Miracle-dz/UniFAR-FTUs huggingface dataset:
A Universal Mariner Transposon System for Forward Genetic Studies in the Genus Clostridium

DNA transposons represent an essential tool in the armoury of the molecular microbiologist. We previously developed a catP-based mini transposon system for Clostridium difficile in which the expression of the transposase gene was dependent on a sigma factor unique to C. difficile, TcdR. Here we have shown that the host range of the transposon is easily extended through the rapid chromosomal insertion of the tcdR gene at the pyrE locus of the intended clostridial target using Allele-Coupled Exchange (ACE). To increase the effectiveness of the system, a novel replicon conditional for plasmid maintenance was developed, which no longer supports the effective retention of the transposon delivery vehicle in the presence of the inducer isopropyl β-D-1-thiogalactopyranoside (IPTG). As a consequence, those thiamphenicol resistant colonies that arise in clostridial recipients, following plating on agar medium supplemented with IPTG, are almost exclusively due to insertion of the mini transposon into the genome. The system has been exemplified in both Clostridium acetobutylicum and Clostridium sporogenes, where transposon insertion has been shown to be entirely random. Moreover, appropriate screening of both libraries resulted in the isolation of auxotrophic mutants as well as cells deficient in spore formation/germination. This strategy is capable of being implemented in any Clostridium species.
Insight into the Earthquake Risk Information Seeking Behavior of the Victims: Evidence from Songyuan, China

Efficient risk communication is a vital way to reduce the vulnerability of individuals when facing emergency risks, especially regarding earthquakes. Efficient risk communication aims at improving the supply of risk information and fulfilling the need for risk information by individuals. Therefore, an investigation into individual-level information seeking behavior within earthquake risk contexts is very important for improved earthquake risk communication. However, at present there are very few studies that have explored the behavior of individuals seeking earthquake risk information. Under the guidance of the Risk Information Seeking and Processing model as well as relevant practical findings using the structural equation model, this study attempts to explore the main determinants of an individual’s earthquake risk information seeking behavior, and to validate the mediator effect of information need during the seeking process. A questionnaire-based survey of 918 valid respondents in Songyuan, China, who had been hit by a small earthquake swarm, was used to provide practical evidence for this study. Results indicated that information need played a noteworthy role in the earthquake risk information seeking process, and was detected both as an immediate predictor and as a mediator. Informational subjective norms drive the seeking behavior on earthquake risk information through both direct and indirect approaches. Perceived information gathering capacity, negative affective responses and risk perception have an indirect effect on earthquake risk information seeking behavior via information need. The implications for theory and practice regarding risk communication are discussed and concluded.
Measurement of Antennas and Microwave Components Using Time-Domain Reflectometry of a Voltage Impulse

Band-pass microwave systems such as ultra-wideband antennas are traditionally characterized in the frequency-domain through a vector network analyzer in an anechoic chamber. A recent study proved antennas could be accurately measured in the time-domain using a step-function time-domain reflectometer (TDR), without the need for an anechoic chamber. We propose a new advance in the TDR characterization method. An impulse generator is employed in place of the step generator in a TDR set-up. The advantage conferred by this change is that more energy is available beyond a given frequency than with a step, and so a higher signal-to-noise ratio is achieved. The theoretical result is compared with measurement.
Does Vocational Education Make a Difference? A Review of Previous Research and Reanalyses of National Longitudinal Data Sets.

were as follows Results showed that dropouts were more frequently black, older, less educated and more likely from public programs than graduates. Also, few men and no women who studied for upper level jobs (accountant, computer programmer, and electronic technician) got those jobs, regardless of whether they had graduated from or dropped out of their vocational programs. However, the majority of women who studied for * An even more recent study of employment outcomes associated with postsecondary education below the baccalaureate level, also using.NLS-72 data, has been conducted by Breneman and Nelson (1981). However, we do not attempt to summarize it here for two reasons, First, oily a draft report on this study is currently available. Second, the draft report provides no indication of the relative benefits of vocational postsecondary education, as opposed to other forms of postsecondary education,
Evaluating the impact of sequencing error correction for RNA-seq data with ERCC RNA spike-in controls

Sequencing errors are a major issue for several next-generation sequencing-based applications such as de novo assembly and single nucleotide polymorphism detection. Several error-correction methods have been developed to improve raw data quality. However, error-correction performance is hard to evaluate because of the lack of a ground truth. In this study, we propose a novel approach which using ERCC RNA spike-in controls as the ground truth to facilitate error-correction performance evaluation. After aligning raw and corrected RNA-seq data, we characterized the quality of reads by three metrics: mismatch patterns (i.e., the substitution rate of A to C) of reads aligned with one mismatch, mismatch patterns of reads aligned with two mismatches and the percentage increase of reads aligned to reference. We observed that the mismatch patterns for reads aligned with one mismatch are significantly correlated between ERCC spike-ins and real RNA samples. Based on such observations, we conclude that ERCC spike-ins can serve as ground truths for error correction beyond their previous applications for validation of dynamic range and fold-change response. Also, the mismatch patterns for ERCC reads aligned with one mismatch can serve as a novel and reliable metric to evaluate the performance of error-correction tools.
Population Diversity of Campylobacter jejuni in Poultry and Its Dynamic of Contamination in Chicken Meat

This study aimed to analyse the diversity of the Campylobacter jejuni population in broilers and to evaluate the major source of contamination in poultry meat. Eight rearing cycles over one year provided samples from three different broiler farms processed at the same slaughterhouse. A total of 707 C. jejuni were isolated from cloacal swabs before slaughter and from the breast skin of carcasses after slaughter and after chilling. All suspected Campylobacter colonies were identified with PCR assays and C. jejuni was genotyped by sequence analysis of the flaA short variable region (SVR) and by pulsed-field gel electrophoresis (PFGE) using SmaI enzyme. Phenotypic antibiotic resistance profiles were also assayed using minimal inhibitory concentration (MIC). The flocks carried many major C. jejuni clones possibly carrying over the rearing cycles, but cross contamination between farms may happen. Many isolates were resistant to fluoroquinolones, raising an issue of high public concern. Specific Campylobacter populations could be harboured within each poultry farm, with the ability to contaminate chickens during each new cycle. Thus, although biosecurity measures are applied, with a persistent source of contamination, they cannot be efficient. The role of the environment needs further investigation to better address strategies to control Campylobacter.
Enhanced Algorithms for Estimating Tree Trunk Diameter Using 2D Laser Scanner

Accurate vehicle localization in forest environments is still an unresolved problem. Global navigation satellite systems (GNSS) have well known limitations in dense forest, and have to be combined with for instance laser based SLAM algorithms to provide satisfying accuracy. Such algorithms typically require accurate detection of trees, and estimation of tree center locations in laser data. Both these operations depend on accurate estimations of tree trunk diameter. Diameter estimations are important also for several other forestry automation and remote sensing applications. This paper evaluates several existing algorithms for diameter estimation using 2D laser scanner data. Enhanced algorithms, compensating for beam width and using multiple scans, were also developed and evaluated. The best existing algorithms overestimated tree trunk diameter by ca. 40%. Our enhanced algorithms, compensating for laser beam width, reduced this error to less than 12%.
Emotion Detection from text: A Survey

This survey describes recent works in the field of Emotion Detection from text, being a part of the broader area of Affective Computing. This survey has been inspired on the well-known fact that, despite there is a lot of work on emotional detection systems, a lot of work is expected to be done yet. The increment of these systems is due to the large amount of emotional data available in Social Web. Detecting emotions from text have attracted the attention of many researchers in computational linguistics because it has a wide range of applications, such as suicide prevention or measuring well-being of a community. This paper mainly collects works based on lexical and machine learning approaches and these works are classificated in accordance with the emotional model and the approach used.
Output Sensitivity of Inflation in the Euro Area: Indirect Evidence from Disaggregated Consumer Prices

We investigate output sensitivity of inflation in the euro area through a disaggregated analysis using price indices at the COICOP 4-digit level and compare cyclical sensitivity of a newly created index of cyclically sensitive items (ICSP) with that of headline HICP and core price indices. We also relate the ICSP to the first common factor extracted from the disaggregated prices, which best reflects the common dynamics of the underlying price indices. Our results indicate that two thirds of the items in the euro area HICP are cyclically sensitive. Categories most robustly related to the business cycle are food items (processed and unprocessed), non-durable industrial goods and services related to recreation. Output sensitivity of the ICSP is significantly higher than that of headline inflation. The difference in output sensitivity is most striking between the ICSP and core inflation because of the rather strong cyclical sensitivity of processed and unprocessed food prices (both in prevalence and the estimated parameter of output sensitivity). The index of cyclically sensitive prices is highly correlated with the first common factor. Given the weak factor structure of disaggregated prices, however, we conclude that the domestic business cycle is an important determinant of inflation but it is only one among a number of nearly equally important factors.
The Long-Run Consequences of Living in a Poor Neighborhood

Many social scientists presume that the quality of the neigborhood to which children are exposed affects a variety of long-run social outcomes. I examine the effect on the long-run labor market outcomes of adults who were assigned, when young, to substantially different public housing projects in Toronto. Administrative data are matched to public housing addresses to track children from the program for over 15 years. The main finding is that neighborhood quality plays little role in determining a youth's adult earnings, education attainment, or welfare participation, but does affect exposure to crime. While living in contrasting housing projects cannot explain large variances in labor market outcomes, family differences, as measured by sibling outcome correlations, account for up to 30 percent of the total variance in the data.
Comparison of Real-Time PCR and Culture for Detection of Porphyromonas gingivalis in Subgingival Plaque Samples

ABSTRACT Porphyromonas gingivalis is a major pathogen in destructive periodontal disease in humans. Detection and quantification of this microorganism are relevant for diagnosis and treatment planning. The prevalence and quantity of P. gingivalis in subgingival plaque samples of periodontitis patients were determined by anaerobic culture and real-time PCR amplification of the 16S small-subunit rRNA gene. The PCR was performed with primers and a fluorescently labeled probe specific for the P. gingivalis 16S rRNA gene. By the real-time PCR assay, as few as 1 CFU of P. gingivalis could be detected. Subgingival plaque samples from 259 adult patients with severe periodontitis were analyzed. P. gingivalis was detected in 111 (43%) of the 259 subgingival plaque samples by culture and in 138 (53%) samples by PCR. The sensitivity, specificity, and positive and negative predictive values of the real-time PCR were 100, 94, 94, and 100%, respectively. We conclude that real-time PCR confirms the results of quantitative culture of P. gingivalis and offers significant advantages with respect to the rapidity and sensitivity of detection of P. gingivalis in subgingival plaque samples.
Prior Knowledge Driven Domain Adaptation

The performance of a natural language system trained on one domain often drops significantly when testing on another domain. Therefore, the problem of domain adaptation remains one of the most important natural language processing challenges. While many different domain adaptation frameworks have been proposed, they have ignored one natural resource – the prior knowledge on the new domain. In this paper, we propose a new adaptation framework called Prior knowledge Driven Adaptation (PDA), which takes advantage of the knowledge on the target domain to adapt the model. We empirically study the effects of incorporating prior knowledge in different ways. On the task of part-of-speech tagging, we show that prior knowledge results in 42% error reduction when adapting from news text to biomedical text. On the task of semantic role labeling, when adapting from one news domain to another news domain, prior knowledge gives 25% error reduction for instances of be verbs (unseen in training domain) and 9% error reduction over instances of all verbs.
Ductal Breast Carcinoma Metastatic to the Stomach Resembling Primary Linitis Plastica in a Male Patient

Breast cancer metastases to the gastrointestinal tract are very rare occurrences. Among the histological subtypes of breast cancer, invasive lobular carcinomas have a high capacity of metastasis to uncommon sites including the stomach. Conversely, there has not been sufficient evidence supporting the gastric metastasis of invasive ductal carcinoma. Herein, we report a unique case of metastatic ductal breast carcinoma mimicking primary linitis plastica in a male patient, particularly focusing on the clinical and pathological features of presentation. Moreover, we propose a immunohistochemical panel of selected antibodies including those for cytokeratin 20, cytokeratin 7, estrogen receptor, progesterone receptor, E-cadherin, gross cystic disease fluid protein 15, and GATA binding protein 3 for an accurate differential diagnosis.
Opening Up International Trade in Eastern Europe

Trade with Eastern Europe Carl B. Hamilton and L Alan Winters Previous economic policy in the Soviet Union and Eastern Europe sought to restrict international trade with market economies. Hence, liberalization and reform should now lead to a huge increase in such trade. This will have a major impact both on the reforming economies and on their new trade partners. First, we develop an empirical model of trade flows between existing market economies, and use this to forecast long-run trade flows as the former Soviet Union and Eastern Europe are reabsorbed into the world economy. Second, we provide a more detailed analysis of one key sector, agricultural trade. We compare and contrast three regime changes: reform in the East, admission of the East to the EC CAP and worldwide success on agricultural liberalization in the GATT. Third, we adduce evidence of high quality human capital in Eastern Europe and argue that this will tend to confer a comparative advantage in quite sophisticated products. We conclude by stressing that since trade cannot be permanently and profoundly unbalanced, Western market economies can enjoy potential gains from trade only if they allow market access to emergent producers from the former Soviet Union and Eastern Europe.
Postoperative Outcomes of Mitral Valve Repair for Mitral Restenosis after Percutaneous Balloon Mitral Valvotomy

Background There have been a number of studies on mitral valve replacement and repeated percutaneous mitral balloon valvotomy for mitral valve restenosis after percutaneous mitral balloon valvotomy. However, studies on mitral valve repair for these patients are rare. In this study, we analyzed postoperative outcomes of mitral valve repair for mitral valve restenosis after percutaneous mitral balloon valvotomy. Methods In this study, we assessed 15 patients (mean age, 47.7±9.7 years; 11 female and 4 male) who underwent mitral valve repair between August 2008 and March 2013 for symptomatic mitral valve restenosis after percutaneous mitral balloon valvotomy. The mean interval between the initial percutaneous mitral balloon valvotomy and the mitral valve repair was 13.5±7 years. The mean preoperative Wilkins score was 9.4±2.6. Results The mean mitral valve area obtained using planimetry increased from 1.16±0.16 cm2 to 1.62±0.34 cm2 (p=0.0001). The mean pressure half time obtained using Doppler ultrasound decreased from 202.4±58.6 ms to 152±50.2 ms (p=0.0001). The mean pressure gradient obtained using Doppler ultrasound decreased from 9.4±4.0 mmHg to 5.8±1.5 mmHg (p=0.0021). There were no early or late deaths. Thromboembolic events or infective endocarditis did not occur. Reoperations such as mitral valve repair or mitral valve replacement were not performed during the follow-up period (39±16 months). The 5-year event-free survival was 56.16% (95% confidence interval, 47.467–64.866). Conclusion On the basis of these results, we could not conclude that mitral valve repair could be an alternative for patients with mitral valve restenosis after percutaneous balloon mitral valvotomy. However, some patients presented with results similar to those of mitral valve replacement. Further studies including more patients with long-term follow-up are necessary to determine the possibility of this application of mitral valve repair.
The Guilty Knowledge Test (GKT) as an application of psychophysiology: Future prospects and obstacles.

Introduction The controversy around the polygraph has been focused almost exclusively on the validity and application of the "Control Questions Test" (see, e. little attention has been paid to research and discussions of other methods of psychophysiological detection. In particular, we are referring to the Guilty Knowledge Test (GKT), also called the Concealed Information Test (CIT). , utilizes a series of multiple-choice questions, each having one relevant alternative (e.g., a feature of the crime under investigation) and several neutral (control) alternatives, chosen so that an innocent suspect would not be able to discriminate them from the relevant alternative (Lykken, 1998). Typically, if the suspect's physiological responses to the relevant alternative are consistently larger than to the neutral alternatives, knowledge about the event (e.g., crime) is inferred. As long as information about the event has not leaked out, the probability that an innocent suspect would show consistently larger responses to the relevant than to the neutral alternatives depends only on the number of questions and the number of alternative answers per question. Thus, the rate of false-positive errors (innocent examinees classified as guilty) can be controlled such that maximal protection for the innocent is provided. Indeed, laboratory research has supported this hypothesis, and most studies conducted to estimate the validity of the GKT have reported high accuracy rates, particularly among innocent examinees. For example, Ben-Shakhar and Furedy (1990) reviewed and summarized 10 GKT laboratory experiments and showed that 3 across these studies, 83.9% of 248 guilty examinees and 94.2% of 208 innocent examinees were correctly classified. They acknowledged that the number of studies they analyzed was too small to allow for a statistical examination of the sources of the between-studies variability, but they speculated that the number of GKT questions used is a natural candidate for accounting for at least some of this variability. They noted that the two studies that used the largest number of questions (Bradley & Ainsworth, 1984; Bradley & Warfield, 1984, nine and ten, respectively) demonstrated the largest rates of correct classifications. Ben-Shakhar and Furedy (1990) concluded that with a sufficiently large number of GKT questions the method could be used quite efficiently. More recently, Elaad (1998) reviewed 15 mock crime studies attempting to estimate the validity of the GKT and reached similar conclusions. Elaad (1998) estimated the accuracy rates among guilty and innocent examinees as 80.6% and 95.9%, respectively, and noted that in 11 of these 15 …
miR-145 inhibits tumor growth and metastasis by targeting metadherin in high-grade serous ovarian carcinoma

High-grade serous ovarian carcinoma (HGSOC), the most common and aggressive subtype of epithelial ovarian cancer, is characterized by TP53 mutations and genetic instability. Using miRNA profiling analysis, we found that miR-145, a p53 regulated miRNA, was frequently down-regulated in HGSOC. miR-145 down-regulation was further validated in a large cohort of HGSOCs by qPCR. Overexpression of miR-145 in ovarian cancer cells significantly suppressed proliferation, migration and invasion in vitro and inhibited tumor growth and metastasis in vivo. Metadherin (MTDH) was subsequently identified as a direct target of miR-145, and was found to be significantly up-regulated in HGSOC. Furthermore, overexpression of MTDH rescued the inhibitory effects of miR-145 in ovarian cancer cells. Finally, we found that high level of MTDH expression correlated with poor prognosis of HGSOC. Therefore, lack of suppression of MTDH by miR-145 when p53 is dysfunctional leads to increased tumor growth and metastasis of HGSOC. Our study established a new link between p53, miR-145 and MTDH in the regulation of tumor growth and metastasis in HGSOC.
The Localization of Deoxyribonucleic Acid in Escherichia coli

The purpose of this study was to localize deoxyribonucleic acid in a bacterial cell. Tri t iumlabelled thymidine was employed to identify the D N A and radioautography was chosen as the method of detection. To insure a high percentage of labelling, a thymine-requiring strain of Escherichia coli, the strain 15 T , was used (1). When whole cells are studied the localization of the label is limited by the resolution of the autograph procedure which, even for tritium, is about 1.5 micron, the same order of magnitude as the cell itself. This difficulty was overcome by studying the distribution of label among thin cross-sections of the cells. The thinness of the sections is then the determining factor in establishing the precise location of isotopic material in the cell.