Miracle-dz/UniFAR-FTUs huggingface dataset:
Engineering Central Metabolic Pathways for High-Level Flavonoid Production in Escherichia coli

ABSTRACT The identification of optimal genotypes that result in improved production of recombinant metabolites remains an engineering conundrum. In the present work, various strategies to reengineer central metabolism in Escherichia coli were explored for robust synthesis of flavanones, the common precursors of plant flavonoid secondary metabolites. Augmentation of the intracellular malonyl coenzyme A (malonyl-CoA) pool through the coordinated overexpression of four acetyl-CoA carboxylase (ACC) subunits from Photorhabdus luminescens (PlACC) under a constitutive promoter resulted in an increase in flavanone production up to 576%. Exploration of macromolecule complexes to optimize metabolic efficiency demonstrated that auxiliary expression of PlACC with biotin ligase from the same species (BirAPl) further elevated flavanone synthesis up to 1,166%. However, the coexpression of PlACC with Escherichia coli BirA (BirAEc) caused a marked decrease in flavanone production. Activity improvement was reconstituted with the coexpression of PlACC with a chimeric BirA consisting of the N terminus of BirAEc and the C terminus of BirAPl. In another approach, high levels of flavanone synthesis were achieved through the amplification of acetate assimilation pathways combined with the overexpression of ACC. Overall, the metabolic engineering of central metabolic pathways described in the present work increased the production of pinocembrin, naringenin, and eriodictyol in 36 h up to 1,379%, 183%, and 373%, respectively, over production with the strains expressing only the flavonoid pathway, which corresponded to 429 mg/liter, 119 mg/liter, and 52 mg/liter, respectively.
Multi-modal Semantic Place Classification

The ability to represent knowledge about space and its position therein is crucial for a mobile robot. To this end, topological and semantic descriptions are gaining popularity for augmenting purely metric space representations. In this paper we present a multi-modal place classification system that allows a mobile robot to identify places and recognize semantic categories in an indoor environment. The system effectively utilizes information from different robotic sensors by fusing multiple visual cues and laser range data. This is achieved using a high-level cue integration scheme based on a Support Vector Machine (SVM) that learns how to optimally combine and weight each cue. Our multi-modal place classification approach can be used to obtain a real-time semantic space labeling system which integrates information over time and space. We perform an extensive experimental evaluation of the method for two different platforms and environments, on a realistic off-line database and in a live experiment on an autonomous robot. The results clearly demonstrate the effectiveness of our cue integration scheme and its value for robust place classification under varying conditions.
THE USE OF PEER ASSESSMENT AND REFLECTIVE DISCUSSION TO IMPROVE STUDENT PARTICIPATION AND ORAL PRESENTATION PERFORMANCE IN A TECHNICAL COMMUNICATION CLASSROOM

21st century classrooms are gearing towards student-centered classrooms where learning is deemed to be more meaningful when students are actively engaged in their learning. In a bid to create more student-centered classrooms, the researcher decided to explore the use of peer assessments and reflective discussions in a Technical Communication classroom as part of an action research to improve student participation and oral presentation performance among thirty 18-year-old diploma students studying in Universiti Tun HusseinOnn Malaysia. The study revealed students in general have a positive perception towards the use of peer assessment and reflective discussion in the classroom. In addition to increased participation and attentiveness in class, improvement in oral presentation performance for the majority of the students (73.3%) was observed. This research shows that with careful planning and scaffolding, positive results can be achieved by employing these two techniques in the teaching and learning process.
Too Many ‘Friends,’ Too Few ‘Likes’? Evolutionary Psychology and ‘Facebook Depression’

Psychologists (and subsequently the media) have defined ‘Facebook depression’ as the affective result of spending too much time on the social networking site (Selfhout et al., 2009; Kross et al., 2013). Some social psychologists have denied that Facebook is causally implicated in any such negative affect (Jelenchick et al., 2013). This article argues that if we want to understand modern mass media and new social media, we need a better understanding of the (old) psychology bequeathed us by natural selection (Barkow et al., 2012). Disentangling the relationship between social media and depression using evolutionary social competition theories of depression, I argue that the mismatch between current social milieu and the environment of evolutionary adaption affords some predictions about the use of social media as a trigger for mild depression or dysphoria. I hypothesize that users of Facebook may be more susceptible to causal triggers for mild depression under the following (specific) circumstances: (a) the greater the number of ‘friends’ that the user has online; (b) the greater the time that the user spends reading updates from this wide pool of friends; (c) the user does so regularly; and (d) the content of the updates tends to a bragging nature. I hypothesize that the frequency and the number of displays of higher status cues observed by the user may incur the perception of low relative social value among users (automatically triggering this response). The article concludes with directions for future research on the behavioral and cognitive effects of social media sites such as Facebook.
Siamese CBOW: Optimizing Word Embeddings for Sentence Representations

We present the Siamese Continuous Bag of Words (Siamese CBOW) model, a neural network for efficient estimation of high-quality sentence embeddings. Averaging the embeddings of words in a sentence has proven to be a surprisingly successful and efficient way of obtaining sentence embeddings. However, word embeddings trained with the methods currently available are not optimized for the task of sentence representation, and, thus, likely to be suboptimal. Siamese CBOW handles this problem by training word embeddings directly for the purpose of being averaged. The underlying neural network learns word embeddings by predicting, from a sentence representation, its surrounding sentences. We show the robustness of the Siamese CBOW model by evaluating it on 20 datasets stemming from a wide variety of sources.
The cognitive neuroscience of human memory since H.M.

Work with patient H.M. , beginning in the 1950s, established key principles about the organization of memory that inspired decades of experimental work. Since H.M. , the study of human memory and its disorders has continued to yield new insights and to improve understanding of the structure and organization of memory. Here we review this work with emphasis on the neuroanatomy of medial temporal lobe and diencephalic structures important for memory, multiple memory systems, visual perception, immediate memory, memory consolidation, the locus of long-term memory storage, the concepts of recollection and familiarity, and the question of how different medial temporal lobe structures may contribute differently to memory functions.
Population Risk of Syringe Reuse: Estimating the Probability of Transmitting Bloodborne Disease

Background. In 2008, the Medical Officer of Health at Alberta Health Services (Edmonton, Canada) was notified that, in some practice settings, a syringe was used to administer medication through the side port of an intravenous circuit and then the syringe, with residual drug, was used to administer medication to other patients in the same manner. This practice has been implicated in several outbreaks of bloodborne infection in hospital and clinic settings. Methods. A risk assessment model was developed to predict the risk of a patient contracting a bloodborne viral infection from the practice. The risk of transmission was defined as the product of 5 factors: (1) the population prevalence of a specific bloodborne pathogen, (2) the probability of finding a viral bloodborne pathogen in an intravenous circuit, (3) the rate of syringe reuse, (4) the probability of causing disease given a bloodborne pathogen exposure, and (5) the susceptibility of the exposed person. Results. The risk was modeled first with consistent use of the proximal port of the intravenous circuit. The risk of transmission of hepatitis B virus was approximately 12–53 transmission events per 1,000,000 exposure events for a range of practice probabilities (ie, frequency of the risk practice) from 20% to 80%, respectively. The risk of transmission of hepatitis C virus was approximately 1.0–4.3 transmission events per 1,000,000 exposure events for the same practice probability range, and the risk of transmission of human immunodeficiency virus was approximately 0.03–0.15 transmission events per 1,000,000 exposure events for the same practice probability range. The use of the distal port was associated with a 10-fold decrease in the risk. Conclusions. Practitioners must practice safe, aseptic injection techniques. The model presented here can be used to estimate the risk of disease transmission in situations where reuse has occurred and can serve as a framework for informing public health action.
Striving for Simplicity: The All Convolutional Net

Most modern convolutional neural networks (CNNs) used for object recognition are built using the same principles: Alternating convolution and max-pooling layers followed by a small number of fully connected layers. We re-evaluate the state of the art for object recognition from small images with convolutional networks, questioning the necessity of different components in the pipeline. We find that max-pooling can simply be replaced by a convolutional layer with increased stride without loss in accuracy on several image recognition benchmarks. Following this finding -- and building on other recent work for finding simple network structures -- we propose a new architecture that consists solely of convolutional layers and yields competitive or state of the art performance on several object recognition datasets (CIFAR-10, CIFAR-100, ImageNet). To analyze the network we introduce a new variant of the "deconvolution approach" for visualizing features learned by CNNs, which can be applied to a broader range of network structures than existing approaches.
Optimizing Human-Computer Interaction for the Electronic Commerce Environment

The paper investigates the interaction effects between the search strategy of software agents and the subject’s product class knowledge. The experimental study consists of a 2 (product class knowledge: high, low) x 4 (agent search strategy: elimination by aspects (EBA), weighted average method (WAD), profile building (PROFILE) , and simple hypertext (HYPERTEXT)) design with product class knowledge as the between groups variable. Significant differences were found for affective reactions of the subjects toward the agent/application depending on the level of product class knowledge possessed by the subjects. Subjects with high product class knowledge had more positive affective reactions towards agents/applications which used the WAD and EBA strategies as compared to the profile building strategy. Subjects with low product class knowledge had more positive affective reactions to agents/applications which used the profile building strategy as compared to the EBA and WAD strategies. When the systems were modified to increase the amount of information provided and to increase the degree of control provided to the subjects, their affective reactions to the agents/applications were found to be different from the original study. Subjects responded more positively to the previously "less preferred" strategy, thus weakening the interaction effect. This research is done in the context of consumers searching for information on the World Wide Web prior to the purchase of cars.
A Role for Top-Down Attentional Orienting during Interference between Global and Local Aspects of Hierarchical Stimuli

Various models of selective attention propose that greater attention is allocated toward target stimuli when conflicting distracters make selection more difficult, but compelling evidence to support this view is scarce. In the present experiment, 15 participants performed a cued global/local selective attention task while brain activity was recorded with event-related functional magnetic resonance imaging. The presence of conflicting versus nonconflicting distracters during target processing activated regions of frontal, parietal, and visual cortices that were also activated when participants oriented attention in response to global- and local-task cues. These findings support models in which conflict between target and distracter stimuli is resolved by more selectively focusing attention upon target stimuli.
Rapid Evaluation of Speech Representations for Spoken Term Discovery

Acoustic front-ends are typically developed for supervised learning tasks and are thus optimized to minimize word error rate, phone error rate, etc. However, in recent efforts to develop zero-resource speech technologies, the goal is not to use transcribed speech to train systems but instead to discover the acoustic structure of the spoken language automatically. For this new setting, we require a framework for evaluating the quality of speech representations without coupling to a particular recognition architecture. Motivated by the spoken term discovery task, we present a dynamic time warping-based framework for quantifying how well a representation can associate words of the same type spoken by different speakers. We benchmark the quality of a wide range of speech representations using multiple frame-level distance metrics and demonstrate that our performance metrics can also accurately predict phone recognition accuracies.
Environmental Nutrient Supply Directly Alters Plant Traits but Indirectly Determines Virus Growth Rate

Ecological stoichiometry and resource competition theory both predict that nutrient rates and ratios can alter infectious disease dynamics. Pathogens such as viruses hijack nutrient rich host metabolites to complete multiple steps of their epidemiological cycle. As the synthesis of these molecules requires nitrogen (N) and phosphorus (P), environmental supply rates, and ratios of N and P to hosts can directly limit disease dynamics. Environmental nutrient supplies also may alter virus epidemiology indirectly by changing host phenotype or the dynamics of coinfecting pathogens. We tested whether host nutrient supplies and coinfection control pathogen growth within hosts and transmission to new hosts, either directly or through modifications of plant tissue chemistry (i.e., content and stoichiometric ratios of nutrients), host phenotypic traits, or among-pathogen interactions. We examined two widespread plant viruses (BYDV-PAV and CYDV-RPV) in cultivated oats (Avena sativa) grown along a range of N and of P supply rates. N and P supply rates altered plant tissue chemistry and phenotypic traits; however, environmental nutrient supplies and plant tissue content and ratios of nutrients did not directly alter virus titer. Infection with CYDV-RPV altered plant traits and resulted in thicker plant leaves (i.e., higher leaf mass per area) and there was a positive correlation between CYDV-RPV titer and leaf mass per area. CYDV-RPV titer was reduced by the presence of a competitor, BYDV-PAV, and higher CYDV-RPV titer led to more severe chlorotic symptoms. In our experimental conditions, virus transmission was unaffected by nutrient supply rates, co-infection, plant stoichiometry, or plant traits, although nutrient supply rates have been shown to increase infection and coinfection rates. This work provides a robust test of the role of plant nutrient content and ratios in the dynamics of globally important pathogens and reveals a more complex relationship between within-host virus growth and alterations of plant traits. A deeper understanding of the differential effects of environmental nutrient supplies on virus epidemiology and ecology is particularly relevant given the rapid increase of nutrients flowing into Earth's ecosystems as a result of human activities.
One History or Many Herstories? Gender politics and the history of physiotherapy's origins in the nineteenth and early twentieth century

Compared to other professional groups in the healthcare sector, physiotherapists seldom use historical references in their efforts to define or empower their profession's identity. This article shows that the gender politics of physiotherapy is central in attempting to answer why this is the case. As illustrated, the gender mechanisms of the professionalizing of physiotherapy consisted of two co-existent developments—homosocial, or professional rivalry between men of differing professional scientific backgrounds—and heterosocial, where women competed against men in order to re-legitimize their professional occupation. Focusing mainly on Sweden but with references to England for comparison, the article brings together masculinity studies with women's history in order to show how the demasculinization of physiotherapy as a profession benefitted women in certain ways while disadvantaging male physiotherapists.
Noninvasive determination of genome size and ploidy level in fishes by flow cytometry: detection of triploid Poecilia formosa.

BACKGROUND In order to understand the evolutionary significance of single triploids among the mostly diploid Poecilia formosa we have developed a simple, noninvasive technique for DNA content and ploidy determination. METHODS From dorsal fin clips of 14 different fish species single cell suspensions were obtained by chopping the material in 2.1% citric acid/0.5% Tween20, passing it through a 0. 6-gauge needle and incubating it for 20 min at room temperature (RT) with gentle agitation. After overnight fixation in 70% ethanol, the cells were treated with 1ml 0.5% pepsin/0.1 M HCl for 15 min at RT before adding DAPI to a final volume of 2 ml. The cells were stained for 1-3 h and then analyzed by flow cytometry. RESULTS We obtained good measurements with CVs ranging from 1.23% to 3.36%. The poeciliid species measured contain from 1.6 to 2.0 pg/nucleus, Oryzias latipes (Medaka) exhibits a nuclear DNA content of 2.2 pg, Danio rerio (zebrafish) 4.6 pg, Tetraodon fluviatilis (freshwater fugu) 0.70 pg. All values except zebrafish are in good agreement with the literature. CONCLUSIONS The identification of living specimens of different ploidy for breeding experiments, behavioral studies and tissue transplantations is now made possible. With slight modifications the method can be extended to a field technique, providing therefore a useful tool for a variety of researchers.
Reversible expression of flagella in Campylobacter jejuni

Campylobacter jejuni 81116 and A3249 undergo a bidirectional transition between flagellated (Fla+) and aflagellated (Fla-) phenotypes. When measured in culture medium, the Fla+----Fla- transition occurred at a rate of 3.1 X 10(-3) to 5.9 X 10(-3) per cell per generation, and the Fla- to Fla+ transition occurred at a rate of 4.0 X 10(-7) to 8.0 X 10(-7) per cell per generation. However, passage through a rabbit intestine markedly favored the Fla+ phenotype.
On inference of control-based imputation for analysis of repeated binary outcomes with missing data

ABSTRACT Missing data are common in longitudinal clinical trials. How to handle missing data is critical for both sponsors and regulatory agencies to assess treatment effect from the trials. Recently, a control-based imputation has been proposed, where the missing data are imputed based on the assumption that patients who discontinued the test drug will have a similar response profile to the patients in the control group. Under control-based imputation, the variance estimation may be biased using Rubin’s formula which could produce biased statistical inferences. We evaluate several statistical methods for obtaining appropriate variances under control-based imputation for analysis of repeated binary outcomes with monotone missing data and show that both the analytical method developed by Robins & Wang and the nonparametric bootstrap method provide more appropriate variance estimates under various simulation settings. We use the methods in an application of an antidepressant Phase III clinical trial and give discussion and recommendations on method performance and preference.
Rotavirus disease, but not infection and development of intestinal histopathological lesions, is age restricted in rabbits.

The rabbit model of rotavirus infection has proved to be useful for assessing active immunity and protection after infection or vaccination with virus or virus-like particles. One limitation of the rabbit model is that after experimental infection of rabbits, clinical diarrhea is not routinely induced. Lack of diarrhea in the rabbit model has been proposed to be due to the fluid absorptive capability of the cecum or attenuation of virus strains through tissue culture adaptation. To test whether a wild-type lapine rotavirus strain BAP (BAPwt) isolated from diarrheic rabbits would cause disease on passage in rabbits, 1-, 2-, 10-, and 16-week-old rabbits were orally inoculated with BAPwt, its tissue culture-adapted counterpart strain (BAP-2), tissue culture-adapted lapine strain ALA, or PBS. Lapine rotavirus infection in 1-week-old, but not >/=2-week-old, rabbits resulted in the development of disease characterized by soft, wet, yellow-to-brownish-green partially formed-to-liquid stools observed only at the time of virus antigen shedding. The level and duration of virus shedding after infection were prolonged in 1-week-old rabbits compared with rabbits >/=2 weeks of age. Although diarrhea was not observed beyond the first 2 weeks of life, histopathological changes, including villus shortening and fusion, increased vacuolation of epithelial cells, and mononuclear infiltration of the lamina propria, were observed throughout the small intestine between 12 and 120 h after ALA infection in 1-week-old, 1- to 2-month-old, and 11-month-old rabbits. In 11-month-old rabbits, onset of intestinal damage appeared to be slightly delayed, was less severe, and was not observed in the duodenum. There were no differences in the immune responses to rotavirus infection in rabbits of different age groups (1 week to 5 years of age). All lapine rotavirus-inoculated rabbits seroconverted and were protected from virus challenge at 28 days postinoculation. Like in mice, rotavirus disease is age restricted in rabbits.
Aflatoxin B1 contamination in sunflower oil collected from sunflower oil refinery situated in Karnataka

In the present study, the aflatoxin B1 contamination at various stages of oil refining and in refined oil were carried out. This was subsequently compared with commercial vegetable oil samples. Among the 23 different sunflower oil samples were tested, 10 of them showed positive results to AFB1 and the remaining 13 showed negative results to AFB1. All the refined oil samples were free from AFB1 contamination.