Miracle-dz/UniFAR-FTUs huggingface dataset:
New Construct Approaches for Efficient Gene Silencing in Plants

An important component of conventional sense, antisense, and double-strand RNA-based gene silencing constructs is the transcriptional terminator. Here, we show that this regulatory element becomes obsolete when gene fragments are positioned between two oppositely oriented and functionally active promoters. The resulting convergent transcription triggers gene silencing that is at least as effective as unidirectional promoter-to-terminator transcription. In addition to short, variably sized, and nonpolyadenylated RNAs, terminator-free cassette produced rare, longer transcripts that reach into the flanking promoter. These read-through products did not influence the efficacy and expression levels of the neighboring hygromycin phosphotransferase gene. Replacement of gene fragments by promoter-derived sequences further increased the extent of gene silencing. This finding indicates that genomic DNA may be a more efficient target for gene silencing than gene transcripts.
Contextual Authority Tagging: Expertise Location via Social Labeling

Terrell G. Russell: Contextual Authority Tagging: Expertise Location via Social Labeling. (Under the direction of Deborah Barreau and Gary Marchionini.) This study investigates the possibility of a group of people making explicit their tacit knowledge about one another’s areas of expertise. Through a design consisting of a modified Delphi Study, group members are asked to label both their own and each others’ areas of expertise over the course of five rounds. Statistical analysis and qualitative evaluation of 10 participating organizations suggest they were successful and that, with simple keywords, group members can convey the salient areas of expertise of their colleagues to a degree that is deemed“similar”and of“high quality” by both third parties and those being evaluated. More work needs to be done to make this information directly actionable, but the foundational aspects have been identified. In a world with a democratization of voices from all around and increasing demands on our time and attention, this study suggests that simple, aggregated third-party expertise evaluations can augment our ongoing struggle for quality information source selection. These evaluations can serve as loose credentials when more expensive or heavyweight reputation cues may not be viable.
Exploiting Knowledge Bases for Multilingual and Cross-lingual Semantic Annotation and Search

The amount of entities in large knowledge bases (KBs) has been increasing rapidly, making it possible to propose new ways of intelligent information access. In addition, there is an impending need for systems that can enable multilingual and cross-lingual information access. In this work, we firstly demonstrate X-LiSA, an infrastructure for multilingual and cross-lingual semantic annotation, which supports interfaces for annotating unstructured text in different languages using resources from KBs. Based on X-LiSA, we demonstrate XKnowSearch! , a novel system for multilingual and cross-lingual semantic search, which supports keyword search on textual data by exploiting its semantics.
Districting for Arc Routing

This paper proposes a heuristic for districting problems arising in an arc routing context. The aim is to design districts by amalgamating edges of a graph as opposed to cells. Solutions must satisfy two hard criteria (complete and exclusive assignment as well as connectedness) and several soft criteria (balance, small deadheading, local compactness, and global compactness). The latter criteria are amalgamated into a weighted objective. The proposed heuristic applies a construction procedure followed by a tabu search improvement phase in which several subroutines are defined and selected according to a roulette wheel mechanism, as in adaptive large neighborhood search. Extensive tests conducted on instances derived from real-world street data confirm the efficiency of the proposed methodology.
Subspace Clustering of Categorical and Numerical Data With an Unknown Number of Clusters

In clustering analysis, data attributes may have different contributions to the detection of various clusters. To solve this problem, the subspace clustering technique has been developed, which aims at grouping the data objects into clusters based on the subsets of attributes rather than the entire data space. However, the most existing subspace clustering methods are only applicable to either numerical or categorical data, but not both. This paper, therefore, studies the soft subspace clustering of data with both of the numerical and categorical attributes (also simply called mixed data for short). Specifically, an attribute-weighted clustering model based on the definition of object-cluster similarity is presented. Accordingly, a unified weighting scheme for the numerical and categorical attributes is proposed, which quantifies the attribute-to-cluster contribution by taking into account both of intercluster difference and intracluster similarity. Moreover, a rival penalized competitive learning mechanism is further introduced into the proposed soft subspace clustering algorithm so that the subspace cluster structure as well as the most appropriate number of clusters can be learned simultaneously in a single learning paradigm. In addition, an initialization-oriented method is also presented, which can effectively improve the stability and accuracy of $k$ -means-type clustering methods on numerical, categorical, and mixed data. The experimental results on different benchmark data sets show the efficacy of the proposed approach.
Micronutrient intake in relation to all-cause mortality in a prospective Danish cohort

Background Few studies have considered source-specific micronutrient intake in relation to mortality under the consideration that dietary and supplemental intake could exhibit different effects. Objective To evaluate the association between intake of vitamin C, E, folate, beta-carotene from diet and supplements, and overall mortality. Furthermore, to examine effect modification by smoking, alcohol intake, and BMI and to investigate if the effect of supplement use differs with dietary micronutrient intake. Methods and Material In a prospective cohort study of 55,453 middle-aged Danes, information regarding diet, supplement use, and lifestyle was collected through questionnaires. During follow-up, 6,767 deaths were identified and incidence rate ratios (IRRs) of mortality related to micronutrient intake were calculated using Cox proportional hazards models. Results The present study found no effect of dietary vitamin C, E, folate, or beta-carotene in relation to mortality. In contrast, supplemental folic acid was associated with a significantly increased mortality, whereas no other micronutrient supplement was associated with mortality. Effect modification by smoking and alcohol intake, but not BMI, was suggested in relation to some dietary micronutrients. The effect of supplements did not differ in groups defined by dietary micronutrient intake. Conclusion This study suggests no effect of dietary micronutrients in relation to overall mortality. Supplemental folic acid was found to be associated with increased mortality, but further studies are required. No other supplemental micronutrient was associated with mortality.
Delayed Hyperbaric Oxygen Therapy Promotes Neurogenesis Through Reactive Oxygen Species/Hypoxia-Inducible Factor-1&agr;/&bgr;-Catenin Pathway in Middle Cerebral Artery Occlusion Rats

Background and Purpose— Hyperbaric oxygen (HBO) has been reported to be neuroprotective and to improve neurofunctional outcomes in acute stroke. However, it is not clear whether delayed HBO enhances endogenous neurogenesis and promotes neurofunctional recovery. The aim of this study is to evaluate the effects of delayed HBO therapy on neurogenesis and its potential mechanisms. Methods— One hundred eleven male Sprague–Dawley rats that survived for 7 days from 2 hours of middle cerebral artery occlusion and reperfusion were used. Delayed and multiple HBO were administrated beginning at 7 days after middle cerebral artery occlusion and lasting for 42 days with 3 HBO-free intervals (5 days each). Motor sensory deficits were measured by foot-fault test, and learning and memory abilities were evaluated by Morris water maze. Neurogenesis was examined by double immunostaining of bromodeoxyuridine and doublecortin, bromodeoxyuridine and neuronal nuclei at day 42. For mechanism studies, inhibitors for reactive oxygen species (ROS), hypoxia-inducible factor (HIF)-1&agr;, and &bgr;-catenin were administrated, and the levels of ROS, HIF-1&agr;, &bgr;-catenin, lymphoid enhancer–binding factor-1, T-cell factor-1, neurogenin-1, doublecortin, and synapsin-1 were assessed by ELISA or Western blot at day 14. Results— Delayed HBO treatment promoted neurogenesis and improved neurofunctional recovery at day 42, and the improvements were reversed by inhibition of ROS and HIF-1&agr;. Delayed HBO significantly increased ROS and HIF-1&agr;, and upregulated the expression of neurogenin-1, doublecortin, and synapsin-1. Inhibition of ROS and HIF-1&agr; removed the effects of delayed HBO. Conclusions— Delayed HBO enhanced endogenous neurogenesis and improved neurofunctional recovery in the late-chronic phase of stroke possibly mediated by ROS/HIF-1&agr;/&bgr;-catenin pathway. Delayed HBO may serve as an alternative treatment to improve long-term recovery of stroke survivors.
Assessment of Probiotic Viability during Cheddar Cheese Manufacture and Ripening Using Propidium Monoazide-PCR Quantification

The use of a suitable food carrier such as cheese could significantly enhance probiotic viability during storage. The main goal of this study was to assess viability of commercial probiotic strains during Cheddar cheesemaking and ripening (4–6 months) by comparing the efficiency of microbiological and molecular approaches. Molecular methods such as quantitative PCR (qPCR) allow bacterial quantification, and DNA-blocking molecules such as propidium monoazide (PMA) select only the living cells’ DNA. Cheese samples were manufactured with a lactococci starter and with one of three probiotic strains (Bifidobacterium animalis subsp. lactis BB-12, Lactobacillus rhamnosus RO011, or Lactobacillus helveticus RO052) or a mixed culture containing B. animalis subsp. lactis BB-12 and L. helveticus RO052 (MC1), both lactobacilli strains (MC2), or all three strains (MC3). DNA extractions were then carried out on PMA-treated and non-treated cell pellets in order to assess PMA treatment efficiency, followed by quantification using the 16S rRNA gene, the elongation factor Tu gene (tuf) or the transaldolase gene (tal). Results with intact/dead ratios of bacteria showed that PMA-treated cheese samples had a significantly lower bacterial count than non-treated DNA samples (P < 0.005), confirming that PMA did eliminate dead bacteria from PCR quantification. For both quantification methods, the addition of probiotic strains seemed to accelerate the loss of lactococci viability in comparison to control cheese samples, especially when L. helveticus RO052 was added. Viability of all three probiotic strains was also significantly reduced in mixed culture cheese samples (P < 0.0001), B. animalis subsp. lactis BB-12 being the most sensitive to the presence of other strains. However, all probiotic strains did retain their viability (log 9 cfu/g of cheese) throughout ripening. This study was successful in monitoring living probiotic species in Cheddar cheese samples through PMA-qPCR.
Molecular characterisation and biomass and metabolite production of Lactobacillus reuteri LPB P01–001: A potential probiotic

Lactobacillus reuteri LPB P01–001 was isolated from the gastrointestinal tract of wild swine and was characterised by biochemical testing and sequencing of gene 16S rRNA. A simple and low-cost culture medium based on cane sugar (2.5% p/v) and yeast extract (1% p/v) was used in the production of this probiotic. The fermentative conditions were a) pH control at 6.5 and b) no pH control; both were set at 37°C in a 12 L slightly stirred tank bioreactor. Fermentation parameters such as the specific growth rate, productivity and yield of biomass, lactic and acetic acid levels were determined. L. reuteri LPB P01–001 behaves as an aciduric bacteria because it grows better in a low pH medium without pH control. However, the lactic acid production yield was practically half (9.22 g.L-1) of that obtained under a constant pH of 6.5, which reached 30.5 g.L-1 after 28 hours of fermentation. The acetic acid production was also higher under pH-controlled fermentation, reaching 10.09 g.L-1after 28 hours of fermentation. These parameters may raise the interest of those committed to the efficient production of a probiotic agent for swine.
Towards Cross-language Application of Dependency Grammar

This paper discusses the adaptation of the Stanford typed dependency model (de Marneffe and Manning 2008), initially designed for English, to the requirements of typologically different languages from the viewpoint of practical parsing. We argue for a framework of functional dependency grammar that is based on the idea of parallelism between syntax and semantics. There is a twofold challenge: (1) specifying the annotation scheme in order to deal with the morphological and syntactic peculiarities of each language and (2) maintaining cross- linguistically consistent annotations to ensure homogenous analysis for similar linguistic phenomena. We applied a number of modifications to the original Stanford scheme in an attempt to capture the language-specific grammatical features present in heterogeneous CoNLL-encoded data sets for German, Dutch, French, Spanish, Brazilian Portuguese, Russian, Polish, Indonesian, and Traditional Chinese. From a multilingual perspective, we discuss features such as subject and object verb complements, comparative phrases, expletives, reduplication, copula elision, clitics and adpositions.
Function of Various Intestinal Bacteria in Converting Germfree Mice to the Normal State

Earlier work had shown that a collection of anaerobic bacteria, in conjunction with facultative anaerobes, may be implanted into germfree mice, thereby rendering the animals “normal” with respect to a variety of parameters tested. The present experiments indicate that a different collection of anaerobic bacteria, isolated from the cecum of normal mice, was necessary to convert germfree mice to the “normal” state when the animals were fed a crude diet, rather than the refined food which had been used in the earlier work. The nature and level of short-chain fatty acids associated with various natural or synthetic “normal” floras in the ceca of mice did not always correlate with the Escherichia coli population present, indicating that fatty acids were not the sole agents inhibiting bacterial populations in the intestine. Experiments are reported which indicate that intestinal anaerobes may under certain circumstances be sufficient to control the populations of other intestinal bacteria such as E. coli. In other instances, such as control of Shigella populations in the mouse intestine, intestinal anaerobes appeared to act synergistically with an E. coli strain, in spite of the fact that the population of the latter was itself suppressed by the anaerobes.
Rapid isolation of bacteria from septicemic patients by use of an antimicrobial agent removal device

The new Antimicrobial Removal Device increased the efficacy of conventional methods for isolating bacteria from the blood of septicemic patients. The device removes as much as 100 microgram of antibiotics per ml from whole blood without a significant decrease in bacteria. Of 51 patients studied, 31 yielded positive cultures, and the Antimicrobial Removal Device permitted earlier isolation of the causative agent from blood. Subcultured within the first 12 h yielded 12 positive isolates, as the 31 agents were isolated more rapidly after Antimicrobial Removal Device permitted earlier isolation of the causative agent from blood. Subcultures within the first 12 h yielded 12 positive isolates, as compared to 2 when subcultured without processing in the device. Overall, 21 of the 31 agents were isolated more rapidly after Antimicrobial Removal Device treatment, and four samples were positive only after such treatment. One agent was not isolated in the treated culture.
SERUM PROTEINS AND BLOOD ALPHA AMINO NITROGEN IN CEREBRAL PALSY

The mean serum proteins of 30 children over the age of 3 suffering from cerebral palsy was 7.20 with a standard deviation of 0.49 g. per 100 ml. No difference was found between children with the spastic and athetoid types of cerebral palsy. The electrophoretic pattern of the serum proteins did not differ in the two types, but the alpha 2 globulin diminished significantly with increasing age. There was no difference that could be considered “clinically significant” between the total serum proteins or their electrophoretic pattern in children with cerebral palsy and in four published series of normal children. The plasma and whole blood alpha amino nitrogen showed no significant difference between the two types of cerebral palsy.
Le prix derrière l’écran : étude netnographique d’une communauté virtuelle professionnelle de Pricing Managers

Tout comme les consommateurs, les professionnels du marketing interagissent à travers des communautés virtuelles. Pour des chargés d’étude, ces communautés sont intéressantes car elles permettent de répondre à des questions concrètes en s’appuyant sur les représentations et les opinions d’experts. La netnographie, une méthode qualitative développée par Kozinets, et adaptée à l’analyse de communautés virtuelles professionnelles, est ici utilisée pour observer la liste de diffusion de la Professional Pricing Society (la Pricinglist ) sur une période de deux ans. L’étude fait ressortir certaines préoccupations et tendances liées la fixation des prix, à la fois jeune discipline et fonction émergente. Peu d’entreprises ont pleinement conscience du levier prix et ce type d’analyse, en privilégiant une approche distanciée et holiste, permet de se familiariser avec la complexité de ces techniques et de rompre un certain isolement des professionnels chargés de cette fonction à l’intérieur de l’entreprise.
Variable selection with Random Forests for missing data

Variable selection has been suggested for Random Forests to improve their efficiency of data prediction and interpretation. However, its basic element, i.e. variable importance measures, can not be computed straightforward when there is missing data. Therefore an extensive simulation study has been conducted to explore possible solutions, i.e. multiple imputation, complete case analysis and a newly suggested importance measure for several missing data generating processes. The ability to distinguish relevant from non-relevant variables has been investigated for these procedures in combination with two popular variable selection methods. Findings and recommendations: Complete case analysis should not be applied as it lead to inaccurate variable selection and models with the worst prediction accuracy. Multiple imputation is a good means to select variables that would be of relevance in fully observed data. It produced the best prediction accuracy. By contrast, the application of the new importance measure causes a selection of variables that reflects the actual data situation, i.e. that takes the occurrence of missing values into account. It's error was only negligible worse compared to imputation.
Bradycardia in perspective—not all reductions in heart rate need immediate intervention

According to Wikipedia, the word ‘bradycardia’ stems from the Greek βραδύς, bradys, ‘slow’, and καρδία, kardia, ‘heart’. Thus, the meaning of bradycardia is slow heart rate but not necessarily too slow heart rate. If looking at top endurance athletes they may have a resting heart rate in the very low thirties without needing emergent intervention with anticholinergics, isoprenaline, epinephrine, chest compressions or the insertion of an emergency pacemaker (Figure 1 ). In fact, they withstand these episodes without incident, accommodating with a compensatory increase in stroke volume to preserve and maintain cardiac output. With this in mind, it is difficult for the authors to fully understand and agree with the general sentiment amongst many pediatric anesthesiologists that all isolated bradycardia portends impending doom and must be immediately treated with resuscitative measures.
Damage mapping based on coherence model using multi-temporal polarimetric-interferometric UAVSAR data

This study aims to evaluate the potential of coherent change detection using multi-temporal polarimetric interferometric SAR data. One of the limitations in damage area extraction is that the decorrelation caused by the disaster is commonly coupled with the natural changes. Also, the interpretation of the coherence is troublesome and requires the coherence model. The approach used in this study is based on the modified coherence model for a case of long-temporal and zero-spatial baseline. The inversion processes yield the temporal decorrelation contributions of ground and volume, respectively, having the physical meaning. We additionally applied simple statistical probability estimation method for the damage area to isolate the contributions of disaster from the natural changes. In this study, we used UAVSAR data acquired over Lake fire which occurred in June, 2015.
Knowledge Transfer to the Subsidiaries: A Case Study of Multinational Enterprise Operating in Overseas

The business opportunities in Southern Africa have justified any effort to learn more about the phenomenon of the transfer of knowledge to the local subsidiaries. We studied four cases with activities in the industrial sector. The results obtained indicate that an efficient transfer of knowledge from the source to the recipient depends on the sourcei¯s ability to transfer this knowledge; the climate of cooperation between the source and the recipient; and the absorptive capacity of the recipient, where the intervention of the expatriates with a profound knowledge of the African reality is fundamental to the creation of a climate of trust.
Color mood grasping in video by state estimation over color space with particle filter

As one possible model for human perception of color cue in vision, state space modeling approach and its particle filter implementation that grasps color mood in video by estimating the state defined over a color space has been proposed. The state space model is formulated over a state vector consisting of color instance and location of a small patch over the image frame. System model represents random fluctuation on each color instance and the location. New generation of color instances copes with emergence of new colors in the scene. Observation model evaluates likeliness of the color instance with the colors contained in the patch region specified by the location factor of the state vector. Experiment over a real image demonstrates performance of the proposed method. The prototype system has been developed for the experiment that works almost real-time for video image captured by a camera installed in PC. Abstraction of the video image becomes possible based on the proposed method that leads to further extension of the human perception model in higher level of knowledge and understanding of real scene.