Miracle-dz/UniFAR-FTUs huggingface dataset:
Phytochrome coordinates with a hnRNP to regulate alternative splicing via an 7 exonic splicing silencer 8

Plants perceive environmental light conditions and optimize their growth and 38 development accordingly by regulating gene activity at multiple levels. Photoreceptors 39 are important for light sensing and downstream gene regulation. Phytochromes, red/far- 40 red light receptors, are believed to regulate light-responsive alternative splicing, but little 41 is known about the underlying mechanism. Alternative splicing is primarily regulated by 42 trans -acting factors, such as splicing regulators, and by cis -acting elements in precursor 43 mRNA. In the moss Physcomitrella patens , we show that phytochrome 4 (PpPHY4) 44 directly interacts with a splicing regulator, heterogeneous nuclear ribonucleoprotein F1 45 (PphnRNP-F1) in the nucleus to regulate light-responsive alternative splicing. RNA 46 sequencing analysis revealed that PpPHY4 and PphnRNP-F1 co-regulate 70% of intron 47 retention events in response to red light. A repetitive GAA motif was identified to be an 48 exonic splicing silencer that controls red light-responsive intron retention. Biochemical 49 studies indicated that PphnRNP-F1 is recruited by the GAA motif to form RNA–protein 50 complexes. Finally, red light elevates PphnRNP-F1 protein levels via PpPHY4, 51 increasing levels of intron retention. We propose that PpPHY4 and PphnRNP-F1 regulate 52 alternative splicing through an exonic splicing silencer to control splicing machinery 53 activity in response to light. These results indicate that a large proportion of RL- responsive IR events PpPHY4 or PphnRNP-F1, that both PpPHY4 and PphnRNP-F1 RL-mediated AS. A comparison of the RL-responsive IR PpPHY4 PphnRNP-F1 RL- RL-responsive IR. RL-responsive IR we further functional enrichment identify potential signaling processes downstream of red light response mediated by PpPHY4 and PphnRNP-F1. Table protein effect these gene transcripts figure out their functions in PpPHY4-mediated RL signaling pathway. These results support the hypothesis that the GAA motif is specifically involved in the recruitment of PphnRNP-F1 for the formation of a RNA-protein complex. We proposed that PphnRNP-F1 is recruited by the GAA motif directly to suppress pre-mRNA splicing. role pre-mRNA splicing, RL and These results indicate that the two proteins modulate AS cooperatively upon RL Our findings thus help a detailed mechanism underlying how regulate AS in conjunction with a potential regulator. provided
Natural allelic variants of bovine ABCG2 transporter: Increased activity of the S581 variant and development of tools for the discovery of new ABCG2 inhibitors

Breast Cancer Resistance Protein ( ABCG2/BCRP) is a member of the ABC transporter superfamily that actively extrudes xenotoxins from cells and is a major determinant of the bioavailability of many compounds. ABCG2 expression is strongly induced during lactation in the mammary gland and is related to the active secretion of drugs into the milk. The presence of drug residues and environmental pollutants in milk is an outstanding problem for human milk consumption and milk industrial processes, involving important risks to Public Health and the Dairy Industry. In cows, an SNP in this protein has been described (Y581S), associated with higher fat and protein percentages and lower milk yield. However, whether this aminoacid substitution affects ABCG2-mediated drug transport in cow, including milk secretion, needed further exploring. We cloned the two variants of bovine ABCG2 and evaluated the effect of this SNP on mitoxantrone accumulation assays performed in ovine primary fibroblasts transiently expressing either of the variants. Interestingly, statistically significant differences in activity between both variants were observed, with the S581 variant being related with an increased efflux activity. In addition, we demonstrated that genistein is a very good inhibitor of bovine ABCG2 and identified new inhibitors of the transporter, such as the macrocyclic lactones, ivermectin and selamectin. Moreover, the inhibitory effect of these compounds on human and murine ABCG2 homologs was confirmed using transduced MDCK-II cells. These findings may have important implications regarding the presence of drug residues in milk and drug interactions affecting the pharmacological behaviour of ABCG2 substrates.
‘On the Electrodynamics of Moving Bodies’ by Albert Einstein is Based on Trickeries Open Letter to Professors, Teachers, Researchers and Students of Physics

The article ‘On the Electrodynamics of Moving Bodies’ by Albert Einstein (1905) is based on trickeries. The Voigt transformation was simply a mathematical possibility which was changed by Lorentz by introducing the Lorentz factor but the Lorentz factor is not real; has been shown in the article Mohammad Shafiq Khan (2012). Thus nature and forces in nature were trivialized and made subservient to mathematics in the theories of relativity, Big Bang Theory, Space-time concept and in all physical sciences which are directly or indirectly based on the ‘On the Electrodynamics of Moving Bodies’. It is unfortunate for humanity that exposing these trickeries took more than one hundred years.
BIROn - Birkbeck Institutional Research Online analytics: density-based social clustering for mobile users.

: We demonstrate how social density-based clustering of WLAN traces can be utilised to detect granular social groups of mobile users within a university campus. Furthermore, the ability to detect such social groups, which can be linked to the learning activities taking place at target locations, provides an invaluable opportunity to understand the presence and movement of people within such an environment. For example, the proposed density-based clustering procedure, which we call Social-DBSCAN, has real potential to support human mo-bility studies such as the optimisation of space usage strategies. It can automatically detect the academic term period, the classes, and the attendance data. From a large Eduroam log of an academic site, we chose as a proof concept, selected locations with known capacity for the evaluation of our proposed method, which we successfully utilise to detect the regular learning activities at those locations, and to provide accurate estimates about the attendance levels over the academic term period.
Learner Analytics in Engineering Education: A Detailed Account of Practices Used in the Cleaning and Manipulation of Learning Management System Data from Online Undergraduate Engineering Courses

in the engineering and manufacturing engineering programs as well as programs in the Engineering Education Systems and Design PhD program. Her research interests include topics related to student persistence, STEM doctoral student experiences, faculty mentorship and development, modeling and analysis of complex manufacturing systems, and the development of new discrete event simulation methodologies. Bekki is the co-director of the interdisciplinary, National Science Foundation supported CareerWISE research program, which strives to: 1) understand the experiences of diverse women who are pursuing and leaving doctoral programs in science and engineering and 2) increase women’s persistence in science and engineering doctoral programs through the development and dissemination of an online resilience and interpersonal communication training program. Engineering Polytechnic in Mechanical Engineering She in Mechanical Engineering from Northeastern University. Dr. Brunhaver’s research examines the career decision-making and professional identity formation of engineering students, alumni, and practicing engineers. She also conducts studies of new engineering pedagogy that help to improve student engagement and understanding. Abstract This is a research paper that provides a concrete example for other engineering education researchers of how Learning Management System (LMS) interaction data from online undergraduate engineering courses can be prepared for analysis. We provide the rationale and details involved in choices related to data preparation, feature creation, and feature selection as part of a larger National Science Foundation-funded study dedicated to developing a theoretical model for online undergraduate engineering student persistence. LMS interaction data provides details about students’ navigations to and submissions of different course elements including quizzes, assignments, discussion forums, wiki pages, attachments, modules, the syllabus, the gradebook, and course announcements. The sample dataset presented here includes 32 courses from three ABET accredited fully online engineering degree programs, electrical engineering, engineering management, and software engineering, offered at a large, public, southwestern university. The analysis demonstrated in this paper will ultimately be combined with associative classification to discover relationships between student-LMS interactions and persistence decisions.
Development of a polyvalent RT-PCR detection assay covering the genetic diversity of Cherry capillovirus A

The variability of Cherry capillovirus A (CVA) was analysed using a short, 275-bp region of the viral RNA-dependent RNA polymerase gene ampliﬁed by a polyvalent RT-PCR assay. As for other members of the family Betaﬂexiviridae , CVA appears to show signiﬁcant diversity, with an average pairwise nucleotide divergence of 9 Æ 4% between isolates in the analysed region. Phylogenetic analyses provide evidence for the existence of at least ﬁve clusters of CVA isolates, one of which is associated with noncherry hosts of the virus, providing evidence that transmission of CVA isolates between cherry and noncherry hosts is probably rare. Comparison of existing detection techniques using a panel of CVA isolates representative of the various phylogenetic groups indicated that dot-blot hybridization assays show high polyvalence but may lack the sensitivity to detect CVA in some samples. On the other hand, available detection primers failed to amplify a wide range of CVA isolates. Partial genome sequencing of two divergent isolates allowed the identiﬁcation of conserved genomic regions and the design of new primer pairs with improved polyvalence. These new primer pairs were used to develop PCR assays allowing the reliable detection of CVA isolates belonging to all phylogenetic clusters. Forty ampliﬁcation of 95 (cid:2) for 54 (cid:2) a ﬁnal extension step 72 (cid:2) ampliﬁcation by nondenaturing agarose gel electrophoresis.Forthetwo-stepRT-PCR Lof TNAsamples
Finger knuckle biometrics for personal identification using statistical and feature based approaches

Texture pattern observed on finger knuckle joint is called as Finger Knuckle Print (FKP). FKP can be extracted from inner side or back side of finger surface. FKP is extremely unique and makes the knuckle surface an emerging biometric modality. The FKP may be useful in user identification and has attracted attention of very few researchers. Our proposed work is based on FKP of back side of finger surface. The objective of this work is to investigate and develop a systematic approach for identifying a person using his/her finger knuckle print. Three different methodologies are employed for FKP identification process. Statistical approach (Principal Component Analysis) and feature based approaches (Gabor based coding scheme and Radon like features) are used to accomplish this objective. Nearest Mean Classification, Angular distance matching and Dynamic Time Warping methods are used for finding similarity between enrolled FKP and test FKP images. Performance comparison of proposed three methodologies is done by computing different performance measures such as FAR, FRR, EER, Di and CRR. Proposed methods are producing EER 0.2 using statistical approach and 0.03 using feature based approach.
Numerical study of TRIP transformation in 35NCD16 steel-effects of plate orientation and some criteria

A BSTRACT . This study aims to analyze the effect of thermo mechanical coupling damage in the presence of a phase change (austenite/martensite) in 35NCD16 steel. The impact of increasing mechanical traction load, accompanied by a martensitic transformation on the scale of a single grain with boundary has been studied. The prediction transformation of induced plasticity (TRIP) was evaluated by taking into account the following parameters: twenty shear directions of the martensitic plates, two values of the shear deformation of the martensitic plates, energetic and thermodynamics criteria for getting in order the transformation of the martensitic plates, elastoplastic behavior of the two areas in the first case (martensitic plate and grain boundary) and elastic behavior for the grain boundary in the second case. The numerical calculation is carried out using the finite element method (FEM), implemented in the Zebulon calculation code. The developed approach is validated using the available experimental results reported in the literature. The numerical results showed that the estimation of TRIP given by the energetics criteria with the values of the shear deformation ( γ 0 = 0.16) are closer to the experiment results . K EYWORDS TRIP; Number of shear
Foundations of Transmathematics: Set Membership

This is a draft for discussion. Comment and collaboration are welcome. In previous work we used a variety of methods from Computer Science to dissolve the Russell Paradox. We constructed the transordinal numbers but without accounting for the Burali-Forti Paradox which establishes that the set of all ordinals does not exist in some circumstances. We deﬁned that nullity is the smallest unordered set but mistakenly wrote this with three pairs of nested set brackets instead of four, when nullity is unordered with respect to the von Neumann ordinals. We discussed a four-valued logic – with the values True, False, Contradiction, Gap – and introduced antinomies as ﬁrst-class objects. Thus we proposed a set theory with three kinds of objects: sets, antinomies and members. All of this is eﬀective at dissolving the Russell Paradox but it is a very large departure from the usual set theories. We now use the empty symbol, epsilon, of Computer Science’s compiler theory to totalise all functions and combine this with Computer Science’s notion of a bag to totalise set membership in a way that uses the usual two-valued logic and is immune to the Russell Paradox. This gives us a trivially consistent set theory, whose universal set is the class of all classes, and which ought to be immune from all paradoxes of logic and set theory. As is the case with the usual set theories, our set theory has just two kinds of objects: sets and members. We call the new set theory Foundations of Transmathematical Logic (FTL) and observe that its deﬁnition of set membership could be adopted by any set theory. We use the properties of the transnumber inﬁnity, ﬁrstly to construct the transnatural numbers, secondly to construct the transordinal numbers, and ﬁnally to dissolve the Burali-Forti Paradox.
Inhibitory e¡ects of broccoli extract on Escherichiacoli O157:H7 quorum sensing and invivovirulence

Broccoli extract (BE) has numerous beneﬁcial effects on human health including anticancer activity. Quorum sensing (QS), mediated by self-produced autoinducer (AI) molecules, is a key process for the production of virulence determinants in pathogenic bacteria. BE suppressed AI-2 synthesis and AI-2-mediated bacterial motility in a dose-dependent manner in Escherichia coli O157:H7. In addition, expression of the ler gene that regulates AI-3 QS system was also diminished in response to treatment with BE. Furthermore, in an in vivo efﬁcacy test using Caenorhabditis elegans as a host organism, C. elegans fed on E. coli O157:H7 in the presence of BE survived longer than those fed solely on the pathogenic bacteria. Quantitative real-time PCR analysis indicated that quercetin was the most active among the tested broccoli-derived compounds in downregulating virulence gene expression, while treatment with myricetin signiﬁcantly suppressed the expression of the eae gene involved in type III secretion system. These data suggest that BE and its ﬂavonoid constituents can inhibit expression of QS-associated genes, thereby downregulating the virulence attributes of E. coli O157:H7 both in vitro and in vivo . This study clearly elucidates BE’s QS-inhibitory activity and suggests that BE has the potential to be developed as an anti-infective agent.
GENETIC VARIABILITY STUDY OF Phytophthora infestans ISOLATES BASED ON MATING TYPE MOLECULAR MARKERS AND METALAXYL RESISTANCE

Isolates of Phytophthora infestans (Mont.) de Bary were collected from potato fields located in main cultivation regions in Egypt during two successive seasons, 2006 and 2007. The ITS4 and ITS5 primers were used to study the genetic variation among the five isolates. Resulted pattern cleared out the differences among isolates concerning the density of the bands and the number in bands for each isolate. A molecular approach was used in order to identify the mating types. Genomic DNA of P. infestans obtained from mycelium grown in pure culture was amplified with the specific primers W16-1/2 and subsequently digested with HaeIII restriction enzyme. The results revealed the presence of the A2 mating type in 1 isolate (Salhia, Behira) among 5 isolates obtained from commercial fields in Egypt. Also, since it is observed that fungicides containing metalaxyl are loosing their efficacy in many fields, when in vitro tests for metalaxyl resistance in P. infestans isolates were performed. Results revealed strong presence of the metalaxyl tolerant and resistant phenotypes in Egyptian P. infestans population. Importance of the genetic studies to follow pathogenicity and population structure of P. infestans was noticed.
A survey on techniques for mining frequent patterns over data stream

—Mining frequent itemsets in a data stream proves to be a difficult problem, as itemset arrives in rapid succession and storing parts of the stream is typically impossible. Finding frequent pattern from data streams have been of importance in many applications such as stock market prediction, sensor data analysis, e-business, network traffic analysis and telecommunication data analysis. In this paper, few recent and popular methods for extracting patterns from stream data have been studied. Also a comparative study of different methods with reference to the conditions in which they work, their benefits and drawbacks of these methods are presented in this work.
InfectionsChoriomeningitis Virus and Influenza Virus Cells Are Generated after Lymphocytic T + Qualitatively Different Memory CD8

Viral infections often induce robust T cell responses that are long-lived and protective. However, it is unclear to what degree systemic versus mucosal infection inﬂuences the generation of effector and memory T cells. In this study, we characterized memory CD8 + T cells generated after respiratory inﬂuenza virus infection and compared the phenotypic and functional qualities of these cells with memory T cells generated after systemic infection with lymphocytic choriomeningitis virus (LCMV). Using a recombinant inﬂuenza virus expressing the LCMV gp 33–41 epitope and TCR transgenic CD8 + T cells with a ﬁxed TCR, we compared responses to the same Ag delivered by mucosal or systemic viral infection. Memory cells generated postinfection with either virus showed only a few phenotypic differences. Yet, inﬂuenza memory T cells produced lower amounts of effector cytokines upon restimulation and displayed reduced proliferation compared with LCMV-induced memory cells. Strikingly, we observed reduced expansion of spleen- and, in particular, lung-derived inﬂuenza memory cells after recall in vivo, which correlated with reduced early protection from secondary infection. These ﬁndings suggest that qualitatively different memory CD8 + T cells are generated after respiratory or systemic virus infections. The Journal of Immunology , 2010, 185: 000–000.
Interaction of RecA Protein with Acidic Phospholipids Inhibits DNA-Binding Activity of RecA

The RecA protein of Escherichia coli binds specifically to acidic phospholipids such as cardiolipin and phosphatidylglycerol. This binding appears to be affected by the presence of divalent cations such as Ca2' and Mg2 . The interaction leads to the inhibition of RecA binding to at least two different conformations of DNA, single-stranded DNA and left-handed Z-DNA, thus suggesting that the phospholipids interact at the DNA-binding site of the RecA protein. Inclusion of a nucleotide cofactor [adenosine 5'-O-(-y-thiotriphosphate)J in the reactions did not prevent the inhibition of DNA-binding activities of RecA protein by the phospholipids. The interaction of RecA protein with cardiolipin and phosphatidylglycerol, which represent two of the three major phospholipids of the E. coli membrane, may be physiologically important, as it provides a possible mechanism for the RecA-membrane association during the SOS response. These observations raise the possibility that the Z-DNA-binding activity of RecA protein is merely a manifestation of its phospholipid- binding property.
Seed Production of Red Clover ( Trifolium pratense L.) under Danish Field Conditions

: High and stable seed yield is critical for red clover ( Trifolium pratense L.) seed production and the commercial exploitation of the crop. A three-year experiment was conducted from 2013 to 2015 under Danish ﬁeld conditions to explore the inﬂuence of precipitation during peak ﬂowering on the seed yield of three red clover cultivars. We investigated the ﬂowering duration and intensity based on a visual scale assessment, seed yield, and thousand seed weight in all three experimental years. In 2014 and 2015 we measured the seed yield components of ﬂoret number per ﬂower head, seed number per ﬂower head, and seed set. During the experimental period, high seed yields of more than 1000 kg ha − 1 were obtained for the diploid cultivars ‘Rajah’ and ‘Suez’. Although a relatively high seed yield of 500 kg ha − 1 was obtained in the tetraploid cultivar ‘Amos’, this was only around half of the seed yield and seed set of the diploid cultivars. Precipitation during peak ﬂowering positively inﬂuenced the seed yield and thousand seed weight for the three cultivars. We conclude that observations of ﬂowering phenology are required to determine the impact of environmental conditions on seed yield in red clover cultivars. Further, adequate water supply during peak ﬂowering is important to obtain the high seed yield of red clover.
A COMPARATIVE STUDY ON THE BIOCHEMICAL COMPOSITION OF HAEMOLYMPH OF THE FIFTH INSTAR LARVAE OF A MULTIVOLTINE BREED AND A BIVOLTINE BREED OF THE MULBERRY SILKWORM,

Changes in the composition of haemolymph reflect the physiological and biochemical transformations taking place in the insect tissues. In this work, the biochemical composition of haemolymph of the fifth instarlarvae of a multivoltine breed (L×CSR2) was compared with that of a bivoltine breed (CSR6×CSR12) of the mulberry silkworm, Bombyx mori . The larval period of the fifth instar larvae of both breeds lasted for 6 days. Increased trend of biochemical properties from the 1 st day to the 6 th day was noticed in both the breeds . The protein concentration of the fifth instar larvae of bivoltine breed was significantly lower than that of the multivoltine breed on all days. But the concentration of amino acid and carbohydrate were greater in the haemolymph of the bivoltine breed than that of the haemolymph of the multivoltine breed on all days. Lipid concentration was lower in the multivoltine breed than that of the bivoltine breed on the first four days whereas on the later days reverse trend was observed. The ‘t’ values indicate that the differences in the biochemical parameters between the two breeds were significant on all days.