients who attempted suicide. Methods: We studied a consecutive series of 377 alcohol-dependent patients in our in-patient clinics. Their alcohol-use histories were assessed through semistructured interviews. The Suicidal Behaviors Questionnaire, the Childhood Trauma Questionnaire, the Michigan Alcoholism Screening Test and the Hamilton Depression Rating Scale were administered to all patients. Serum total cholesterol levels, mean corpuscular volume, the liver enzymes gamma glutamyl transferase, aspartate aminotransferase and alanine aminotransferase were routinely measured. In the statistical analyses, Student's t-test and chi-squared tests were applied. Results: Of the 377 alcohol-dependent patients, 89 (23.6%) had histories of attempted suicide. Thirty-four (42.5%) of the 80 female alcohol-dependent patients and 55 (18.5%) of the 297 male alcohol-dependent patients had attempted suicide; this gender difference was statistically significant (χ2 = 27.7, P < 0.001). A greater proportion of the suicide attempters than of the non-attempters met the Diagnostic Statistical Manual IV criteria for another psychiatric disorder (60.6%, n = 54, vs. 40.6%, n = 117; χ2 = 14.8; df = 6; P < 0.05). The difference of total cholesterol levels between female (mean = 144.0, SD = 58.3; mean = 158.0, SD = 83.9; t = 4.5; P < 0.05) and male (mean = 133.7, SD = 50.5; mean = 163.6, SD = 69.7; t = 11.7; P < 0.01) attempters and non-attempters was statistically significant. Conclusion: These results suggest that suicide attempts in alcohol-dependent patients are associated with more profound biopsychosocial pathology and decreased serum cholesterol levels.
Prevalence of Axial Spondyloarthritis in United States Rheumatology Practices: Assessment of SpondyloArthritis International Society Criteria Versus Rheumatology Expert Clinical Diagnosis

New classification criteria for axial spondyloarthritis (SpA) have been validated by the Assessment of SpondyloArthritis international Society (ASAS) working group. We applied these criteria to estimate prevalence of SpA in randomly selected, retrospectively reviewed medical records from representative US rheumatology practices.
Rzeczpospolita blogów [Republic of Blog]: Examining Polish Bloggers Through Content Analysis

While researchers are increasingly interested in understanding the social context of weblogs, or blogs, most existing studies rely on analysis of English-language content. This study is a quantitative content analysis of Polish blogs (N=358) aimed at understanding the content elements and user-initiated features, such as hyperlinks, of blogs under the theoretical framework of uses and gratifications. Results indicate that self-expression is the primary motivation for blog posts. Furthermore, Polish bloggers appear to be driven more by self-expression than by social interaction motivations. Additional findings explored the relationship among motivations, gender, and topics discussed in blogs.
Performances of the Assessment of SpondyloArthritis International Society Axial Spondyloarthritis Criteria for Diagnostic and Classification Purposes in Patients Visiting a Rheumatologist Because of Chronic Back Pain: Results From a Multicenter, Cross‐Sectional Study

To evaluate the performances (sensitivity, specificity, and positive and negative predictive values) at diagnosis and study visit of the Assessment of SpondyloArthritis international Society (ASAS) criteria in axial spondyloarthritis in patients with chronic back pain (CBP). A secondary objective was to identify the most contributory item to diagnosis/classify spondyloarthritis.
Alexithymia, Depression, Inflammation, and Pain in Patients With Rheumatoid Arthritis

We previously reported that depression and inflammation have independent effects on pain severity in patients with rheumatoid arthritis (RA). Alexithymia is a personality trait characterized by deficits in cognitive processing and regulation of emotions. A broad association between alexithymia and various health problems has been suggested, including depression, inflammation, and pain. The objective of this study was to examine the independent influence of alexithymia on pain perception and its relationship to depression and inflammation.
Change of Psychological Distress and Physical Disability in Patients With Rheumatoid Arthritis Over the Last Two Decades

During the past decades, a more cautious approach with respect to prescribing medication and physical exercise progressed toward evidence‐based guidelines regarding the management of rheumatoid arthritis (RA). Currently, physical activity and other means to improve well‐being and functioning are encouraged, and the disease is targeted earlier with more intensive and aggressive pharmacologic treatment. The current study examined whether psychological distress and physical disability in patients with RA reduced over the last 2 decades and whether this is explained by a reduction of disease activity.
A novel nuclear receptor superfamily member in Xenopus that associates with RXR, and shares extensive sequence similarity to the mammalian vitamin D3 receptor

We report the isolation of xONR1, a novel member of the nuclear receptor superfamily from Xenopus laevis. xONR1 shares a high degree of amino acid sequence identity with the mammalian receptor for 1 alpha, 25-dihydroxy vitamin D3, particularly within the DNA-binding domain, although it does not bind this ligand. xONR1 DNA binding is stimulated by association with retinoid X receptor gamma (RXR gamma).
Feasibility of Gait Event Detection Using Intramuscular Electromyography in the Child with Cerebral Palsy

The objective of this study was to develop and test the feasibility of a model that employs electromyographic (EMG) signals to predict the occurrence of gait events in the child with cerebral palsy (CP). This model could be the basis of a future functional electrical stimulation (FES) control system to assist gait. Two children were implanted with bifilar intramuscular electrodes into the quadriceps muscle bilaterally. Muscle activity and gait parameters were recorded, and a fuzzy inference system was used to correlate EMG to five distinct gait events. For nine of the 10 gait events evaluated, the model predicted gait events to within 82 ms on average, as referenced to the VICON motion analysis system. For eight of the 10 events, prediction errors were 0.3% or less. Results indicate that EMG from the proximal musculature could be used to predict the occurrence of gait events in these two children with CP.
Double bands in DNA gel electrophoresis caused by bis-intercalating dyes

Many bis-intercalating dyes used for fluorescence detection of DNA in electrophoresis have been reported to give band-splitting and band-broadening, which results in poor resolution and a decreased detection sensitivity. We have studied the dimeric dye YOYO-1, and to some extent also TOTO-1 and EthD-1, and found that in complex with DNA these dyes give rise to two components with different electrophoretic mobilities. Electrophoresis experiments and spectroscopic measurements on the two components show that they differ in that the DNA molecules have different amounts of dye bound. Our results exclude that the extra bands are caused by intermolecular cross-linking. Incubation of the samples for increasing times before electrophoresis makes the bands move closer and closer to each other as the dye molecules become more homogeneously distributed among the DNA molecules. Finally, the two bands merge into one at an intermediate position. This equilibration process is extremely slow at room temperature (days), and is therefore not a practical method to eliminate band-splitting in routine analysis. However, we find that if the temperature is raised to 50 degrees C, the dye-DNA complexes equilibrate completely in only 2 h.
The HSSP database of protein structure-sequence alignments

HSSP is a derived database merging structural (3-D) and sequence (1-D) information. For each protein of known 3-D structure from the Protein Data Bank (PDB), the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family. The list of homologues is the result of a database search in SwissProt using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). The database is updated frequently. The listed homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of aligned sequence families, but also a database of implied secondary and tertiary structures covering 29% of all SwissProt-stored sequences.
Identification of an RNA-dependent ATPase activity in mammalian U5 snRNPs.

Nuclear pre-mRNA splicing requires ATP at several steps from spliceosome assembly to product release. Here, we demonstrate that an integral component of the 20S U5 snRNP is an RNA-dependent ATPase. The ATPase activity of 20S U5 and 25S [U4/U6.U5] snRNPs purified by glycerol gradient centrifugation is strongly stimulated by homopolymeric RNA but not ssDNA. Purified 12S Ul and U2 snRNPs do not exhibit ATPase activity. Moreover, the U5-associated NTPase specifically hydrolyzes ATP and dATP. The additional purification of 20S U5 snRNPs by Mono Q chromatography does not affect the efficiency of ATP hydrolysis. Both U5 and tri-snRNPs bind ATP stoichiometrically in an RNA-independent manner. A candidate ATPase was identified by UV-irradiation of purified snRNPs with radiolabeled ATP. In the presence of homopolymeric RNA, the 200 kDa U5-specific protein is the major crosslinked protein, even in Mono Q-purified U5 snRNPs. The correlation between RNA-dependent ATPase activity in the U5 snRNP and the RNA-dependent onset of this crosslink strongly suggests that the 200 kDa protein is an RNA-dependent ATPase. Furthermore, both the formation of the crosslink and ATPase activity appear with a similar substrate specificity for ATP.
Post chemoradiation re-staging of rectal cancer using MRI

4 PUBLICATION . 5 Original Papers: . 5 Review articles:. 5 Invited presentations: . 6 TABLE OF CONTENTS . 7 ACKNOWLEDGEMENTS . 13 1 BACKGROUND AND LITERATURE REVIEW . 18 1.
Explaining Physical Activity Maintenance After a Theory‐Based Intervention Among Patients With Rheumatoid Arthritis: Process Evaluation of a Randomized Controlled Trial

Regular physical activity (PA) benefits patients with rheumatoid arthritis (RA), particularly when maintained over time. Research in this area has largely focused on factors associated with initiating PA, while factors contributing to PA maintenance, particularly after lifestyle interventions, have received less attention. This study examined whether higher levels of autonomous motivation, self‐efficacy for PA, and greater use of self‐regulation skills mediated PA initiation and maintenance 6 months after a theory‐based motivational interviewing and self‐regulation coaching intervention.