Miracle-dz/UniFAR-FTUs huggingface dataset:
Splicing- and cleavage-independent requirement of RNA polymerase II CTD for mRNA release from the transcription site

Eukaryotic cells have a surveillance mechanism that identifies aberrantly processed pre-mRNAs and prevents their flow to the cytoplasm by tethering them near the site of transcription. Here we provide evidence that mRNA release from the transcription site requires the heptad repeat structure of the C-terminal domain (CTD) of RNA polymerase II. The mammalian CTD, which is essential for normal co-transcriptional maturation of mRNA precursors, comprises 52 heptad repeats. We show that a truncated CTD containing 31 repeats (heptads 1–23, 36–38, and 48–52) is sufficient to support transcription, splicing, cleavage, and polyadenylation. Yet, the resulting mRNAs are mostly retained in the vicinity of the gene after transcriptional shutoff. The retained mRNAs maintain the ability to recruit components of the exon junction complex and the nuclear exosome subunit Rrp6p, suggesting that binding of these proteins is not sufficient for RNA release. We propose that the missing heptads in the truncated CTD mutant are required for binding of proteins implicated in a final co-transcriptional maturation of spliced and 3′ end cleaved and polyadenylated mRNAs into export-competent ribonucleoprotein particles.
Constituents from the testas of Castanea mollissima Blume with α-glucosidase inhibitory activity

In the screening of biologically active constituents from medicinal plants, the 75% EtOH extract of the testas of Castanea mollissima Blume showed potent α-glucosidase inhibitory activity. By means of various chromatographic methods, the extract gave a new dammarane-type triterpene 1 along with 17 known compounds. The structure of 1 was determined to be 3β-acetoxy-20-oxo-21-nordammaran-23-oic acid by HRMS and NMR studies including 2D NMR experiments. The new compound and some known compounds showed potent α-glucosidase inhibitory activity with acarbose as a positive control.
Effect of a protein and energy dense n-3 fatty acid enriched oral supplement on loss of weight and lean tissue in cancer cachexia: a randomised double blind trial

Aim: N-3 fatty acids, especially eicosapentaenoic acid (EPA), may possess anticachectic properties. This trial compared a protein and energy dense supplement enriched with n-3 fatty acids and antioxidants (experimental: E) with an isocaloric isonitrogenous control supplement (C) for their effects on weight, lean body mass (LBM), dietary intake, and quality of life in cachectic patients with advanced pancreatic cancer. Methods: A total of 200 patients (95 E; 105 C) were randomised to consume two cans/day of the E or C supplement (480 ml, 620 kcal, 32 g protein ± 2.2 g EPA) for eight weeks in a multicentre, randomised, double blind trial. Results: At enrolment, patients’ mean rate of weight loss was 3.3 kg/month. Intake of the supplements (E or C) was below the recommended dose (2 cans/day) and averaged 1.4 cans/day. Over eight weeks, patients in both groups stopped losing weight (Δ weight E: −0.25 kg/month versus C: −0.37 kg/month; p = 0.74) and LBM (Δ LBM E: +0.27 kg/month versus C: +0.12 kg/month; p = 0.88) to an equal degree (change from baseline E and C, p<0.001). In view of evident non-compliance in both E and C groups, correlation analyses were undertaken to examine for potential dose-response relationships. E patients demonstrated significant correlations between their supplement intake and weight gain (r = 0.50, p<0.001) and increase in LBM (r = 0.33, p = 0.036). Such correlations were not statistically significant in C patients. The relationship of supplement intake with change in LBM was significantly different between E and C patients (p = 0.043). Increased plasma EPA levels in the E group were associated with weight and LBM gain (r = 0.50, p<0.001; r = 0.51, p = 0.001). Weight gain was associated with improved quality of life (p<0.01) only in the E group. Conclusion: Intention to treat group comparisons indicated that at the mean dose taken, enrichment with n-3 fatty acids did not provide a therapeutic advantage and that both supplements were equally effective in arresting weight loss. Post hoc dose-response analysis suggests that if taken in sufficient quantity, only the n-3 fatty acid enriched energy and protein dense supplement results in net gain of weight, lean tissue, and improved quality of life. Further trials are required to examine the potential role of n-3 enriched supplements in the treatment of cancer cachexia.
On the Estimation of Detection Probabilities for Sampling Stream-Dwelling Fishes.

To examine the adequacy of fish probability of detection estimates, I examined distributional properties of survey and monitoring data for bull trout (Salvelinus confluentus), brook trout (Salvelinus fontinalis), westslope cutthroat trout (Oncorhynchus clarki lewisi), chinook salmon parr (Oncorhynchus tshawytscha), and steelhead /redband trout (Oncorhynchus mykiss spp.), from 178 streams in the Interior Columbia River Basin. Negative binomial dispersion parameters varied considerably among species and streams, but were significantly (P<0.05) positively related to fish density. Across streams, the variances in fish abundances differed greatly among species and indicated that the data for all species were overdispersed with respect to the Poisson (i.e., the variances exceeded the means). This significantly affected Poisson probability of detection estimates, which were the highest across species and were, on average, 3.82, 2.66, and 3.47 times greater than baseline values. Required sample sizes for species detection at the 95% confidence level were also lowest for the Poisson, which underestimated sample size requirements an average of 72% across species. Negative binomial and Poisson-gamma probability of detection and sample size estimates were more accurate than the Poisson and generally less than 10% from baseline values. My results indicate the Poisson and binomial assumptions often are violated, which results inmore » probability of detection estimates that are biased high and sample size estimates that are biased low. To increase the accuracy of these estimates, I recommend that future studies use predictive distributions than can incorporate multiple sources of uncertainty or excess variance and that all distributional assumptions be explicitly tested. « less
Electromagnetic Compatibility (EMC) of Power Converters as a Problem of Parametric Optimization

In this paper a problem of parametric opti­ mization of power semiconductor converters is considered. It is shown that an account of EMC parameters takes to a significant increase in dimension of elements mathematical models of converter and to generogeneity of their para­ meters variations and to multiextremums of cost functions. Algorithm of quasilinear app­ roximation of a cost function is proposed, allowing to use a finite-difference analogue of gradient methods, having high quickoperation. The check of global character of cost function extremum is made by random search me­ thods .
Building Change Detection from Historical Aerial Photographs Using Dense Image Matching and Object-Based Image Analysis

A successful application of dense image matching algorithms to historical aerial photographs would offer a great potential for detailed reconstructions of historical landscapes in three dimensions, allowing for the efficient monitoring of various landscape changes over the last 50+ years. In this paper we propose the combination of image-based dense DSM (digital surface model) reconstruction from historical aerial imagery with object-based image analysis for the detection of individual buildings and the subsequent analysis of settlement change. Our proposed methodology is evaluated using historical greyscale and color aerial photographs and numerous reference data sets of Andermatt, a historical town and tourism destination in the Swiss Alps. In our paper, we first investigate the DSM generation performance of different sparse and dense image matching algorithms. They demonstrate the superiority of dense matching algorithms and of the resulting historical DSMs with root mean square error values of 1–1.5 GSD (ground sampling distance) and yield point densities comparable to those of recent airborne LiDAR DSMs. In the second part, we present an object-based building detection workflow mainly based on the historical DSMs and the historical imagery itself. Additional inputs are a current digital terrain model and a cadastral building database. For the case of densely matched DSMs, the evaluation yields building detection rates of 92% for grayscale and 94% for color imagery.
Tissue-dependent expression of heat shock factor 2 isoforms with distinct transcriptional activities

Heat shock factor 2 (HSF2) functions as a transcriptional regulator of heat shock protein gene expression in mammalian cells undergoing processes of differentiation and development. Our previous studies demonstrated high regulated expression and unusual constitutive DNA-binding activity of the HSF2 protein in mouse testes, suggesting that HSF2 functions to regulate heat shock protein gene expression in spermatogenic cells. The purpose of this study was to test whether HSF2 regulation in testes is associated with alterations in the HSF2 polypeptide expressed in testes relative to other mouse tissues. Our results show that mouse cells express not one but two distinct HSF2 proteins and that the levels of these HSF2 isoforms are regulated in a tissue-dependent manner. The testes express predominantly the 71-kDa HSF2-alpha isoform, while the heart and brain express primarily the 69-kDa HSF2-beta isoform. These isoforms are generated by alternative splicing of HSF2 pre-mRNA, which results in the inclusion of an 18-amino-acid coding sequence in the HSF2-alpha mRNA that is skipped in the HSF2-beta mRNA. HSF2 alternative splicing is also developmentally regulated, as our results reveal a switch in expression from the HSF2-beta mRNA isoform to the HSF2-alpha isoform during testis postnatal developmental. Transfection analysis shows that the HSF2-alpha protein, the predominant isoform expressed in testis cells, is a more potent transcriptional activator than the HSF2-beta isoform. These results reveal a new mechanism for the control of HSF2 function in mammalian cells, in which regulated alternative splicing is used to modulate HSF2 transcriptional activity in a tissue-dependent manner.
Characterization of the inhibitory prostanoid receptors on human neutrophils

1 We have evaluated the effects of various prostanoid agonists on the release of leukotriene B4 (LTB4) and superoxide anions (O2−) from human neutrophils stimulated with opsonized zymosan (OZ) and formyl‐methionyl‐leucyl‐phenylalanine (FMLP), respectively. 2 Prostaglandin E2 (PGE2) and PGD2 inhibited both OZ‐induced LTB4 release (EC50 0.72 μm and 0.91 μm respectively), and FMLP‐induced O2− release (EC50 0.42 μm and 0.50 μm respectively). PGF2α, the TP‐receptor agonist, U46619, and the IP‐receptor agonist, iloprost, were also active, but were all at least an order of magnitude less potent than PGE2 and PGD2. 3 The EP2/EP3‐receptor agonist, misoprostol, and the selective EP2‐agonist, AH13205, were both effective inhibitors of LTB4 release, being approximately equipotent with and 16‐times less potent than PGE2, respectively. In contrast, the EP1/EP3‐receptor agonist, sulprostone, had no inhibitory activity at concentrations of up to 10 μm. 4 The selective DP‐receptor agonist, BW245C, inhibited LTB4 release, (EC50 0.006 μm) being approximately 50 times more potent than PGD2. BW245C also inhibited O2− release, and this inhibition was antagonized competitively by the DP‐receptor blocking drug, AH6809 (pA2 6.6). 5 These data indicate the presence of both inhibitory EP‐ and DP‐receptors on the human neutrophil. The rank order of potency of EP‐receptor agonists suggest that the EP‐receptors are of the EP2‐subtype. ;
A Joint Motion-Image Inpainting Method for Error Concealment in Video Coding

In this paper, we propose a new method for spatial-temporal error concealment in video coding using joint motion-image inpainting. The proposed method combines motion inpainting and adaptive Markov random field (MRF) based diffusion as robust motion inpainting. Image inpainting is employed to refine the result. With robust motion inpainting, effective compromise between temporal and spatial method is achieved for each point in the missing marcroblock (MB), which provides satisfactory visual quality of the restored frame with complex motion in video.
Comprehensive Evaluation of OpenCL-based Convolutional Neural Network Accelerators in Xilinx and Altera FPGAs

Deep learning has significantly advanced the state of the art in artificial intelligence, gaining wide popularity from both industry and academia. Special interest is around Convolutional Neural Networks (CNN), which take inspiration from the hierarchical structure of the visual cortex, to form deep layers of convolutional operations, along with fully connected classifiers. Hardware implementations of these deep CNN architectures are challenged with memory bottlenecks that require many convolution and fully-connected layers demanding large amount of communication for parallel computation. Multi-core CPU based solutions have demonstrated their inadequacy for this problem due to the memory wall and low parallelism. Many-core GPU architectures show superior performance but they consume high power and also have memory constraints due to inconsistencies between cache and main memory. FPGA design solutions are also actively being explored, which allow implementing the memory hierarchy using embedded BlockRAM. This boosts the parallel use of shared memory elements between multiple processing units, avoiding data replicability and inconsistencies. This makes FPGAs potentially powerful solutions for real-time classification of CNNs. Both Altera and Xilinx have adopted OpenCL co-design framework from GPU for FPGA designs as a pseudo-automatic development solution. In this paper, a comprehensive evaluation and comparison of Altera and Xilinx OpenCL frameworks for a 5-layer deep CNN is presented. Hardware resources, temporal performance and the OpenCL architecture for CNNs are discussed. Xilinx demonstrates faster synthesis, better FPGA resource utilization and more compact boards. Altera provides multi-platforms tools, mature design community and better execution times.
Estimated HIV Trends and Program Effects in Botswana

Background This study uses surveillance, survey and program data to estimate past trends and current levels of HIV in Botswana and the effects of treatment and prevention programs. Methods/Principal Findings Data from sentinel surveillance at antenatal clinics and a national population survey were used to estimate the trend of adult HIV prevalence from 1980 to 2007. Using the prevalence trend we estimated the number of new adult infections, the transmission from mothers to children, the need for treatment and the effects of antiretroviral therapy (ART) and adult and child deaths. Prevalence has declined slowly in urban areas since 2000 and has remained stable in rural areas. National prevalence is estimated at 26% (25–27%) in 2007. About 330,000 (318,000–335,000) people are infected with HIV including 20,000 children. The number of new adult infections has been stable for several years at about 20,000 annually (12,000–26,000). The number of new child infections has declined from 4600 in 1999 to about 890 (810–980) today due to nearly complete coverage of an effective program to prevent mother-to-child transmission (PMTCT). The annual number of adult deaths has declined from a peak of over 15,500 in 2003 to under 7400 (5000–11,000) today due to coverage of ART that reaches over 80% in need. The need for ART will increase by 60% by 2016. Conclusions Botswana's PMTCT and treatment programs have achieved significant results in preventing new child infections and deaths among adults and children. The number of new adult infections continues at a high level. More effective prevention efforts are urgently needed.
Cross-cultural study of posttraumatic growth following childbirth

Posttraumatic growth describes positive changes following challenging events. Although such changes are well documented there remain a number of important areas for further research, some of which are addressed in this thesis. In particular, this thesis aimed to clarify the relationship between growth and adjustment following health events, explore growth in different cultures (UK and Africa), and examine growth following childbirth using a prospective design. First, two systematic reviews were carried out to examine (i) growth following health events and (ii) maternal wellbeing in African women. The first meta-analytic review found that growth following cancer and HIV/AIDS was associated with higher levels of positive mental health, higher subjective physical health, and lower levels of negative mental health. Moderating variables were time since the event, age, ethnicity, and type of negative mental health outcome. The second review found that maternal psychological problems in African women have a similar or slightly higher prevalence than reported in developed countries. Risk factors were broadly comparable although some culture-specific factors were also found. Three research studies were conducted. The first study qualitatively explored 55 Gambian women’s experiences of pregnancy, childbirth, and the postnatal period. Thematic analysis identified five themes: (1) transition to adulthood, (2) physical difficulties, (3) value of children in relation to others, (4) children as a strain, and (5) going through it alone. Prospective studies of growth following childbirth were then carried out in the UK (N=125) and The Gambia (N=101). Women completed questionnaires during their third trimester of pregnancy and up to 12 weeks after birth. A proportion of women in both countries reported growth following childbirth. In the UK, higher levels of growth were associated with caesarean sections and prenatal posttraumatic stress symptoms. In The Gambia, higher growth was associated with lower income, lower education, and higher postnatal social support.
Characterizing and Modeling the Dropbox Workload

This paper presents a characterization and modeling of the workload of the currently most popular cloud storage system, Drop box. The workload is analyzed from two complementary perspectives. On one side, characteristics of the Drop box folders of a set of 333 volunteers, including number, type and sizes of files, replication level, and file update dynamics are analyzed. On the other side, the client behavior patterns are modeled based on the analysis of Drop box traffic collected from 3 universities. Our results can be explored to design realistic synthetic workloads, which in turn can support the design and evaluation of more cost-effective cloud storage services.
An Adaptive Edge-Detection Method Based on the Canny Operator

On the basis of analyzing the conventional Canny algorithm, this paper advanced an adaptive edge-detection method based on the canny operator. This method not only keeps the Canny’s good performance in good detection, good localization and only one response to a single edge, but also improves the capability of restraining the fake edge and the automaticity of edge-detection based on the Otsu’s thresholding method. Through experiments, it is demonstrated that the adaptive edge-detection method in this paper is very effective.
A Phylogenetic Analysis of the Brassicales Clade Based on an Alignment-Free Sequence Comparison Method

Phylogenetic analyses reveal the evolutionary derivation of species. A phylogenetic tree can be inferred from multiple sequence alignments of proteins or genes. The alignment of whole genome sequences of higher eukaryotes is a computational intensive and ambitious task as is the computation of phylogenetic trees based on these alignments. To overcome these limitations, we here used an alignment-free method to compare genomes of the Brassicales clade. For each nucleotide sequence a Chaos Game Representation (CGR) can be computed, which represents each nucleotide of the sequence as a point in a square defined by the four nucleotides as vertices. Each CGR is therefore a unique fingerprint of the underlying sequence. If the CGRs are divided by grid lines each grid square denotes the occurrence of oligonucleotides of a specific length in the sequence (Frequency Chaos Game Representation, FCGR). Here, we used distance measures between FCGRs to infer phylogenetic trees of Brassicales species. Three types of data were analyzed because of their different characteristics: (A) Whole genome assemblies as far as available for species belonging to the Malvidae taxon. (B) EST data of species of the Brassicales clade. (C) Mitochondrial genomes of the Rosids branch, a supergroup of the Malvidae. The trees reconstructed based on the Euclidean distance method are in general agreement with single gene trees. The Fitch–Margoliash and Neighbor joining algorithms resulted in similar to identical trees. Here, for the first time we have applied the bootstrap re-sampling concept to trees based on FCGRs to determine the support of the branchings. FCGRs have the advantage that they are fast to calculate, and can be used as additional information to alignment based data and morphological characteristics to improve the phylogenetic classification of species in ambiguous cases.
Understanding the Continued Usage Intention of Educators toward an e-Learning System

The tremendous development of technologies over recent decades has offered many e-learning systems to faculty educators to support teaching. The advantage of using such systems in connection with on-site courses is that it increases flexibility in teaching/learning by making resources available online. However, there is little empirical evidence to suggest which factors shape educatorsâ€™ continuance intention to use such systems. This study builds a model, based on the Unified Theory of Acceptance and Use of Technology to identify the factors. The model was tested among university educators who use the popular e-learning system, Moodle. The results suggest that the continuance intention is driven by perceived usefulness and access. Perceived ease of use, perceived behavioral control, compatibility, and social influence do not have a significant direct impact on continuance intention, although perceived ease of use and compatibility significantly affect perceived usefulness. Taken together, the core determinants of the continuance intention explained around 70% of the total variance in intention in this study.
Functional limitations and survival following stroke: Psychological and clinical predictors of 3-year outcome

Previous studies predicting functional outcomes of stroke have mainly used clinical and demographic measures. This study examines the additional predictive value of psychological predictors. A cohort of patients were assessed on 6 occasions between admission to hospital and 3 years post-stroke, with 40 of the original sample of 101 being available at the final assessment. Demographic variables, clinical indexes, and psychological measures were used to predict survival to 3 years and 3-year functional recovery was assessed using measures derived from the Barthel Index which took account of initial levels of performance. For functional recovery, multiple regression analyses showed that fixed clinical and demographic indexes explained 16% to 40% of the variance in recovery. Perceptions of control 6 months after discharge added significantly to the predictive equations. Because these cognitions are modifiable, they offer opportunities for intervention to improve patient outcomes. Multiple regression showed that no psychological variables predicted survival.