Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Neural Networks for Multiword Recognition in IR

In this paper, a supervised neural network has been used to classify pairs of terms as being multiwords or non-multi words. Classification is based on the values yielded by different estimators, cUlTently available in literature, used as inputs for the neural network. Lists of multiwords and non-multiwords have been built to train the net. Afterward, many other pairs of tenns have been classified using the trained net. Results obtained in this classification have been used to perfonu information retrieval tasks. Experiments show that detecting multiwords results in better performance of the IR methods.
Spirocyclic Drimanes from the Marine Fungus Stachybotrys sp. Strain MF347

A novel spirocyclic drimane coupled by two drimane fragment building blocks 2 and a new drimane 1 were identified in mycelia and culture broth of Stachybotrys sp. MF347. Their structures were established by spectroscopic means. This is the first example of spirocyclic drimane coupled by a spirodihydrobenzofuranlactam unit and a spirodihydroisobenzofuran unit; and the connecting position being N-C instead of an N and N connecting unit. Strain MF347 produced also the known spirocyclic drimanes stachybocin A (12) and stachybocin B (11) featured by two sesquiterpene-spirobenzofuran structural units connected by a lysine residue; the known spirocyclic drimanes chartarlactam O (5); chartarlactam K (6); F1839A (7); stachybotrylactam (8); stachybotramide (9); and 2α-acetoxystachybotrylactam acetate (10); as well as ilicicolin B (13), a known sesquiterpene. The relative configuration of two known spirobenzofuranlactams (3 and 4) was determined. All compounds were subjected to biological activity tests. The spirocyclic drimane 2, 11, and 12, as well as the sesquiterpene 13, exhibited antibacterial activity against the clinically relevant methicillin-resistant Staphylococcus aureus (MRSA).
Antigenotoxic Effect of Piperine in Broiler Chickens Intoxicated with Aflatoxin B1

Piperine is an abundant amide extracted from black pepper seeds which has been shown to have protective effects against cytotoxic and genotoxic carcinogenesis induced by certain chemical carcinogens and aflatoxin B1 (AFB1) in vitro. The aim of this work was to study, in vivo, the antigenotoxic potential of feed-added piperine on broiler chickens experimentally intoxicated with AFB1, using micronucleus and comet assays. The antigenotoxicity assessment of 9-day-old chicks was performed on a total of 60 chickens divided into four groups of 15 broilers each: (C) control, (P) 60 mg·piperine kg−1 feed, (A) 0.5 mg·AFB1·kg−1 body weight, (daily by oral route), and (P + A) co-treatment with piperine and AFB1. The experiment was conducted for 26 days. Chicks intoxicated with AFB1 showed significant genotoxic effects in the first 24 h post intoxication, and the effects remained in the other periods analyzed (48, 72, and 96 h and 26 days of treatment). The DNA damage in peripheral blood cells, the number of erythrocytes with micronuclei, and polychromatic-to-normochromatic erythrocyte ratio were significantly reduced or absent in the piperine/AFB1 group. No significant differences were observed between the group piperine/AFB1 and the control and piperine-alone groups. The addition 60 mg·kg−1 of piperine to the diet of the broiler chicks was safe, promoting beneficial effects in poultry health with respect to the toxic effects 0.5 mg·AFB1·kg−1 body weight.
Prediction of atherosclerotic cardiovascular disease mortality in a nationally representative cohort using a set of risk factors from pooled cohort risk equations

The American College of Cardiology/American Heart Association developed Pooled Cohort equations to estimate atherosclerotic cardiovascular disease (ASCVD) risk. It is unclear how well the equations predict ASCVD mortality in a nationally representative cohort. We used the National Health and Nutrition Examination Survey (NHANES) 1988–1994 and Linked Mortality through 2006 (n = 6,644). Among participants aged 40–79 years without ASCVD at baseline, we used Cox proportional hazard models to estimate the 10-year probability of ASCVD death by sex and race-ethnicity (non-Hispanic white (NHW), non-Hispanic black (NHB) and Mexican American (MA)). We estimated the discrimination and calibration for each sex-race-ethnicity model. We documented 288 ASCVD deaths during 62,335 person years. The Pooled Cohort equations demonstrated moderate to good discrimination for ASCVD mortality, with modified C-statistics of 0.716 (95% CI 0.663–0.770), 0.794 (0.734–0.854), and 0.733 (0.654–0.811) for NHW, NHB and MA men, respectively. The corresponding C-statistics for women were 0.781 (0.718–0.844), 0.702 (0.633–0.771), and 0.789 (CI 0.721–0.857). Modified Hosmer-Lemeshow χ2 suggested adequate calibration for NHW, NHB and MA men, and MA women (p-values: 0.128, 0.295, 0.104 and 0.163 respectively). The calibration was inadequate for NHW and NHB women (p<0.05). In this nationally representative cohort, the Pooled Cohort equations performed adequately to predict 10-year ASCVD mortality for NHW and NHB men, and MA population, but not for NHW and NHB women.
A multispecies dependent double‐observer model: A new method for estimating multispecies abundance

Abstract Conservation of biological communities requires accurate estimates of abundance for multiple species. Recent advances in estimating abundance of multiple species, such as Bayesian multispecies N‐mixture models, account for multiple sources of variation, including detection error. However, false‐positive errors (misidentification or double counts), which are prevalent in multispecies data sets, remain largely unaddressed. The dependent‐double observer (DDO) method is an emerging method that both accounts for detection error and is suggested to reduce the occurrence of false positives because it relies on two observers working collaboratively to identify individuals. To date, the DDO method has not been combined with advantages of multispecies N‐mixture models. Here, we derive an extension of a multispecies N‐mixture model using the DDO survey method to create a multispecies dependent double‐observer abundance model (MDAM). The MDAM uses a hierarchical framework to account for biological and observational processes in a statistically consistent framework while using the accurate observation data from the DDO survey method. We demonstrate that the MDAM accurately estimates abundance of multiple species with simulated and real multispecies data sets. Simulations showed that the model provides both precise and accurate abundance estimates, with average credible interval coverage across 100 repeated simulations of 94.5% for abundance estimates and 92.5% for detection estimates. In addition, 92.2% of abundance estimates had a mean absolute percent error between 0% and 20%, with a mean of 7.7%. We present the MDAM as an important step forward in expanding the applicability of the DDO method to a multispecies setting. Previous implementation of the DDO method suggests the MDAM can be applied to a broad array of biological communities. We suggest that researchers interested in assessing biological communities consider the MDAM as a tool for deriving accurate, multispecies abundance estimates.
Real world activity recognition with multiple goals

Recognizing and understanding the activities of people from sensor readings is an important task in ubiquitous computing. Activity recognition is also a particularly difficult task because of the inherent uncertainty and complexity of the data collected by the sensors. Many researchers have tackled this problem in an overly simplistic setting by assuming that users often carry out single activities one at a time or multiple activities consecutively, one after another. However, so far there has been no formal exploration on the degree in which humans perform concurrent or interleaving activities, and no thorough study on how to detect multiple goals in a real world scenario. In this article, we ask the fundamental questions of whether users often carry out multiple concurrent and interleaving activities or single activities in their daily life, and if so, whether such complex behavior can be detected accurately using sensors. We define several classes of complexity levels under a goal taxonomy that describe different granularities of activities, and relate the recognition accuracy with different complexity levels or granularities. We present a theoretical framework for recognizing multiple concurrent and interleaving activities, and evaluate the framework in several real-world ubiquitous computing environments.
Unleashing the potential of the root hair cell as a single plant cell type model in root systems biology

Plant root is an organ composed of multiple cell types with different functions. This multicellular complexity limits our understanding of root biology because -omics studies performed at the level of the entire root reflect the average responses of all cells composing the organ. To overcome this difficulty and allow a more comprehensive understanding of root cell biology, an approach is needed that would focus on one single cell type in the plant root. Because of its biological functions (i.e., uptake of water and various nutrients; primary site of infection by nitrogen-fixing bacteria in legumes), the root hair cell is an attractive single cell model to study root cell response to various stresses and treatments. To fully study their biology, we have recently optimized procedures in obtaining root hair cell samples. We culture the plants using an ultrasound aeroponic system maximizing root hair cell density on the entire root systems and allowing the homogeneous treatment of the root system. We then isolate the root hair cells in liquid nitrogen. Isolated root hair yields could be up to 800 to 1000~mg of plant cells from 60 root systems. Using soybean as a model, the purity of the root hair was assessed by comparing the expression level of genes previously identified as soybean root hair specific between preparations of isolated root hair cells and stripped roots, roots devoid in root hairs. Enlarging our tests to include other plant species, our results support the isolation of large quantities of highly purified root hair cells which is compatible with a systems biology approach.
A Simple Approach to Dynamic Optimisation of Flexible Optical Networks with Practical Application

This paper provides an initial introduction to, and definition of, the ‘Dynamically Powered Relays for a Flexible Optical Network’ (DPR-FON) problem for opto-electro-optical (OEO) regenerators used in optical networks. In such networks, optical transmission parameters can be varied dynamically as traffic patterns change. This will provide different bandwidths, but also change the regeneration limits as a result. To support this flexibility, OEOs (‘relays’) may be switched on and off as required, thus saving power. DPR-FON is shown to be NP-complete; consequently, solving such a dynamic problem in real-time requires a fast heuristic capable of delivering an acceptable approximation to the optimal configuration with low complexity. In this paper, just such an algorithm is developed, implemented, and evaluated against more computationally-demanding alternatives for two known cases. A number of real-world extensions are considered as the paper develops, combining to produce the ‘Generalised Dynamically Powered Relays for a Flexible Optical Network’ (GDPR-FON) problem. This, too, is analysed and an associated fast heuristic proposed, along with an exploration of the further research that is required.
Functional and Structural Methods With Mixed Measurement Error and Misclassification in Covariates

Covariate measurement imprecision or errors arise frequently in many areas. It is well known that ignoring such errors can substantially degrade the quality of inference or even yield erroneous results. Although in practice both covariates subject to measurement error and covariates subject to misclassification can occur, research attention in the literature has mainly focused on addressing either one of these problems separately. To fill this gap, we develop estimation and inference methods that accommodate both characteristics simultaneously. Specifically, we consider measurement error and misclassification in generalized linear models under the scenario that an external validation study is available, and systematically develop a number of effective functional and structural methods. Our methods can be applied to different situations to meet various objectives.
Autophagy of metallothioneins prevents TNF-induced oxidative stress and toxicity in hepatoma cells

Lysosomal membrane permeabilization (LMP) induced by oxidative stress has recently emerged as a prominent mechanism behind TNF cytotoxicity. This pathway relies on diffusion of hydrogen peroxide into lysosomes containing redox-active iron, accumulated by breakdown of iron-containing proteins and subcellular organelles. Upon oxidative lysosomal damage, LMP allows relocation to the cytoplasm of low mass iron and acidic hydrolases that contribute to DNA and mitochondrial damage, resulting in death by apoptosis or necrosis. Here we investigate the role of lysosomes and free iron in death of HTC cells, a rat hepatoma line, exposed to TNF following metallothionein (MT) upregulation. Iron-binding MT does not normally occur in HTC cells in significant amounts. Intracellular iron chelation attenuates TNF and cycloheximide (CHX)-induced LMP and cell death, demonstrating the critical role of this transition metal in mediating cytokine lethality. MT upregulation, combined with starvation-activated MT autophagy almost completely suppresses TNF and CHX toxicity, while impairment of both autophagy and MT upregulation by silencing of Atg7, and Mt1a and/or Mt2a, respectively, abrogates protection. Interestingly, MT upregulation by itself has little effect, while stimulated autophagy alone depresses cytokine toxicity to some degree. These results provide evidence that intralysosomal iron-catalyzed redox reactions play a key role in TNF and CHX-induced LMP and toxicity. The finding that chelation of intralysosomal iron achieved by autophagic delivery of MT, and to some degree probably of other iron-binding proteins as well, into the lysosomal compartment is highly protective provides a putative mechanism to explain autophagy-related suppression of death by TNF and CHX.
Personality and intentional binding: an exploratory study using the narcissistic personality inventory

When an individual estimates the temporal interval between a voluntary action and a consequent effect, their estimates are shorter than the real duration. This perceived shortening has been termed “intentional binding”, and is often due to a shift in the perception of a voluntary action forward towards the effect and a shift in the perception of the effect back towards the action. Despite much work on binding, there is virtually no consideration of individual/personality differences and how they affect it. Narcissism is a psychological trait associated with an inflated sense of self, and individuals higher in levels of subclinical narcissism tend to see themselves as highly effective agents. Conversely, lower levels of narcissism may be associated with a reduced sense of agency. In this exploratory study, to assess whether individuals with different scores on a narcissism scale are associated with differences in intentional binding, we compared perceived times of actions and effects (tones) between participants with high, middle, and low scores on the narcissistic personality inventory (NPI). We hypothesized that participants with higher scores would show increased binding compared to participants with lower scores. We found that participants in our middle and high groups showed a similar degree of binding, which was significantly greater than the level of binding shown by participants with the lowest scores. To our knowledge, these results are the first to demonstrate that different scores on a personality scale are associated with changes in the phenomenological experience of action, and therefore underscore the importance of considering individual/personality differences in the study of volition. Our results also reinforce the notion that intentional binding is related to agency experience.
A Distributed Stream Library for Java 8

Java 8 has introduced new capabilities such as lambda expressions and streams which simplify data-parallel computing. However, as a base language for Big Data systems, it still lacks a number of important capabilities such as processing very large datasets and distributing the computation over multiple machines. This paper gives an overview of the Java 8 Streams API and proposes extensions to allow its use in Big Data systems. It also shows how the API can be used to implement a range of standard Big Data paradigms. Finally, it compares performance with that of Hadoop and Spark. Despite being a proof-of-concept implementation, results indicate that it is a lightweight and efficient framework, comparable in performance to Hadoop and Spark, and is up to 5 times faster for the largest input sizes tested.
Serine/threonine kinase 15 gene polymorphism and risk of digestive system cancers: A meta-analysis

Previous studies have reported an association between the two coding polymorphisms (91T>A and 169G>A) of the serine/threonine kinase 15 (STK15) gene and the risk of digestive system cancers; however, the results are inconsistent. In the present study, a meta-analysis was carried out to assess the association between the two STK15 polymorphisms and the risk of digestive system cancers. Relevant studies were identified using PubMed, Web of Science, China National Knowledge Infrastructure, WanFang and VIP databases up to February 18, 2014. The pooled odds ratio (OR) with a 95% confidence interval (CI) was calculated using the fixed or random effects model. A total of 15 case-control studies from 14 publications were included. Of these, 15 studies concerned the 91T>A polymorphism and included 7,619 cases and 7,196 controls and four studies concerned the 161G>A polymorphism and included 826 cases and 713 controls. A significantly increased risk of digestive system cancers was observed for the 91T>A polymorphism (recessive model: OR, 1.19; 95% CI, 1.07–1.31). In subgroup analysis by ethnicity, a significant association was detected in Asian populations (recessive model: OR, 1.21; 95% CI, 1.08–1.36) but not in Caucasian and mixed populations. Stratification by tumor type indicated that the 91T>A polymorphism was associated with an increased risk of esophageal and colorectal cancers under the recessive model (OR, 1.19; 95% CI, 1.03–1.38; and OR, 1.24; 95% CI, 1.04–1.46; respectively); however, no significant association was observed between the 169G>A polymorphism and the risk of digestive system cancers in any of the genetic models. Furthermore, in subgroup analysis by ethnicity, similar results were observed in the Asian and Caucasian populations. The present meta-analysis demonstrated that the STK15 gene 91T>A polymorphism, but not the 169G>A polymorphism, may be a risk factor for digestive system cancers, particularly for esophageal and colorectal cancers.
Formin1 Mediates the Induction of Dendritogenesis and Synaptogenesis by Neurogenin3 in Mouse Hippocampal Neurons

Neurogenin3, a proneural transcription factor controlled by Notch receptor, has been recently shown to regulate dendritogenesis and synaptogenesis in mouse hippocampal neurons. However, little is known about the molecular mechanisms involved in these actions of Ngn3. We have used a microarray analysis to identify Ngn3 regulated genes related with cytoskeleton dynamics. One of such genes is Fmn1, whose protein, Formin1, is associated with actin and microtubule cytoskeleton. Overexpression of the Fmn1 isoform-Ib in cultured mouse hippocampal neurons induced an increase in the number of primary dendrites and in the number of glutamatergic synaptic inputs at 4 days in vitro. The same changes were provoked by overexpression of Ngn3. In addition downregulation of Fmn1 by the use of Fmn1-siRNAs impaired such morphological and synaptic changes induced by Ngn3 overexpression in neurons. These results reveal a previously unknown involvement of Formin1 in dendritogenesis and synaptogenesis and indicate that this protein is a key component of the Ngn3 signaling pathway that controls neuronal differentiation.
Immunocytochemical localization of factor VIII/von Willebrand factor antigen in human platelets

Specific antibodies against anti‐human FVIII/vW protein were isolated by affinity chromatography on glutaraldehyde‐activated gel (Ultrogel AcA22). They were coupled directly with peroxidase or visualized with anti‐rabbit IgG (sheep)‐peroxidase (Institut Pasteur). Fab fragments of the same specific antibodies were prepared to enhance the intracellular penetration and coupled to peroxidase. In washed human platelets, staining was observed on the plasma membrane and in the canalicular system, whereas in previous studies whole specific antibodies incubated with fixed platelets showed the labeling only on the plasma membrane. After thrombin activation, the release of granules containing FVIII/vW protein was better visualized in the surface canalicular system. This localization was discussed in regard to the exocytosis process: membrane fusion, granule labeling.
Temporal Coding in Olfaction

Knowledge about the molecular organization principles of the sense of smell in different species has greatly improved in the last decade (Bargmann 2006; Mombaerts 2004a, 2004b; Rodriguez 2007). It is now well established that in many species, odorant molecules are detected by large families of G-protein-coupled receptors (Buck and Axel 1991), whose molecular sequence and structure may vary across species and phyla, but that essentially implement the same function (Bargmann 2006). Interestingly, the insect olfactory receptors display a unique and unconventional membrane topology in comparison to the mammalian receptors, questioning the existence of a coupling with G-proteins (Benton et al. 2006; Vosshall and Stocker 2007). Nevertheless, understanding how odorant information generated by these large arrays of receptors is interpreted by the brain to produce a great variety of behaviors will be the challenge of the next decade. A few questions, which may appear basic with regard to the complexity of the entire olfactory system, are still not answered. Among these, how olfactory information is encoded in brain networks downstream to receptors, remains poorly understood. In recent years, there have been strong debates on this question and it seems that the answer is not as simple as recording from the neurons of these networks. The ambition of this chapter is not to provide a definitive answer, but to present the most relevant results on this question and put them in perspective, helping the reader to appreciate where the field stands in terms of olfactory coding. Since a certain similarity in the olfactory system organization has been observed across species (Kay and Stopfer 2006), we will endeavor to compare between different animal models. Our focus will primarily be on temporal coding, as temporal dynamics, in our opinion, are currently the main aspect of neuronal activity in the olfactory system that is difficult to integrate in a convincing and unanimously recognized theory of olfactory coding.