Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Feature Selection Strategy for Enhanced Biomedical Event Extraction Using the Turku System

Feature selection is of paramount importance for text-mining classifiers with high-dimensional features. The Turku Event Extraction System (TEES) is the best performing tool in the GENIA BioNLP 2009/2011 shared tasks, which relies heavily on high-dimensional features. This paper describes research which, based on an implementation of an accumulated effect evaluation (AEE) algorithm applying the greedy search strategy, analyses the contribution of every single feature class in TEES with a view to identify important features and modify the feature set accordingly. With an updated feature set, a new system is acquired with enhanced performance which achieves an increased F-score of 53.27% up from 51.21% for Task 1 under strict evaluation criteria and 57.24% according to the approximate span and recursive criterion.
Skimmed Classi ers

Most Inductive Logic Programming (ILP) systems use a greedy covering algorithm to nd a set of clauses that best model positive examples. This set of clauses is called a theory and can be seen as an ensemble of clauses. It turns out that the search for a theory within the ILP system is very time consuming and often yields overly complex classi ers. One alternative approach to obtain a theory is to use the ILP system to non deterministically learn one clause at a time, several times, and to combine the obtained clauses using ensemble methods.
Functional Genomics: New Insights into the 'Function' of Low Levels of Gene Expression in Stem Cells

Understanding the global gene expression profile of stem cells and their multilineage differentiation will be essential for their ultimate therapeutic application. Efforts to characterize stem cells have relied on analyzing the genome-wide expression profiles that are biased towards the identification of genes that display the most pronounced differential expression. Rather than being viewed as a “blank” state, recent studies suggest that stem cells express low levels of multiple lineage specific genes prior to differentiation, a phenomenon known as “lineage priming. ” It is not likely that low levels of lineage-specific genes produce sufficient amounts of differentiation factors, but rather to provide rapid transcription to a wide range of lineage programs prior to differentiation. Thus, stem cell differentiation may involve the elimination of other potential pathways and the activation of a specific lineage program.
E-Shadow: Lubricating Social Interaction Using Mobile Phones

In this paper, we propose E-Shadow, a distributed mobile phone-based local social networking system. E-Shadow has two main components: (1) Local profiles. They enable EShadow users to record and share their names, interests, and other information with fine-grained privacy controls. (2) Mobile phone based local social interaction tools. E-Shadow provides mobile phone software that enables rich social interactions. The software maps proximate users' local profiles to their human owners and enables user communication and content sharing. We have designed and implemented E-Shadow on mobile phones. In our E-Shadow system, we allow users to perform dynamic and layered information publishing, making use of interpersonal relevance. Our system also provides a mechanism to help users perform direction-driven localization of an E-Shadow and match it with its owner. Experiments on real world Windows Mobile phones and large-scale simulations show that our system disseminates information efficiently and helps receivers find the direction of a specific E-Shadow with accuracy. We believe our E-Shadow concept and system can lead to a more tightly-knit temporary community in one's physical vicinity.
The importance of the 5′‐region in regulating the stability of sdh mRNA in Bacillus subtilis

The decay of the polycistronic Bacillus subtilis sdh mRNA was analysed using probes specific for each of the component cistrons, sdhC, sdhA and sdhB. In exponentially growing cells, the entire sdh mRNA seems to decay with an ‘all or nothing’ mechanism and with a uniform half‐life of 2–3 min for all cistrons. In stationary‐phase cells, the half‐life of the 5′‐part had dropped to about 0.6 min whereas that of the 3′‐part was about 1.2 min. Decay of sdh mRNA was also measured in exponentially growing cells containing a ‘down‐mutation’ in the ribosomal binding site preceding sdhC which decreases the expression of sdhC by about 90%. The mutation has a moderate effect on expression of the downstream cistron sdhA. In this mutant, the half‐life of the 5′‐part of sdh mRNA was about 0.5 min (i.e. the same as in stationary phase wild‐type cells) and the half‐life of the 3′‐part about 1.3 min. Also, analysis of the decay of an sdh‐cat fusion transcript revealed that the sdh (5′) part decayed more rapidly than the cat part and this difference was more pronounced in stationary‐phase cells compared to exponentially growing cells. The results of these experiments demonstrate the importance of the 5‐ segment of sdh mRNA in controlling the stability of the transcript under different growth conditions.
When New Technology is an Answer for Old Problems: The Use of Videoconferencing in Cognitive Aging Assessment

People living with cognitive impairment and dementia require regular screening of their symptomatology and needs. Brief cognitive screening is crucial for assessing these conditions. Such screening can give health professionals a snapshot of the patient’s cognitive abilities and help in their monitoring and adaptation. An appropriate administration of brief cognitive screening using telemedicine technology, such as videoconference, can improve access to care and treatment planning. Moreover, the burden that rural and underserved communities often suffer because of limited access to specialty mental health services is also of concern. Herein, in this review, we describe the existing and relevant research regarding the administration of neuropsychological instruments via videoconferencing, and suggest methodological improvements for further studies. To date, only a handful of scientific studies have been published documenting the feasibility and acceptability of videoconferencing among older people and health professionals. Varying in their assessment tools, the studies demonstrate the reliability of cognitive testing and clinical diagnosis of dementia via videoconferencing, as noted by the associations between results of several cognitive tests using it as compared to face-to-face interviews. Further research is required to replicate findings and bring new solutions for their adaptation to a wide range of individuals, health professionals, areas of practice and settings.
Investigation of the Vitamin D Receptor Polymorphisms in Acromegaly Patients

Objective. The genetic structural alterations in the majority of somatotroph adenomas are not clarified and the search for novel candidate genes is still a challenge. We aimed to investigate possible associations between vitamin D receptor (VDR) polymorphisms and acromegaly. Design, Patients, and Methods. 52 acromegaly patients (mean age 45.7 ± 1.9 years) and 83 controls (mean age 43.1 ± 2.6 years) were recruited to the study. VDR polymorphism was determined by polymerase chain reaction-based restriction fragment length polymorphism methods. Results. The distribution of VDR genotypes showed a significant difference in the frequencies of VDR FokI genotypes between patients and controls (P = 0.034). VDR FokI ff genotype was significantly decreased in acromegaly patients (P = 0.035) and carriers of FokI Ff genotype had a 1.5-fold increased risk for acromegaly (OR: 1.5, 95% CI: 1.07–2.1; P = 0.020). IGF1 levels after treatment were significantly higher in patients carrying the Ff genotype compared to carrying ff genotype (P = 0.0049). 25(OH)D3 levels were significantly lower in acromegaly patients (P < 0.001). Conclusions. Our study suggests that VDR FokI genotypes might affect the development of acromegaly and VDR polymorphisms may play a role in the course of acromegaly as a consequence of altering hormonal status.
Effect of thinning on the above ground biomass of (Conocarpus erectus L.) trees in the western region of Saudi Arabia.

Benefiting from introduced exotic trees in Saudi Arabia is mostly limited to municipal uses. In order to establish forest plantations of those species, studies should be conducted concerning the effect of silvicultural practices on the plantations productivity. In the present study, we studied the effect of three thinning treatments, on 7 years old short rotation intensively cultured Buttonwood (Conocarpus erectus L.) plantation after 2 years of application. The thinning treatments were 0, 50 and 67% of stock. In exception of the increase in the dry matter (DM) of foliage, no significant influence of thinning was observed on the above ground dry matter (AGDM) of individual tree components. The average total above ground dry matter (TAGDM) ranged between 15.79 kg for unthinned to 22.44 kg for 67% treatment. In all treatments, stem wood accounted for the largest proportion of AGDM with the highest value for the unthinned (71.72 %), differing significantly from the other two treatments (62.88 and 63.05%). Of all tree dimension parameters, only crown diameter (CrD) and stand basal area (BA) were significantly influenced by the treatments. The 67% thinning treatment had the highest mean CrD (2.16 m), while the unthinned was the highest in BA (17.93 m 2 ha -1 ). Several allometric equations were constructed relating DM of tree components and stem volume of individual trees with their diameter or diameter and total height. Except foliage DM all the relations were highly significant. The coefficients of determination (R 2 ) were 0.882, 0.899, 0.945, 0.996, 0.987 and 0.990 for twigs, branches, bark, stem wood, total DM and stem volume respectively.
Game theoretic analysis for video transmission in simulated WLANs

Real-time video transmission over Wireless Local Area Networks (WLANs) is a new challenge for wireless network research. This work solves the problem of video streaming transmission encoded with H.264/SVC (Scalable Video Coding). Firstly, we analyze the common theoretical foundations of video transmission in WLANs. Second, we present a review of the game model and use it to develop a mathematical method for understanding the relationship among workstations. Game theory is applied to analyze individual and group activities of workstations. The solution to Carrier Sense Multiple Access Scheme (CSMA)/Collision Avoid (CA) based on game theory presents a strategy for workstations to choose the back-off windows and reaches the equilibrium points. Third, the new module "System-in-the-Loop (SITL)" for OPNET Modeler is examined in this study to facilitate the video streaming transmission between real and simulated devices. The simulation results establish analytical statistics and provide insights for the process of the real response of transmission.
Toward Scalable Transaction Processing

Designing scalable transaction processing systems on modern multicore hardware has been a challenge for almost a decade. The typical characteristics of transaction processing workloads lead to a high degree of unbounded communication on multicores for conventional system designs. In this tutorial, we initially present a systematic way of eliminating scalability bottlenecks of a transaction processing system, which is based on minimizing the unbounded communication. Then, we show several techniques that apply the presented methodology to minimize logging, locking, latching etc. related bottlenecks of transaction processing systems. In parallel, we demonstrate the internals of the Shore-MT storage manager and how they have evolved over the years in terms of scalability on multicore hardware through such techniques. We also teach how to use Shore-MT with the various design options it offers through its application layer Shore-Kits and Metadata Frontend.
Co-Inflammatory Roles of TGFβ1 in the Presence of TNFα Drive a Pro-inflammatory Fate in Mesenchymal Stem Cells

High plasticity is a hallmark of mesenchymal stem cells (MSCs), and as such, their differentiation and activities may be shaped by factors of their microenvironment. Bones, tumors, and cardiomyopathy are examples of niches and conditions that contain MSCs and are enriched with tumor necrosis factor α (TNFα) and transforming growth factor β1 (TGFβ1). These two cytokines are generally considered as having opposing roles in regulating immunity and inflammation (pro- and anti-inflammatory, respectively). Here, we performed global gene expression analysis of human bone marrow-derived MSCs and identified overlap in half of the transcriptional programs that were modified by TNFα and TGFβ1. The two cytokines elevated the mRNA expression of soluble factors, including mRNAs of pro-inflammatory mediators. Accordingly, the typical pro-inflammatory factor TNFα prominently induced the protein expression levels of the pro-inflammatory mediators CCL2, CXCL8 (IL-8), and cyclooxygenase-2 (Cox-2) in MSCs, through the NF-κB/p65 pathway. In parallel, TGFβ1 did not elevate CXCL8 protein levels and induced the protein expression of CCL2 at much lower levels than TNFα; yet, TGFβ1 readily induced Cox-2 and acted predominantly via the Smad3 pathway. Interestingly, combined stimulation of MSCs by TNFα + TGFβ1 led to a cooperative induction of all three inflammatory mediators, indicating that TGFβ1 functioned as a co-inflammatory cytokine in the presence of TNFα. The cooperative activities of TNFα + TGFβ1 that have led to CCL2 and CXCL8 induction were almost exclusively dependent on p65 activation and were not regulated by Smad3 or by the upstream regulator TGFβ-activated kinase 1 (TAK1). In contrast, the TNFα + TGFβ1-induced cooperative elevation in Cox-2 was mostly dependent on Smad3 (demonstrating cooperativity with activated NF-κB) and was partly regulated by TAK1. Studies with MSCs activated by TNFα + TGFβ1 revealed that they release factors that can affect other cells in their microenvironment and induce breast tumor cell elongation, migration, and scattering out of spheroid tumor masses. Thus, our findings demonstrate a TNFα + TGFβ1-driven pro-inflammatory fate in MSCs, identify specific molecular mechanisms involved, and propose that TNFα + TGFβ1-stimulated MSCs influence the tumor niche. These observations suggest key roles for the microenvironment in regulating MSC functions, which in turn may affect different health-related conditions.
Economic Analysis of Greenhouse Lighting: Light Emitting Diodes vs. High Intensity Discharge Fixtures

Lighting technologies for plant growth are improving rapidly, providing numerous options for supplemental lighting in greenhouses. Here we report the photosynthetic (400–700 nm) photon efficiency and photon distribution pattern of two double-ended HPS fixtures, five mogul-base HPS fixtures, ten LED fixtures, three ceramic metal halide fixtures, and two fluorescent fixtures. The two most efficient LED and the two most efficient double-ended HPS fixtures had nearly identical efficiencies at 1.66 to 1.70 micromoles per joule. These four fixtures represent a dramatic improvement over the 1.02 micromoles per joule efficiency of the mogul-base HPS fixtures that are in common use. The best ceramic metal halide and fluorescent fixtures had efficiencies of 1.46 and 0.95 micromoles per joule, respectively. We also calculated the initial capital cost of fixtures per photon delivered and determined that LED fixtures cost five to ten times more than HPS fixtures. The five-year electric plus fixture cost per mole of photons is thus 2.3 times higher for LED fixtures, due to high capital costs. Compared to electric costs, our analysis indicates that the long-term maintenance costs are small for both technologies. If widely spaced benches are a necessary part of a production system, the unique ability of LED fixtures to efficiently focus photons on specific areas can be used to improve the photon capture by plant canopies. Our analysis demonstrates, however, that the cost per photon delivered is higher in these systems, regardless of fixture category. The lowest lighting system costs are realized when an efficient fixture is coupled with effective canopy photon capture.
Delta-Notch signalling and the patterning of sensory cell differentiation in the zebrafish ear: evidence from the mind bomb mutant.

Mechanosensory hair cells in the sensory patches of the vertebrate ear are interspersed among supporting cells, forming a fine-grained pattern of alternating cell types. Analogies with Drosophila mechanosensory bristle development suggest that this pattern could be generated through lateral inhibition mediated by Notch signalling. In the zebrafish ear rudiment, homologues of Notch are widely expressed, while the Delta homologues deltaA, deltaB and deltaD, coding for Notch ligands, are expressed in small numbers of cells in regions where hair cells are soon to differentiate. This suggests that the delta-expressing cells are nascent hair cells, in agreement with findings for Delta1 in the chick. According to the lateral inhibition hypothesis, the nascent hair cells, by expressing Delta protein, would inhibit their neighbours from becoming hair cells, forcing them to be supporting cells instead. The zebrafish mind bomb mutant has abnormalities in the central nervous system, somites, and elsewhere, diagnostic of a failure of Delta-Notch signalling: in the CNS, it shows a neurogenic phenotype accompanied by misregulated delta gene expression. Similar misregulation of delta ; genes is seen in the ear, along with misregulation of a Serrate homologue, serrateB, coding for an alternative Notch ligand. Most dramatically, the sensory patches in the mind bomb ear consist solely of hair cells, which are produced in great excess and prematurely; at 36 hours post fertilization, there are more than ten times as many as normal, while supporting cells are absent. A twofold increase is seen in the number of otic neurons also. The findings are strong evidence that lateral inhibition mediated by Delta-Notch signalling controls the pattern of sensory cell differentiation in the ear.
Peripheral tolerance to an islet cell‐specific hemagglutinin transgene affects both CD4+ and CD8+ T cells

To study the basis for immunological tolerance of peripheral tissue‐specific antigens, a transgenic mouse line was established that expresses the influenza hemagglutinin (HA) on pancreatic islet β cells (Ins‐HA transgenic mice). When followed up to 14 months of age, Ins‐HA transgenic mice did not develop spontaneous autoimmune disease. Upon immunization with HA‐expressing viruses, high titers of HA‐specific circulating antibody were detected; however, T cell responses by both the T helper and T cytolytic compartment were markedly reduced as compared with transgene‐negative littermates, and no evidence could be found for islet infiltrates. Adoptive transfer of histocompatible lymphocytes from transgene‐negative mice plus virus into irradiated Ins‐HA hosts resulted in islet inflammation dominated by CD4+ T cells, indicating that the HA antigen was accessible to activated T cells. These results suggest that T cells can be rendered tolerant of antigens expressed outside the thymus.
The Robust Network Loading Problem Under Hose Demand Uncertainty: Formulation, Polyhedral Analysis, and Computations

We consider the network loading problem (NLP) under a polyhedral uncertainty description of traffic demands. After giving a compact multicommodity flow formulation of the problem, we state a decomposition property obtained from projecting out the flow variables. This property considerably simplifies the resulting polyhedral analysis and computations by doing away with metric inequalities. Then we focus on a specific choice of the uncertainty description, called the “hose model,” which specifies aggregate traffic upper bounds for selected endpoints of the network. We study the polyhedral aspects of the NLP under hose demand uncertainty and use the results as the basis of an efficient branch-and-cut algorithm. The results of extensive computational experiments on well-known network design instances are reported.
Imitation Learning Based Talking Heads in Humanoid Robotics

The main goal of this Chapter is to describe a novel approach for the control of Talking Heads in Humanoid Robotics. In a preliminary section we will discuss the state of the art of the research in this area. In the following sections we will describe our research results while in the final part some experimental results of our approach are reported. With the goal of controlling talking heads in mind, we have developed an algorithm which extracts articulatory features from human voice. In fact, there is a strong structural linkage between articulators and facial movements during human vocalization; for a robotic talking head to have human-like behavior, this linkage should be emulated. Exploiting the structural linkage, we used the estimated articulatory features to control the facial movements of a talking head. Moreover, the articulatory estimate is used to generate artificial speech which is by construction synchronized with the facial movements. Hence, the algorithm we describe aims at estimating the articulatory features from a spoken sentence using a novel computational model of human vocalization. Our articulatory features estimator uses a set of fuzzy rules and genetic optimization. That is, the places of articulation are considered as fuzzy sets whose degrees of membership are the values of the articulatory features. The fuzzy rules represent the relationships between places of articulation and speech acoustic parameters, and the genetic algorithm estimates the degrees of membership of the places of articulation according to an optimization criteria. Through the analysis of large amounts of natural speech, the algorithm has been used to learn the average places of articulation of all phonemes of a given speaker. This Chapter is based upon the work described in [1]. Instead of using known HMM based algorithms for extracting articulatory features, we developed a novel algorithm as an attempt to implement a model of human language acquisition in a robotic brain. Human infants, in fact, acquire language by imitation from their care-givers. Our algorithm is based on imitation learning as well. Nowadays, there is an increasing interest in service robotics. A service robot is a complex system which performs useful services with a certain degree of autonomy. Its intelligence emerges from the interaction between data gathered from the sensors and the management algorithms. The sensorial subsystem furnishes environment information useful for motion tasks (dead reckoning), auto-localization and obstacle avoidance in order to introduce
Review of state-of-the-arts in artificial intelligence with application to AI safety problem

Here, I review current state-of-the-arts in many areas of AI to estimate when it's reasonable to expect human level AI development. Predictions of prominent AI researchers vary broadly from very pessimistic predictions of Andrew Ng to much more moderate predictions of Geoffrey Hinton and optimistic predictions of Shane Legg, DeepMind cofounder. Given huge rate of progress in recent years and this broad range of predictions of AI experts, AI safety questions are also discussed.