Miracle-dz/UniFAR-FTUs huggingface dataset:
The Polyadenylation of RNA in Plants

Poly(A) tracts are a nearly ubiquitous feature of mRNAs in eukaryotes. The poly(A) tail is an important determinant of the function of a eukaryotic mRNA, because it is intimately involved in processes that determine the translatability (Sachs and Wahle, 1993) and lifetime (Jacobson and Peltz, 1996) of mRNAs. From this perspective, the addition of the poly(A) tail to an mRNA is an important, even necessary, step in the expression of eukaryotic genes. However, although the functions of a poly(A) tail are largely manifest in the cytoplasm, the process of polyadenylation itself is an important component of mRNA metabolism. A growing body of evidence indicates that mRNA polyadenylation may be physically linked to the processes of intron remova1 (e.g. Niwa et al., 1990) and transcription termination (McCracken et al., 1997), and other studies imply an interplay between polyadenylation and transport of mRNA (Huang and Carmichael, 1996). Thus, it may be more appropriate to consider mRNA 3'-end formation as part of a larger series of events that begins with the initiation of transcription by RNA polymerase I1 and ends with the delivery of a mature, polyadenylated mRNA to the cytoplasm. In this context, the individual components that mediate mRNA polyadenylation may be expected to have an impact on other nuclear processes (splicing, trankription termination, and transport) as well. Several recent reviews may be consulted for a detailed picture of the process by which mRNAs are polyadenylated in animals and yeast (Wahle, 1995; Proudfoot, 1996; Wahle and Keller, 1996). Briefly, poly(A) tails are nontemplated and are thus added to nuclear mRNA precursors in a posttranscriptional process. Moreover, polyadenylation in the nucleus is usually viewed as an RNA processing event; in other words, the 3' end of the mRNA to which poly(A) i s added is generated, not by termination of transcription by RNA polymerase 11, but rather by processing of a larger RNA that is generated by transcription beyond the poly(A) site. In mammals and yeast a finite series of factors (5-6) cooperate to recognize, process, and polyadenylate precursor mRNAs in the nucleus. Several of the
Nodal Marginal Zone Lymphoma: A Heterogeneous Tumor: A Comprehensive Analysis of a Series of 27 Cases

We have reviewed the clinical, morphologic, immunophenotypical, and molecular features of a series of 27 cases of nodal marginal zone lymphoma with the aim of defining this entity more precisely. The series was characterized by a relatively favorable clinical course, with a low clinical stage at diagnosis (59% patients with clinical stage I–II) and a 5-year overall survival probability of 79%. However, the disease persisted in a relatively large fraction of the patients, thus yielding a 5-year failure-free survival probability of 22%. Molecular and immunohistochemical analyses of the series revealed heterogeneity in the frequency of IgVH somatic mutation and in the expression of IgD, CD43, MUM1, and CD38. Apart from the absence of nuclear Bcl10, no clear distinction could be made from the expression profiling of other B-cell lymphomas claimed to be derived from marginal zone B cells. Additionally, the immunophenotype of the tumoral cells in all cases but one differed from that described in monocytoid B cells. It was characterized by a Bcl2−, p21+, cyclin E+ profile. The analysis of apoptosis-regulator proteins disclosed abnormalities in the expression of survivin and active caspase 3, which could partially explain the abnormal regulation of apoptosis observed in these tumors. Molecular and immunohistochemical data obtained in this study strongly imply that there is significant heterogeneity among the cases included in the category termed nodal marginal zone lymphoma.
Lifetime Cognitive Performance is Associated With Midlife Physical Performance in a Prospective National Birth Cohort Study

Objectives: To examine whether measures of cognitive performance across life are related to physical performance at age 53 years, allowing for potential confounders. Methods: In a large representative British birth cohort of men and women (N = 2135) the associations between cognitive performance across life (i.e., standardized cognition scores at ages 15, 43, and 53 years and changes in verbal memory and search speed scores between 43 and 53 years) and measures of physical performance at age 53 years (i.e., standing balance, chair rising, and grip strength) were examined. Adjustments were made for body size, physical activity levels, health status, and socioeconomic conditions at age 53 years. Results: Higher cognitive scores on all childhood and adult tests, and a slower decline in verbal memory and search speed, were associated with better standing balance. Higher verbal fluency scores and a slower decline in verbal memory and search speed were more strongly related than scores on tests of general cognitive ability to chair rising. The relationships between cognitive performance and grip strength were inconsistent and weak. Conclusions: The differential patterns of association found are consistent with the degree to which each is dependent on central nervous system function. Our findings suggest that initial developmental differences as well as shared ageing processes may underlie associations found between cognitive and physical performance. CNS = central nervous system; MRC = Medical Research Council; NSHD = National Survey of Health and Development; NART = National Adult Reading Test.
Role of the transcriptional activator, VirF, and temperature in the expression of the pYV plasmid genes of Yersinia enterocolitica

Upon incubation at 37°C in the absence of Ca2+ ions, pathogenic yersiniae release high amounts of pYV plasmid‐encoded proteins called Yops, involved in pathogenesis. Yersinia enterocolitica also express two outer membrane proteins, an adhesin called YadA and a lipoprotein called YIpA. The production of the Yops is co‐ordinately regulated by a 20kb region of the plasmid referred to as the ‘Ca2+ dependence region’ and containing at least four loci called virA, virB, virC, and virF. The 8.5kb virC region, involved in the specific transport of the Yops, is a single operon containing 13 open reading frames called yscA to yscM. Gene virF encodes a key transcriptional activator of the yop, yadA and ylpA genes. It is only transcribed at 37°C and its expression is modulated by a chromosome‐encoded histone‐like protein called YmoA. We show here that virF also controls the virC operon. By contrast, VirF is not essential for the induction of virA and virB. The VirF protein binds specifically to yop promoters. In particular, it protects the region spanning nucleotides ‐64 to ‐34 of yopH. In order to analyse the role of temperature in the induction of the yop regulon, we constructed Y. enterocolitica strains expressing virF from the tac promoter. In spite of the fact that virF was transcribed at 25°C, neither the Yops nor YadA were expressed at that temperature. This poor response to VirF at 25°C was at least partially due to a weak and slow transcription of the genes controlled by virF. Surprisingly, when cloned on pACYC184, gene yadA was expressed even in absence of VirF, but remained thermodependent. Hence temperature and virF are both required for the induction of the yop regulon. Among other possible roles, temperature could modify the structure of either the activator itself or the yop promoter. The fact that VirF binds in vitro to yop promoters at 25°C rules out the first hypothesis. In order to test the second hypothesis, we studied, in vivo, the activity of the yopH promoter in ymoA mutants. The yopH promoter became active in the absence of VirF, indicating that yop promoter activity depends upon chromatin structure. We conclude from these two observations that, in vivo, temperature is required to modify the DNA structure of the yop promoters in order to allow the action of the transcriptional activator.
Fast Palmprint Identification Using Orientation Pattern Hashing

A palmprint identification system recognizes a query palmprint image by searching for its nearest neighbor from among all the templates in a database. When applied on a large-scale identification system, it is often necessary to speed up the nearest-neighbor searching process. In this paper, by viewing the palmprint feature as a high-dimension binary vector, we present a palmprint identification method using orientation pattern hashing. We propose three properties required by the hash function and demonstrate that the orientation pattern has all of these properties. Under some simple assumptions we give the parameter selection method for fast and accurate palmprint identification. Experimental results on the Hong Kong large scale database (9667 palms) show that the proposed method is over 16 times faster than brute force searching, while its accuracy is slightly higher. Evaluations on the CASIA palmprint database (600 palms) plus a synthetic database (100,000 palms) show a speedup of 6.8 over brute force searching and a negligible loss of accuracy.
Identification of Novel Hepatitis C Virus NS3-4A Protease Inhibitors byVirtual Screening Approach

Hepatitis C Virus (HCV) is a leading cause of cirrhosis and liver cancer worldwide. The replication and viral polyprotein maturation of HCV crucially depends on the cleavage of the polyprotein precursor into 10 viral proteins. The NS3-4A serine protease cleaves the nonstructural region of the polyprotein at four out of five junctions, thus is a promising target for the development of antiviral inhibitors. There are many inhibitors of HCV NS3/4A protease in the clinical trial and improvement indicating significant reduction in the viral infection rate. However, most PIs develop resistance associated variants while treatment and are restricted to one or two HCV genotypes. The second generation PI, MK-5172, is the only exception, which potently inhibits most variants associated with resistance to first generation PIs and is pan-genotypic. In this study, we investigated the potent lead compound(s) based on similarity search using the most potent proved protease inhibitor, MK-5172. We have performed virtual screening techniques using PubChem database available in NCBI to identify lead like molecules. The database has yielded 32 hits for 95% similarity search and the pharmacokinetic analysis (ADME) was performed for screened compounds. This structure based drug design identified three lead compounds that can work better against NS3/4A protease.
Diethyl 4-(4,5-dihydrofuran-2-yl)-3,5-dimethyl-1-phenyl-1,4-dihydropyrazine-2,6-dicarboxylate

In the title compound, C22H26N2O5, the central 1,4-dihydropyrazine ring adopts a boat conformation, while the benzene ring and the two disordered components of the furan ring are inclined at angles of 77.9 (5) and 61.9 (7)°. Three of the C atoms of the furan ring are disordered over two positions with occupancies of 0.655 (18) and 0.345 (18). In the crystal structure, weak intermolecular C—H⋯O hydrogen bonds link the molecules into chains propagating in [010].
Interrelationship between Attachment Styles and Facebook Addiction

Social networking sites have started to become one of the most frequently used online communication types in the world. It is reported that one of the commonly used social networking sites is Facebook. Since Facebook use is new yet, it can be stated that researches on the Facebook addiction are at the beginning level. For this reason, determining factors leading to the Facebook addiction has gained importance. In this context, in this study, relationships between attachment styles and the Facebook addiction were examined. The participants of the study were 322 university students [145 (45%) male, 177 (55%) female, M age =20.61 years, SD=1.82]. In the study, the Personal Information Form, the Relationship Scales Questionnaire and the Facebook Addiction Scale were administered. The relationships between attachment styles and the Facebook addiction were calculated via using the Pearson correlation analysis. The Pearson correlation analysis results indicated that the Facebook addiction was negatively related with the secure and dismissing attachment style and positively related with the preoccupied attachment style. No relationship was found between the fearful attachment style and the Facebook addiction. If the attachment styles predicted the Facebook addiction was examined via using the stepwise regression analysis. The research findings indicated that the secure and dismissing attachment style negatively predicted and the preoccupied attachment style positively predicted the Facebook addiction. However, it was determined that the fearful attachment style did not predict Facebook addiction. The research findings were discussed under the light of related literature.
A High Embedding Efficiency Steganography Scheme for Wet Paper Codes

In this paper, a good data hiding scheme has been proposed. This scheme embeds messages into a still image based on (7,4) Hamming Codes oriented wet paper codes . It embeds a segment of three secret bits into a group of seven cover pixels at a time. The experimental results show that the proposed scheme achieves high embedding efficiency and acceptable capacity.
Intermédiaires graphiques et Conception Assistée par Ordinateur - Étude des processus d'enseignement-apprentissage à l'œuvre en technologie au collège

Au niveau du college, la technologie est une discipline generale qui s'adresse a tous les eleves. Ainsi, plus que jamais, au 21eme siecle, la connaissance du monde des objets fait partie de la culture du citoyen. Pour autant la technologie au college est une discipline encore en construction, les objets de savoir sont partiellement definis et la recherche en didactique de la technologie a encore de nombreux terrains a explorer. Cette these s'interesse aux enseignements technologiques au college et particulierement a la conception d'objet. Dans un premier temps, notre but est de repondre, de maniere empirique, a la question suivante : quelles sont les difficultes rencontrees par les eleves en situation de conception ? A titre exploratoire, nous analysons l'activite d'eleves en train de resoudre collectivement un probleme de conception. Nous envisageons dans un deuxieme temps d'analyser plus particulierement les difficultes liees a la production de representations des solutions possibles au travers du role que jouent les outils informatiques de conception assistee par ordinateur. Il s'agit donc de reflechir a l'integration de ces outils dans l'enseignement de la technologie au college. L'utilisation d'intermediaires graphiques modifierait-elle et dans quel sens les performances des eleves de 5eme dans la phase de recherche de solutions ? Le recours aux theories de l'action pour observer l'activite conjointe de l'enseignant et de l'eleve se revele pertinent et au travers des resultats qu'elle propose, cette these contribue a la communaute des didacticiens des sciences et de la technologie.
Proposal and Analysis of a Silicon MMI Coupler-Based Electronically Controllable Photonic Switch

In this paper, we propose and analyze an electronically controllable 2 × 2 multimode interference (MMI) coupler-based photonic switch (PS) in form of a lateral p-i-n diode, which is realized on the silicon-on-insulator platform. The switching has been achieved by applying external bias voltage, which induces free carrier dispersion effect-based refractive index change. Theoretical analysis of the proposed PS based on perturbation theory is presented, and the results are verified by numerical simulations and full vectorial analysis. Analysis and simulation show that the proposed multimode interference photonic switch (MMIPS) can offer maximum 22.7 dB extinction ratio (ER) and '1.5 dB of maximum excess loss (EL). The maximum switching voltage is found to be '2.25 V. Optimization in terms of device length, doping concentrations, width of the intrinsic region, and position of the access waveguides for achieving desired values of ER and EL has been presented. Analysis also indicates strong polarization dependence of the proposed switch. Steady-state analysis of the proposed MMIPS confirms its operation over entire C-band (1530-1565 nm) with maximum 0.25 and 0.35 dB optical power variation in bar and cross port, respectively. It is found that the MMIPS can easily withstand a temperature variation of 20 K. Moreover, we show that change in switching performance due to temperature variation can also be compensated by adjusting external bias voltage. This paper also investigates the fabrication tolerances of MMIPS in terms of imperfections in device length, width, and doping concentrations. Study shows that ±100 nm variation in device length and ±50 nm variation in device width introduce maximum optical power variations of 0.3 and 0.1 dB in cross port (and 0.2 and 0.07 dB in bar port), respectively. The doping concentration variation, as permissible in state-of-the-art fabrication process, is found to introduce negligible penalty on the switching performance. Transient analysis and equivalent circuit model of the proposed switch confirms more than 1 GHz of switching speed. Small-signal equivalent circuit of the proposed MMIPS predicts power dissipation in the orders of tens of milliwatts.
Keyword Extraction From Chinese Text Based On Multidimensional Weighted Features

This paper proposed to solve the problems of incomplete coverage and low accuracy in keyword extraction of Chinese text based on intrinsic feature of the Chinese language and an extraction method of multidimensional information weighted eigenvalues. This method combined theoretical analysis and experimental calculation to study the parts of speech, word position, word length, semantic similarity and word co-occurrence frequency in Chinese texts. By combining multidimensional data related to word frequency, word feature values, word similarity and word co-occurrence probability, we calculated that the weighted eigenvalues obtained by comparing precision rate, recall rate and F measure and concluded that the proposed method can give a better measure of the word accuracy than using word frequency or the basic eigenvalue methods alone. The conclusions obtained in this study provide reference values for keyword extraction and text mining. Subject Categories and Descriptors I.2. 7 [Artificial intelligence]: Natural Language Processing Text analysis; H.2. 8 [Database Applications]: Data mining; General Terms: Chinese text mining, sentiment analysis
The CTX-M-15-producing Escherichia coli diffusing clone belongs to a highly virulent B2 phylogenetic subgroup.

OBJECTIVES A clone of CTX-M-15-producing Escherichia coli has recently been reported to be spreading through Europe and Africa. The aim of this work was to thoroughly characterize this clone. MATERIALS AND METHODS Representative isolates of this clone were subjected to multilocus sequence typing, O typing, virulence gene detection, adhesion assay on human cells, biofilm production assay and mouse lethality assay. RESULTS The clone: (i) belongs to a unique B2 phylogenetic subgroup encompassing the pyelonephritogenic diffusely adhering EC7372 strain; (ii) exhibits a specific O25b molecular subtype; (iii) is identical to the E. coli clone O25:H4-ST131 producing CTX-M-15; (iv) produces biofilm; and (v) is highly virulent in mice despite lacking classical extraintestinal pathogenicity islands (except for high pathogenicity island) and the afa/dra gene. CONCLUSIONS The CTX-M-15-producing E. coli diffusing clone is associated with a high level of antibiotic resistance and with high virulence, showing that, under certain selective pressures, the previously observed trade-off between resistance and virulence may not apply.
A long-distance sea wave height measurement based on 3D image measurement technique

This paper constructed a sea wave height measurement system based on 3-D image measurement technique. As existing calibration [1] and matching algorithms cannot be applied to this system with distance extension (more than 20 km). Setting cameras maximally horizontal and fixing the focal length of the cameras can simplify the process of calibration, with information of a target object from a sequence of continuous images, calibration for a long distance can be realized. Meanwhile, we search corresponding points based on corresponding sea waves. This method extracts sea waves from the original images firstly and then matches the corresponding points according to the corresponding sea waves. Experiments of real-time sea wave photography using long focal length cameras were conducted to testify the proposed methods. Combine the position of massive corresponding points and the calibration parameters, calculate the sea level at daytime, graphs of tide trend can be drawn. Comparison between the calculating trend and data from Japan Meteorological Agency implies that the proposed methods has feasibility in long-distance sea wave height measuring.
Developing a logistics strategy through participative business modelling

Introduces the participative business modelling method (PBM), a management consulting method based on a synergetic mix of (system dynamics) modelling, group knowledge elicitation techniques and a process consultation attitude. PBM is a method well‐suited to support managers in their strategic decision‐making processes, in particular in the field of operations management, because it provides support in dealing with both the technical and organizational complexities of strategic decision making. Presents a case study where PBM was used to assist in the development of a European logistics strategy for an American pharmaceutical firm setting up operations in Europe. Discusses findings from the analysis of the evaluation interviews with project participants, which contain valuable lessons, not just for the PBM method itself, but also for the theory of strategic decision making that lies at the basis of the PBM method.
Biotin-streptavidin cross-bridging: a novel and feasible approach for targeting transplanted cells to damaged tissue

Background: Accumulating evidence indicates the positive impact of endothelium-derived cell therapy in vascular repair. However, low cell transplantation efficiency inevitably and greatly reduces the treatment efficacy of cell transplants. Purpose: To modify the surfaces of cells with polypeptides or small-molecule proteins that specifically recognize and bind to damaged tissue. Methods: We used a biotin-streptavidin binding approach to attach annexin V, which recognizes apoptotic cells, onto bEnd.3 cells that express vascular endothelial growth factor receptor 2 (VEGFR2) and verified that the modified cells could efficiently bind to dead cells in vitro. Results: We analyzed biotinylated VEGFR2-bEnd.3 cells, streptavidin-biotinylated VEGFR2-bEnd.3 cells, and biotinylated annexin V-streptavidin-biotinylated VEGFR2-bEnd.3 cells. Our results from flow cytometry analysis and immunofluorescent examination demonstrated that we successfully labeled the cells in a three-step process. Furthermore, we determined that the positive binding rate correlated with reagent concentration. Immunofluorescent examination illustrated that adding the biotinylated annexin V-streptavidin-biotinylated VEGFR2-bEnd.3 cells to dead cells led to the clustering and aggregation of the modified cells and the dead cells. Conclusions: Annexin V can be attached to bEnd.3 cells using a biotin-streptavidin binding approach, and the modified cells can specifically recognize and bind to dead cells.