Miracle-dz/UniFAR-FTUs huggingface dataset:
The Caulobacter heat shock sigma factor gene rpoH is positively autoregulated from a sigma32-dependent promoter

Sigma factor sigma32, encoded by rpoH, is required for the recognition of heat shock genes during normal growth conditions and in response to heat shock and other stresses. Unlike the well-studied Escherichia coli rpoH gene, which is transcribed from four promoters recognized by either a sigma70 (sigmaD)- or sigma24 (sigmaE)-containing RNA polymerase, the Caulobacter crescentus rpoH gene is transcribed from two promoters, P1 and P2. In this study, we have examined the structure and expression of these promoters and shown that the rpoH P2 promoter is sigma32 dependent. We present evidence here that P2 is specifically recognized and transcribed by the reconstituted C. crescentus Esigma32 RNA polymerase holoenzyme. We show that site-directed mutations within either the -10 or the -35 regions of P2 have substantial effects on the levels of transcription by the Esigma32 polymerase predicted from the sigma32 promoter consensus sequence. The mutations have similar effects in vivo as assayed with rpoH-lacZ transcription fusions. Analysis of the rpoH P1 promoter provided evidence that it is sigma70 dependent. S1 nuclease protection assays of rpoH P1- and P2-specific expression after heat shock at 42 or 50 degrees C and during synchronous cell division cycles under normal growth conditions showed that the two promoters are differentially regulated. Mutations within the rpoH P2 promoter consensus sequences abolished the response to heat shock induction in C. crescentus. We conclude from these results that, unlike rpoH genes studied previously in other bacteria, the major transcriptional response of the C. crescentus rpoH gene to heat shock depends on positive autoregulation of the sigma32-dependent promoter.
Control of hnRNP A1 Alternative Splicing: an Intron Element Represses Use of the Common 3′ Splice Site

ABSTRACT Alternative splicing of exon 7B in the hnRNP A1 pre-mRNA produces mRNAs encoding two proteins: hnRNP A1 and the less abundant A1B. We have reported the identification of several intron elements that contribute to exon 7B skipping. In this study, we report the activity of a novel element, conserved element 9 (CE9), located in the intron downstream of exon 7B. We show that multiple copies of CE9 inhibit exon 7B-exon 8 splicing in vitro. When CE9 is inserted between two competing 3′ splice sites, a single copy of CE9 decreases splicing to the distal 3′ splice site. Our in vivo results also support the conclusion that CE9 is a splicing modulator. First, inserting multiple copies of CE9 into an A1 minigene compromises the production of fully spliced products. Second, one copy of CE9 stimulates the inclusion of a short internal exon in a derivative of the human β-globin gene. In this case, in vitro splicing assays suggest that CE9 decreases splicing of intron 1, an event that improves splicing of intron 2 and decreases skipping of the short internal exon. The ability of CE9 to act on heterologous substrates, combined with the results of a competition assay, suggest that the activity of CE9 is mediated by atrans-acting factor. Our results indicate that CE9 represses the use of the common 3′ splice site in the hnRNP A1 alternative splicing unit.
Downregulation of miR-21 Enhances Chemotherapeutic Effect of Taxol in Breast Carcinoma Cells

The successful of anti-cancer treatment are often limited by the development of drug resistance. Recent work has highlighted the involvement of non-coding RNAs, microRNAs(miRNAs) in cancer development, and their possible involvement in the evolution of drug resistance has been proposed. In this study, we combine taxol chemotherapy and miR-21 inhibitor treatment via polyamidoamine (PAMAM) dendrimers vector to evaluate the effects of combination therapy on suppression of breast cancer cells. The 50% inhibitory concentration (IC50) values for taxol were significantly decreased to a greater extent in the cells transfected with miR-21 inhibitor compared with cells treated with taxol alone. Taxol treatment also increased the percentage of apoptotic breast cancer cells in miR-21 inhibitor transfected cells compared with control cells. Furthermore, treatment of the miR-21 inhibitor-transfected cells with the anti-cancer drugs taxol resulted in significantly reduced cell viability and invasiveness compared with control cells. These results indicated that the miR-21 plays an important role in the resistance of breast carcinoma cells to chemotherapeutic drugs. Therefore, miR-21 inhibitor gene therapy combined with taxol chemotherapy might represent a promising novel therapeutic approach for the treatment of breast malignancies.
Submerged macrophyte zonation in a Mediterranean salt marsh: a facilitation effect from established helophytes?

Abstract The relationship between communities of submerged annual macrophytes (predominately Chara spp.) and environmental characteristics is studied in three habitats with different dominant perennial species (Arthrocnemum, Juncus, Scirpus) and areas of bare soil. The distribution of submerged annual macrophytes is significantly dependent on two independent environmental factors: a dominant gradient of flooding/salinity, and a secondary gradient of nutrients related exclusively to the combined abundance of helophytes of the genus Scirpus (S. maritimus and S. litoralis). The results suggest that these emergent helophytes (1) are able to modify water column parameters (such as concentration of nitrates, phosphates, potassium, and bicarbonates) which are important for the communities of submerged macrophytes, and (2) play a fundamental role in the generation of secondary sources of environmental variability which, superimposed on the main gradient of flooding/salinity, favours the appearance of new compositional equilibria in such communities. The existence of a process of facilitation is discussed by which the emergent helophytes induce changes in nutrient availability that would favour relatively nutrient-demanding charophyte species (such as Chara connivens and Nitella hyalina), altering the established relationships with other coexisting charophytes (such as Chara canescens and C. galioides) that dominate in the absence of the facilitating species. Nevertheless, the increased nutrient concentration associated to the presence of helophytes would not introduce significant changes in the total biomass of submerged aquatic macrophytes. Abbreviations: SBM = Seasonal biomass maximum; SOM = Soil organic matter; STN = Total nitrogen; STP = Total phosphorus. Nomenclature: Valdés et al. (1987); Corillion (1961) for Charophytes.
Book retrieval based on Near-Duplicate image matching

Image Near-Duplicate (IND) detection and retrieval are both useful techniques in a variety of applications. There exist several detectors demonstrated high effectiveness and efficiency in IND detection and retrieval such as Scale Invariant Feature Transform (SIFT) detector and Histograms of Oriented Gradients (HOG) detector. We notice that any artificially taken book cover photo is a variant of the standard image about the identical book, and their relationship can be considered as IND. We propose a method for searching any book from numerous books based on IND retrieval. One of application contexts of this method is selecting a book from several similar ones. That means consumers can take photos of any book they want to have a general idea of by their cellphones to obtain some basic information by searching the corresponding book. We adopt the SIFT algorithm as our feature extraction algorithm and improve it in details to be faster and more accurate in book cover image retrieval. A two-level structure is designed in the matching stage, namely the “routine matching” and the “refining matching”. In the experiment, we establish a database of 2,000 standard image as template images and 1,200 artificially taken photos as query images. For evaluation the results, we use precision metric. The experimental results indicate that our method shows high effectiveness and efficiency.
Adaptive coding-unit size selection based on hierarchical quad-tree correlations for high-efficiency video coding

Abstract. The latest high-efficiency video coding (HEVC) standard adopts a recursive quad-tree block structure with the coding-unit (CU) size variable depending on video content. It substantially improves the coding efficiency and also dramatically increases complexity. Therefore, a fast CU size selection algorithm based on hierarchical quad-tree correlations (HQTCs) is proposed. First, for each coding tree unit, the partition information at each depth is recorded in a table that reflects the appearance of the quad-tree structure. Then, by using two techniques called top omitting and bottom pruning, the size of the current CU can be determined according to the subtree distributions of adjacent CUs instead of traversing all the depths. Additionally, a gray level co-occurrence matrix-based method is also introduced to further speedup the searching process. Experimental results show that the proposed algorithm can achieve on average a 26% computational time reduction under all configurations with a negligible BD-rate (Bjøntegaard Delta bitrate) increase of 0.47% compared with the original encoding scheme in HEVC test model HM13.0.
Fault diagnosis model for power transformer based on statistical learning theory and dissolved gas analysis

After thoroughly analyzing the relationships between indications and faults, it has been found that there are no explicit mapping functions between the faults of oil-immersed power transformer. To handle this problem, a multilevel decision-making model for power transformer fault diagnosis based on statistical learning theory is presented. Based on the concentration distribution of some typical fault gases, the proposed approach is to determine the optimal solution with a few training samples. The output of this model is improved by approaching exactly with K-nearest neighbor search classification for the SVM classification results, which is adjacent to optimal separating hyperplan. So the dependability of this model is enhanced greatly, and its effectiveness and usefulness is proved.
Turning around schools: A view from the superintendent / central office as policy implementers

This single case study examines how stakeholders of a local education agency (LEA) understand and implement state turnaround policy for its chronically underperforming schools. While there is ample research on how to improve chronically underperforming schools, a research gap exists specifically around addressing implementation of mandated turnaround policy. This qualitative study uses the theory frame of policy sense-making to identify how implementers come to understand turnaround policy and to explore how that sense-making impacts their implementation decisions. This study seeks to understand the role of central office in turnaround policy sense-making by collecting data on superintendent and central office administrator sense-making and its impact on policy implementation. While recent research on school improvement has focused on school improvement actions and responsibilities of principals and teachers, this study seeks to address the research gap of the essential role of school district offices in school turnaround. In seeking to understand how district TURNING AROUND SCHOOLS: A VIEW FROM IMPLEMENTERS ii leaders make sense of turnaround policy implementation to support school turnaround, the findings revealed that the superintendent and central office administrators identified strong superintendent leadership, monitoring and supporting schools, strategic distribution of resources, and management of human capital as key implementer actions and areas of influence. TURNING AROUND SCHOOLS: A VIEW FROM IMPLEMENTERS iii TURNING AROUND SCHOOLS: A VIEW FROM POLICY IMPLEMENTERS A single case study which examines how turnaround policy implementation is influenced by policy sense-making. EXECUTIVE SUMMARY DISSERTATION IN PRACTICE BOSTON COLLEGE Jamie B. Chisum Anna Carollo Cross Jill S. Geiser Charles A. Grandson IV
Randomized trial of continuing care enhancements for cocaine-dependent patients following initial engagement.

OBJECTIVE The effects of cognitive-behavioral relapse prevention (RP), contingency management (CM), and their combination (CM + RP) were evaluated in a randomized trial with 100 cocaine-dependent patients (58% female, 89% African American) who were engaged in treatment for at least 2 weeks and had an average of 44 days of abstinence at baseline. METHOD The participants were from intensive outpatient programs, which provide 10 hr per week of group counseling. The CM protocol provided gift certificates (maximum value $1,150; mean received = $740) for cocaine-free urines over 12 weeks on an escalating reinforcement schedule, and weekly individual RP sessions were offered for up to 20 weeks. Average number of RP sessions attended was 3 in RP and 13 in CM + RP. RESULTS Generalizing estimation equation analyses over 18 months postrandomization showed significant effects for CM (but not RP) on urine toxicology and self-reported cocaine use (p = .05), with no significant CM x RP interactions. Secondary analyses indicated CM + RP produced better cocaine urine toxicology outcomes at 6 months than treatment as usual, odds ratio [OR] = 3.96 (1.33, 11.80), p < . 01, and RP, OR = 4.89 (1.51, 15.86), p < . 01, and produced better cocaine urine toxicology outcomes at 9 months than treatment as usual, OR = 4.21 (1.37, 12.88), p < . 01, and RP, OR = 4.24 (1.32, 13.65), p < . 01. Trends also favored CM + RP over CM at 6 months, OR = 2.93 (0.94, 9.07), p = . 06, and 9 months, OR = 2.93 (0.94, 9.10), p = . 06. Differences between the conditions were not significant after 9 months. CONCLUSIONS These results suggest CM can improve outcomes in cocaine-dependent patients in intensive outpatient programs who have achieved initial engagement, particularly when it is combined with RP.
The Elasticity of a Single Supercoiled DNA Molecule

Single linear DNA molecules were bound at multiple sites at one extremity to a treated glass cover slip and at the other to a magnetic bead. The DNA was therefore torsionally constrained. A magnetic field was used to rotate the beads and thus to coil and pull the DNA. The stretching force was determined by analysis of the Brownian fluctuations of the bead. Here, the elastic behavior of individual λ DNA molecules over- and underwound by up to 500 turns was studied. A sharp transition was discovered from a low to a high extension state at a force of ∼0.45 piconewtons for underwound molecules and at a force of ∼3 piconewtons for overwound ones. These transitions, probably reflecting the formation of alternative structures in stretched coiled DNA molecules, might be relevant for DNA transcription and replication.
Growth and fabrication of carbon-based three-dimensional heterostructure in through-silicon vias (TSVs) for 3D interconnects

Carbon nanomaterials such as graphene and carbon nanotubes (CNTs) have recently received much attention as potential materials proposed for integration in the future semiconductor technologies because of the advantageous properties particularly in thermal and electrical conductivities. Among them, three-dimensional (3D) pillared CNT-graphene nanostructures are especially attractive due to the desirable out-of-plane and in-plane properties. In this work, a growth and fabrication process flow of CNT-graphene heterostructure as filler of TSV for 3D interconnects was designed and explored. First, experiments for the fabrication of top wafer with unfilled TSV of various diameters (5–50μm) and bottom wafer with patterned graphene electrodes and catalyst deposition were completed successfully. Next, top TSV wafer and bottom graphene wafer were bonded and manually ground followed by wet and dry etching to completely remove the handling wafer and buried oxide, exposing the underlying TSV. CNT growth was conducted for both within TSV and free standing on the graphene. Compared to the free-standing growth with sufficient length (∼334μm) and high density (∼1011 cm−2 estimated), few via holes have CNTs grown and none was completely filled by CNTs. The inhibited growth of CNTs within unfilled TSV can possibly be attributed to several process-engineering steps involved in wafer-bonding, grinding and wet/dry etching. Further modification and optimization of the process steps need to be done in order to attain higher CNT fillings within the unfilled TSV.
Prospects of Voltage-Sourced Converters (VSC) applications in DC transmission systems

Fundamental changes are affecting the power transmission industry. Markets are being deregulated and liberalized, urbanization is continuing around the world accompanied by a constantly growing demand for energy and renewable energy sources are playing an increasingly important role. For these reasons, new and efficient solutions for power transmission are required. This paper will present the prospects and technology issues of the latest developments in Voltage-Sourced Converters (VSC) for advanced power transmission systems. A new technology Modular Multilevel Converters (MMC) will be described and all the benefits of the VSC for transmission systems enhancement will be highlighted.
Bayesian Optimization Combined with Successive Halving for Neural Network Architecture Optimization

The choice of hyperparameters and the selection of algorithms is a crucial part in machine learning. Bayesian optimization methods and successive halving have been applied successfully to optimize hyperparameters automatically. Therefore, we propose to combine both methods by estimating the initial population of incremental evaluation, our variation of successive halving, by means of Bayesian optimization. We apply the proposed methodology to the challenging problem of optimizing neural network architectures automatically and investigate how state of the art hyperparameter optimization methods perform for this task. In our evaluation of these automatic methods, we are able to achieve human expert performance on the MNIST data set but we are not able to achieve similar good results for the CIFAR-10 data set. However, the automated methods find shallow convolutional neural networks that outperform human crafted shallow neural networks with respect to classification error and training time.
Organofluorine Isoselenocyanate Analogues of Sulforaphane: Synthesis and Anticancer Activity

A series of previously unknown sulforaphane analogues with organofluorine substituents bonded to the sulfinyl sulfur atom, an isoselenocyanate moiety in place of the isothiocyanate group, the central sulfur atom in various oxidation states, and different numbers of methylene groups in the central alkyl chain were synthesized and fully characterized. All new compounds were tested for their biological properties in vitro and demonstrated much higher anticancer activity against two breast cancer cell lines than that shown by native sulforaphane; at the same time, the compounds were less toxic for normal cells. The influence of the particular structural changes in the molecules on the cytotoxicity is discussed.
Bayesian Startup Phase Mean Monitoring of an Autocorrelated Process That Is Subject to Random Sized Jumps

In this work we will provide a monitoring scheme for the mean of an autocorrelated process which can experience bidirectional jumps of random size and occurrence and has a steady state. Our interest focuses in the start up phase and short-run scenarios, where traditional SPC techniques fail to provide formal testing. Furthermore, we will provide a framework where prior information regarding the process can be employed. These will be achieved by adopting a Bayesian sequentially updated scheme that will allow inference in an online fashion. The performance of the proposed model will be compared against other methods which can be applied in similar settings. A simulation study along with a real data application from the dairy business will conclude this work. Supplemental files are available online, with technical details and the code for applying the proposed methodology in R.
Stroke associated with cardiac surgery. Determinants, timing, and stroke subtypes.

OBJECTIVE To determine the nature of strokes complicating cardiac surgery. DESIGN A medical record review was undertaken of all patients who underwent cardiac surgery (either coronary bypass, valvular surgery, or both) between January 1990 and July 1995. Univariate and multivariate analyses were done using odds ratios (ORs) and logistic regression. RESULTS A total of 2211 patients underwent cardiac surgery. A total of 44 patients (2%) had postoperative strokes. They were compared with 104 surgical controls. Univariate analysis revealed that the patients with stroke were significantly older and had significantly higher rates of transient ischemic attack, congestive heart failure, and peripheral vascular disease by history. A multivariate logistic regression revealed the significant variables associated with stroke were congestive heart failure (OR, 6.8) and transient ischemic attack (OR, 1.2). Analyses of surgical variables revealed that bypass pump time of more than 120 minutes (OR, 1.40) was the only significant predictor. The majority of strokes (61%) had occurred by postoperative day 2, but 39% occurred between postoperative days 3 to 9. Hemispheric syndromes occurred in 70%, brain stem and cerebellar syndromes in 14%, and lacunar syndromes in 16%. Computed tomographic scans revealed that 29 patients had new infarcts, of which 20 (69%) were territorial, 5 (17%) were small deep, and 4 (14%) were border zone. Hemorrhagic infarction was found in 2 cases (5%). One patient (2.5%) had a cardiorespiratory arrest while undergoing computed tomography. Discharge disposition was good in 88% of patients with stroke (12% with poor outcomes) vs 97% of controls with good outcomes (3% with poor outcomes) (P = .04). CONCLUSIONS Strokes may be delayed following cardiac surgery perhaps because of ongoing risk of embolism or a hypercoagulable state. A surprisingly high proportion of patients have lacunar syndromes or small-deep infarcts shown on computed tomography. Early computed tomographic imaging may be useful to exclude hemorrhage if anticoagulation is considered, but is not without risk in these potentially unstable patients. Greater understanding of risk factors for stroke, timing, and subtypes may ultimately allow identification of patients at particularly high risk for perioperative stroke.
Compact Dual-Band Hybrid Dielectric Resonator Antenna With Radiating Slot

A miniature independent dual-band hybrid dielectric resonator antenna (DRA) fed by a coplanar waveguide (CPW) inductive slot is proposed. In this configuration, the CPW inductive slot performs the functions of an effective radiator and the feeding structure of the DR. By optimizing the structure parameters, the hybrid structure resonates at two different frequencies independently. One is from the DRA with the broadside patterns and the other from the inductive slot with the dipole-like patterns. In order to determine the performance of varying design parameters on bandwidth and resonance frequency, parametric study is carried out using simulation software HFSS and experimental results. The measured and simulated results show excellent agreement.