Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting contrastive information from negation patterns in biomedical literature

Expressions of negation in the biomedical literature often encode information of contrast as a means for explaining significant differences between the objects that are so contrasted. We show that such information gives additional insights into the nature of the structures and/or biological functions of these objects, leading to valuable knowledge for subcategorization of protein families by the properties that the involved proteins do not have in common. Based on the observation that the expressions of negation employ mostly predictable syntactic structures that can be characterized by subclausal coordination and by clause-level parallelism, we present a system that extracts such contrastive information by identifying those syntactic structures with natural language processing techniques and with additional linguistic resources for semantics. The implemented system shows the performance of 85.7% precision and 61.5% recall, including 7.7% partial recall, or an F score of 76.6. We apply the system to the biological interactions as extracted by our biomedical information-extraction system in order to enrich proteome databases with contrastive information.
Tumor markers in cancer diagnosis and prognosis

A tumor marker is a biochemical indicator for the presence of a tumor. In clinical usage, the term usually refers to a molecule that can be detected in plasma or other body fluids. Table I summarizes the major concep tual developments in the history of tumor markers. Bence Jones proteins in urine and the serum levels of acid phosphatase have been employed for many years as indica tors for multiple myeloma and prostatic adenocarcinoma, respectively. Although efforts were made in the early decades of this century to identify tumor-specific anti gens, the number of markers in clinical use remained limited, and almost none were available for the more common cancers. The discovery of alpha-feto@@t@Th' (AFP) as a marker for hepatomas, and car cinoembryonic antigen2 (CEA) as a marker for colon carcinoma, provided a fresh im petus for the search for specific tumor
Beyond fairness: the ethics of inclusion for transgender and intersex athletes

Abstract Sporting communities remain entangled in debate over whether and how to include transgender and intersex athletes in competition with cisgender athletes. Of particular concern is that transgender and intersex athletes may have unfair physiological advantages over their cisgender opponents. Arguments for inclusion of transgender and intersex athletes in sport attempt to demonstrate that such inclusion does not threaten the presumed physiological equivalence among competitors and is therefore fair to all. This article argues that the physiological equivalency rationale has significant limitations, including an inordinate emphasis on sport as a comparative test. Instead, this article contends that arguments for narrativity rather than physiological equivalency show that exclusion is not only misguided but also undesirable: it is detrimental not only to the excluded athletes but to sport itself. The article yields several important consequences including calls for revisions to policies on transgender and intersex athletes.
Multiple start codons and phosphorylation result in discrete Rad52 protein species

The sequence of the Saccharomyces cerevisiae RAD52 gene contains five potential translation start sites and protein-blot analysis typically detects multiple Rad52 species with different electrophoretic mobilities. Here we define the gene products encoded by RAD52. We show that the multiple Rad52 protein species are due to promiscuous choice of start codons as well as post-translational modification. Specifically, Rad52 is phosphorylated both in a cell cycle-independent and in a cell cycle-dependent manner. Furthermore, phosphorylation is dependent on the presence of the Rad52 C terminus, but not dependent on its interaction with Rad51. We also show that the Rad52 protein can be translated from the last three start sites and expression from any one of them is sufficient for spontaneous recombination and the repair of gamma-ray-induced double-strand breaks.
From Business Model to Process Pattern in e-commerce

The basic notions in e-commerce are communicative, institutional, and deontic notions such as obligation, responsibility, and trust. The Language Action approach, therefore, seems to be a most promising framework for designing e-commerce systems. However, the penetration of the Language Action approach in industrial practice is still limited. We discuss some reasons for this state of affairs by identifying a number of problems that hinder an effective application of the Language Action approach. We propose modelling techniques and methodological guidelines that can contribute to the solution of these problems. These techniques and guidelines are based on three building blocks: a business model describing the values exchanged in an e-commerce process, a formal and executable language based on communicating state machines, and an automated designer’s assistant that guides a user from a business model to an executable process model. The copyright of this paper belongs to the paper’s authors. Permission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage. Proceedings of the Sixth International Workshop on the Language-Action Perspective on Communication Modelling (LAP 2001) Montreal, Canada, July 21-22, 2001 (M. Schoop, J. Taylor, eds.) http://www-i5.informatik. rwth-aachen.de/conf/lap2001/ P. Jayaweera, P. Johannesson, and P. Wohed 88 The Language-Action Perspective on Communication Modelling 2001
Global warming will reshuffle the areas of high prevalence and richness of three genera of avian blood parasites

The importance of parasitism for host populations depends on local parasite richness and prevalence: usually host individuals face higher infection risk in areas where parasites are most diverse, and host dispersal to or from these areas may have fitness consequences. Knowing how parasites are and will be distributed in space and time (in a context of global change) is thus crucial from both an ecological and a biological conservation perspective. Nevertheless, most research articles focus just on elaborating models of parasite distribution instead of parasite diversity. We produced distribution models of the areas where haemosporidian parasites are currently highly diverse (both at community and at within‐host levels) and prevalent among Iberian populations of a model passerine host: the blackcap Sylvia atricapilla; and how these areas are expected to vary according to three scenarios of climate change. On the basis of these models, we analysed whether variation among populations in parasite richness or prevalence are expected to remain the same or change in the future, thereby reshuffling the geographic mosaic of host‐parasite interactions as we observe it today. Our models predict a rearrangement of areas of high prevalence and richness of parasites in the future, with Haemoproteus and Leucocytozoon parasites (today the most diverse genera in blackcaps) losing areas of high diversity and Plasmodium parasites (the most virulent ones) gaining them. Likewise, the prevalence of multiple infections and parasite infracommunity richness would be reduced. Importantly, differences among populations in the prevalence and richness of parasites are expected to decrease in the future, creating a more homogeneous parasitic landscape. This predicts an altered geographic mosaic of host‐parasite relationships, which will modify the interaction arena in which parasite virulence evolves.
Spatiotemporal Profiles of Proprioception Processed by the Masseter Muscle Spindles in Rat Cerebral Cortex: An Optical Imaging Study

Muscle spindles in the jaw-closing muscles, which are innervated by trigeminal mesencephalic neurons (MesV neurons), control the strength of occlusion and the position of the mandible. The mechanisms underlying cortical processing of proprioceptive information are critical to understanding how sensory information from the masticatory muscles regulates orofacial motor function. However, these mechanisms are mostly unknown. The present study aimed to identify the regions that process proprioception of the jaw-closing muscles using in vivo optical imaging with a voltage-sensitive dye in rats under urethane anesthesia. First, jaw opening that was produced by mechanically pulling down the mandible evoked an optical response, which reflects neural excitation, in two cortical regions: the most rostroventral part of the primary somatosensory cortex (S1) and the border between the ventral part of the secondary somatosensory cortex (S2) and the insular oral region (IOR). The kinetics of the optical signal, including the latency, amplitude, rise time, decay time and half duration, in the S1 region for the response with the largest amplitude were comparable to those in the region with the largest response in S2/IOR. Second, we visualized the regions responding to electrical stimulation of the masseter nerve, which activates both motor efferent fibers and somatosensory afferent fibers, including those that transmit nociceptive and proprioceptive information. Masseter nerve stimulation initially excited the rostral part of the S2/IOR region, and an adjacent region responded to jaw opening. The caudal part of the region showing the maximum response overlapped with the region responding to jaw opening, whereas the rostral part overlapped with the region responding to electrical stimulation of the maxillary and mandibular molar pulps. These findings suggest that proprioception of the masseter is processed in S1 and S2/IOR. Other sensory information, such as nociception, is processed in a region that is adjacent to these pulpal regions and is located in the rostral part of S2/IOR, which receives nociceptive inputs from the molar pulps. The spatial proximity of these regions may be associated with the mechanisms by which masseter muscle pain is incorrectly perceived as dental pain.
Detecting Emergency Events and Geo-Location Awareness from Twitter Streams

the rapidly increasing number of messages on twitter is quite interesting. Through twitter streaming, this paper is capable of delivering tweets for any keywords from clients all around the world or Hashtag in real-time. However, semantic topic extraction and tracking the userinterested news events from messages on twitter can be considered as a challenging task. In this paper focused on detecting unusual behaviors and geo-social events in Twitter streams. The proposed method is able to provide/manage notifications and awareness (i.e., alerts) for users. In general, there are 4 steps in the process of identifying alerts and current awareness as follows: 1) Applying the set of realtime streaming APIs offered by Twitter for retrieving the public live stream of Twitter messages, 2) Utilizing an online clustering method to form the group of similar messages based on a corpus of text messages, 3) Applying an algorithm to compare the newly extracted event-term candidate with the list of event-term based on timestamp and calculate ranking indicating real-world events by frequent re-tweets, and 4) Identifying the alerts and current awareness based on the user's geo-location. Into the bargain, the proposed method is evaluated using high-volume Twitter data and as a result the findings are reported.
An efficient GSC VSS-APA beamformer with integrated log-energy based VAD for noise reduction in speech reinforcement systems

This paper presents an efficient time-domain Generalized Sidelobe Canceller (GSC) with low signal distortion capabilities using the variable step size affine projection algorithm (VSS-APA) and a log-energy based voice activity detector (VAD). The performance of the proposed VSS-APA based GSC method with integrated log-energy VAD, is illustrated in the context of speech reinforcement application using different signals with low signal-to-noise ratio and different types of noise.
The relationship between environmental exposure to cadmium and lead and blood selenium concentration in randomly selected population of children inhabiting industrial regions of Silesian Voivodship (Poland)

This study aimed at determining the relationship between environmental exposure to lead (Pb) and cadmium (Cd) and blood selenium (Se) concentration in randomly selected population of children inhabiting the industrial regions of Silesian Voivodship, Poland. The study was conducted on a group of consecutive randomly selected 349 children aged below 15 years and inhabiting the industrial regions in Upper Silesia. The examined variables included whole blood Cd concentration (Cd-B), whole blood Pb concentration (Pb-B) and whole blood Se concentration (Se-B). The concentration of Cd-B, Pb-B and Se-B in the studied group of children amounted to 0.26 ± 0.14, 37.62 ± 25.30 and 78.31 ± 12.82 μg/L, respectively. In the entire examined group a statistically significant negative linear relationship was noted between Pb-B and Se-B (r = −0.12, p < 0.05). Also, a statistically insignificant negative correlation was detected between Cd-B and Se-B (r = −0.02, p > 0.05) and a statistically insignificant positive correlation between Pb-B and Cd-B (r = 0.08, p > 0.05). A multivariate backward stepwise regression analysis demonstrated that in the studied group of children higher Pb-B and a more advanced age-represented independent risk factors for a decreased Se-B. Environmental exposure to Pb may represent an independent risk factor for Se deficit in blood of the studied population of children. In children, the lowered Se-B may create one of the mechanisms in which Pb unfavourably affects human body.
Oxidative Stress and Diabetic Vascular Complications

Long-term vascular complications still represent the main cause of morbidity and mortality in diabetic patients. Although prospective randomized long-term clinical studies comparing the effects of conventional and intensive therapy have demonstrated a clear link between diabetic hyperglycemia and the development of secondary complications of diabetes, they have not defined the mechanism through which excess glucose results in tissue damage. Evidence has accumulated indicating that the generation of reactive oxygen species (oxidative stress) may play an important role in the etiology of diabetic complications. This hypothesis is supported by evidence that many biochemical pathways strictly associated with hyperglycemia (glucose autoxidation, polyol pathway, prostanoid synthesis, protein glycation) can increase the production of free radicals. Furthermore, exposure of endothelial cells to high glucose leads to augmented production of superoxide anion, which may quench nitric oxide, a potent endothelium-derived vasodilator that participates in the general homeostasis of the vasculature. In further support of the consequential injurious role of oxidative stress, many of the adverse effects of high glucose on endothelial functions, such as reduced endothelial-dependent relaxation and delayed cell replication, are reversed by antioxidants. A rational extension of this proposed role for oxidative stress is the suggestion that the different susceptibility of diabetic patients to microvascular and macrovascular complications may be a function of the endogenous antioxidant status.
Environment Specific Pleiotropy Facilitates Divergence at the Ectodysplasin Locus in Threespine Stickleback

Adaptive radiation occurs when divergent natural selection in different environments leads to phenotypic differentiation. The pleiotropic effects of underlying genes can either promote or constrain this diversification. Identifying the pleiotropic effects of genes responsible for divergent traits, and testing how the environment influences these effects, can therefore help to provide an understanding of how ecology drives evolutionary change between populations. Positive selection on low-armor alleles at the Ectodysplasin (Eda) locus in threespine stickleback has led to the repeated evolution of reduced armor in populations following freshwater colonization by fully armored marine sticklebacks. Here, we demonstrate that Eda has environmentally determined pleiotropic effects on armor and growth. When raised in freshwater, reduced armor sticklebacks carrying “low” alleles at Eda had increased growth rate relative to fully armored sticklebacks carrying “complete” alleles. In saltwater treatments this growth advantage was present during juvenile growth but lost during adult growth, suggesting that in this environment stickleback are able to develop full armor plates without sacrificing overall growth rate. The environment specific pleiotropic effects of Eda demonstrate that ecological factors can mediate the influence of genetic architecture in driving phenotypic evolution. Furthermore, because size is important for mate choice in stickleback, the growth rate differences influenced by Eda may have effects on reproductive isolation between marine and freshwater populations.
Variation in serum immunoglobulin levels in acute trichinosis

ABSTRACT An early rise in serum IgE levels was observed in five of seven patients with acute primary trichinosis. Parallel increases in the total IgG, IgM and IgA levels, as well as specific IgG and IgM antibody titres to Trichinella spiralis larval antigen, were detected in two. The elevated levels persisted long after the clinical recovery of the patients.
On stability and stabilisation for uncertain stochastic systems with time-delay and actuator saturation

This article concerns the stability analysis and design for uncertain stochastic systems with time-varying delays in state and actuator saturation. The parameter uncertainties belong to a convex polytopic set, and the delays are time varying. A sufficient condition is obtained in terms of a priori designed feedback matrix for determining if a given set is in inside the domain of attraction. Using the linear matrix inequality (LMI) approach, an estimate of the domain of attraction is presented. The problem of designing a state feedback controller such that the domain of attraction is enlarged is formulated through solving an optimisation problem with LMI constraints. A numerical example is given to illustrate the effectiveness of the proposed results.
Regulation of secreted protein production by filamentous fungi: recent developments and perspectives.

Filamentous fungi, typically, are saprophytic organisms which, unlike yeasts, secrete a wide array of enzymes involved in the breakdown and recycling of complex polymers from both plant and animal tissues. This makes them attractive hosts for the production of secreted heterologous proteins (Jeenes et al., 1991; van den Hondel et al., 1991). In only a few examples, however, have the secreted yields of heterologous protein reached the gram per litre levels of many homologous fungal enzymes. In many cases, the problem does not appear to be at the level of transcription but, rather, occurs within the secretory pathway. Although the secretory process has barely been explored in filamentous fungi, we have attempted to identify areas upon which attention should be focused based on current knowledge gained from other systems. We also discuss recent developments in the dissection of transcriptional control in these organisms with particular reference to the interaction of regulatory proteins with fungal promoter regions and to the need for targeting expression cassettes to specific locations in the fungal genome. Understanding the detailed mechanisms of transcriptional control will help in designing modified promoter elements or regulatory factors optimized for a given set of growth conditions. Coupled with the proposed study of the secretory pathway, this should improve the yields of secreted heterologous proteins produced by filamentous fungi.
CERTAIN DEMOGRAPHIC VARIABLES

It is inconsistently reported that despite equal cognitive ability, girls outperform boys is schools. In several methodological steps, the present s tudy examined the level of achievementmotivation, differences in achievementmotivation across gender, academic streams and to find out the significant differences in achievement motivation of students studying in government and private higher secondary s
Anomaly Detection Using Convolutional Sparse Models

where λ > 0 is the parameter balancing the reconstruction error and the sparsity of the feature maps, and ‖dm‖2 = 1 ∀m. Solutions of (2) can be obtained via the Alternating Direction Method of Multipliers (ADMM) algorithm [3], exploiting an efficient formulation [4] in the Fourier domain. Filters can be learned from training images [2]. Our contribution is the design of an anomaly-detection approach monitoring also the local group sparsity of the feature maps, which is shown to be a relevant prior for anomaly detection.
Where is multicast today?

Multicast has been a very active area of research in the nineties. Multicast is uniquely qualified to deliver data in a scalable and efficient manner to a large number of receivers. Steve Deering in his thesis showed how to support multicast routing [1]. Since multicast routing was not supported directly by the routers, the first experiments were carried out building overlays such as the Mbone [2]. In the following, innovative applications using multicast were developed. For a survey of the various aspects of multicast and its applications see the book by S. Paul [3]. In multicast communication, the sender sends data to potentially a large number of receivers, as compared to unicast where there is only one receiver. The fact that there are multiple receivers that may experience heterogeneous transmission conditions with repect to bandwidth, loss and delay poses a number of challenges for the design of multicast error control and congestion control schemes.
Assessing the Gaming Experience using Puppetry

In this paper we address the question: What factors of game experience are measured and have to be measured? by proposing a concept called Puppetry to assess the experience while playing videogames. Puppetry was obtained using qualitative methods on the experiences of players. The main characteristic of Puppetry is that it looks at the common elements of videogames that allow the user to build the experience.
Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila

The polyhomeotic (ph) locus in Drosophila melanogaster consists of the two tandemly duplicated genes ph-d (distal) and ph-p (proximal). They code for transcriptional repressors belonging to the Polycomb group proteins, which regulate homeotic genes and hundreds of other loci. Although the duplication of ph occurred at least 25 million to 30 million years ago, both copies are very similar to each other at both the DNA and the protein levels, probably because of the action of frequent gene conversion. Despite this homogenizing force, differential regulation of both transcriptional units suggests that the functions of the duplicates have begun to diverge. Here, we provide evidence that this functional divergence is driven by positive selection. Based on resequencing of an ≈30-kb region around the ph locus in an African sample of D. melanogaster X chromosomes, we identified a selective sweep, estimated its age and the strength of selection, and mapped the target of selection to a narrow interval of the ph-p gene. This noncoding region contains a large intron with several regulatory elements that are absent in the ph-d duplicate. Our results suggest that neofunctionalization has been achieved in the Drosophila ph genes through the action of strong positive selection and the inactivation of gene conversion in part of the gene.