Miracle-dz/UniFAR-FTUs huggingface dataset:
Health and Quality of Life Outcomes

Background: To examine the associations between vision-targeted health-related quality of life (VT-HRQ) and ocular surface parameters in patients with Sjögren's syndrome, a systemic autoimmune disease characterized by dry eye and dry mouth. Methods: Forty-two patients fulfilling European / American diagnostic criteria for Sjögren's syndrome underwent Schirmer testing without anesthesia, ocular surface vital dye staining; and measurement of tear film breakup time (TBUT). Subjects were administered the Ocular Surface Disease Index (OSDI) and the 25-item National Eye Institute Vision Functioning Questionnaire (NEI-VFQ). Main outcome measures included ocular surface parameters, OSDI subscales describing ocular discomfort (OSDI-symptoms), vision-related function (OSDI-function), and environmental triggers, and NEI-VFQ subscales. Results: Participants (aged 31–81 y; 95% female) all had moderate to severe dry eye. Associations of OSDI subscales with the ocular parameters were modest (Spearman r (ρ) < 0.22) and not statistically significant. Associations of NEI-VFQ subscales with the ocular parameters reached borderline significance for the near vision subscale with TBUT (ρ = 0.32, p = .05) and for the distance vision subscale with van Bijsterveld score (ρ = 0.33, p = .04). The strongest associations of the two questionnaires were for: ocular pain and mental function with OSDI-symptoms (ρ = 0.60 and 0.45, respectively); and general vision, ocular pain, mental function, role function, and driving with OSDI-function (ρ = 0.60, 0.50, 0.61, 0.64, 0.57, and 0.67, respectively). Conclusions: Associations between conventional objective measures of dry eye and VT-HRQ were modest. The generic NEI-VFQ was similar to the disease-specific OSDI in its ability to measure the impact of Sjögren's syndrome-related dry eye on VT-HRQ. Background Dry eye is a common disorder of the ocular surface and tear film and is estimated to affect from 2% to over 15% of persons in surveyed populations, depending on the definition used [1-6]. Symptoms of dry eye are a major reason to seek ophthalmic care: a study by Nelson and coworkers found that 1.3% of Medicare patients had a primary diagnosis of keratoconjunctivitis sicca or dry eye [7]. Dry eye can range from mild to severe disease; although the majority of patients with dry eye experience ocular Published: 01 September 2004 Health and Quality of Life Outcomes 2004, 2:44 doi:10.1186/1477-7525-2-44 Received: 07 July 2004 Accepted: 01 September 2004 This article is available from: http://www.hqlo. com/content/2/1/44 © 2004 Vitale et al; licensee BioMed Central Ltd. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Lexical Access in Chinese Speech Comprehension and Production

This paper offers a description of Chinese speech comprehension and production processes that demonstrates why the word is the unit of lexical access-the Lexical Unit-in Chinese natural speech. It is argued that an access model which posits the morpheme as the Lexical Unit would be unlikely, as it must assume for Chinese either a real-time morpheme combination algorithm (i.e., an on-line grammar that takes morphemes as basic combinatory units) or an improbable lexical processing mechanism in which morphemes are identified as the first step in accessing precompiled words.
Neuromotor Effects of Acute Ethanol Inhalation Exposure in Humans: A Preliminary Study

Neuromotor Effects of Acute Ethanol Inhalation Exposure in Humans: A Preliminary Study: Véronique Nadeau, et al. TOXHUM (Groupe de Recherche en Toxicologie Humaine), Département de Santé Environnementale et Santé au Travail, Université de Montréal, Canada— Ethanol (ETOH) is added to unleaded gasoline to decrease environmental levels of carbon monoxide from automobiles emissions. Therefore, addition of ETOH in reformulated fuel will most likely increase and the involuntarily human exposure to this chemical will also increase. This preliminary study was undertaken to evaluate the possible neuromotor effects resulting from acute ETOH exposure by inhalation in humans. Five healthy non‐smoking adult males, with no history of alcohol abuse, were exposed by inhalation, in a dynamic, controlled‐environment exposure chamber, to various concentrations of ETOH (0, 250, 500 and 1,000 ppm in air) for six hours. Reaction time, body sway, hand tremor and rapid alternating movements were measured before and after each exposure session by using the CATSYSTM 7.0 system and a diadochokinesimeter. The concentrations of ETOH in blood and in alveolar air were also measured. ETOH was not detected in blood nor in alveolar air when volunteers were exposed to 250 and 500 ppm, but at the end of exposure to 1,000 ppm, blood and alveolar air concentrations were 0.443 mg/100ml and 253.1 ppm, respectively. The neuromotor tests did not show conclusively significant differences between the exposed and non‐exposed conditions. In conclusion, this study suggests that acute exposure to ethanol at 1,000 ppm or lower or to concentrations that could be encountered upon refueling is not likely to cause any significant neuromotor alterations in healthy males.
The role of intrinsic motivations in learning sensorimotor vocal mappings: a developmental robotics study

Learning complex mappings between various modalities (typically articulatory, somato­sensory and auditory) is a central issue in computationally modeling speech acquisition. These mappings are generally non­linear and redundant, involving high dimensional sensorimotor spaces. Classical approaches consider two separate phases: a relatively pre-determined exploration phase analogous to infant babbling followed by an exploitation phase involving higher level communicative motivations. In this paper, we consider the problem as a developmental robotics one, in which an agent actively learns sensorimotor mappings of an articulatory vocal model. More specifically, we show how intrinsic motivations can allow the emergence of efficient exploration strategies, driving the way a learning agent will interact with its environment to collect an adequate learning set.
MHC Class II Tetramers

MHC class II tetramers have emerged as an important tool for characterization of the specificity and phenotype of CD4 T cell immune responses, useful in a large variety of disease and vaccine studies. Issues of specific T cell frequency, biodistribution, and avidity, coupled with the large genetic diversity of potential class II restriction elements, require targeted experimental design. Translational opportunities for immune disease monitoring are driving the rapid development of HLA class II tetramer use in clinical applications, together with innovations in tetramer production and epitope discovery.
TinyRNG: A Cryptographic Random Number Generator for Wireless Sensors Network Nodes

Wireless sensors network (WSN) security is a major concern and many new protocols are being designed. Most of these protocols rely on cryptography, and therefore, require a cryptographic pseudo-random number generator (CPRNG). However, designing an efficient and secure CPRNG for wireless sensor networks is not trivial since most of the common source of randomness used by standard CPRNGs are not present on a wireless sensor node. We present TinyRNG, a CPRNG for wireless sensor nodes. Our generator uses the received bit errors as one of the sources of randomness. We show that transmission bit errors on a wireless sensor network are a very good source of randomness. We demonstrate that these errors are randomly distributed and uncorrelated from one sensor to another. Furthermore, we show that these errors are difficult to observe and manipulate by an attacker.
The Agent-Environment Interface: Simon's Indirect or Gibson's Direct Coupling?

A fundamental problem for ecological and cognitive psychology alike is to explain how agents are situated, that is, functionally coupled to their environments so as to facilitate adaptive actions. Herbert Simon (1969/1996) argued that such coupling is artifactual (rule governed), being mediated by symbol functions and necessarily involving information processing. An alternative to this computational approach is offered by James Gibson's (1979/1986) view that the interface is natural (law governed), being a direct informational coupling rather than a symbolically mediated one. This latter view necessarily involves the agent's awareness, whereas the former, being mechanistic, does not. I review the coupling problem from historical, logical, and semantic perspectives. I give arguments that the computational approach provides an inadequate account of situated adaptive actions and founders on the symbol grounding problem, whereas the ecological approach does a better job on both. Personal comments are interspersed throughout, providing an autobiographical perspective on issues germane to these topics.
Distributed and Hierarchical Storage Systems

We discuss issues and technologies for implementing and applying distributed, high-performance storage systems. We review a range of software systems for distributed storage management, and summarise what we believe to be the most important issues and the outstanding problems in distributed storage research. We outline our vision for integrated storage management that is compatible with our DISCWorld wide-area service-based metacomputing environment. Very large on-line archives present a challenge and our driving force for developing a distributed storage system. In addition, robotic tape silos form the lowest level of many of these archives. Their integration into the storage hierarchy is often non-trivial, proprietary and expensive. We describe how our system can provide the necessary infrastructure for such applications.
Modeling human corneal polarization properties and comparison with PS-OCT measurements

Polarization sensitive optical techniques such as Scanning Laser Polarimetry (SLP) or Polarization Sensitive Optical Coherence Tomography (PS-OCT) must take into account corneal polarization changes when imaging the eye fundus. Information about corneal structure is also basic in the diagnosis of corneal disorders. Histological analysis shows that cornea is layered, with fibrils oriented at varying angles. However, this information does not refer to fibril orientation in a macrostructural sense. In this work, we propose a corneal structural model with different fibril arrangements and compare them with in vivo and in vitro PS-OCT measurements. The model is based on a stack of lamellae, represented by Jones theory. Each lamella has a preferred fast axis orientation according to the fibril structure and a birefringence. Optical radiation is parallel to the eye optical axis. A third of the lamellae are arbitrarily oriented. Several fibril configurations were modeled: preferentially horizontal and vertical fibrils; preferentially vertical and radial fibrils; circularly and radially oriented fibrils; and a configuration in which fibrils form arcs that join opposite points of a cross defined over the corneal surface. We also modeled the rotation of the previous configurations and compared them with PS-OCT measurements of in vitro tilted corneas.
Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis

We carried out a systematic evaluation of target selectivity profiles across three recent large-scale biochemical assays of kinase inhibitors and further compared these standardized bioactivity assays with data reported in the widely used databases ChEMBL and STITCH. Our comparative evaluation revealed relative benefits and potential limitations among the bioactivity types, as well as pinpointed biases in the database curation processes. Ignoring such issues in data heterogeneity and representation may lead to biased modeling of drugs' polypharmacological effects as well as to unrealistic evaluation of computational strategies for the prediction of drug-target interaction networks. Toward making use of the complementary information captured by the various bioactivity types, including IC50, K(i), and K(d), we also introduce a model-based integration approach, termed KIBA, and demonstrate here how it can be used to classify kinase inhibitor targets and to pinpoint potential errors in database-reported drug-target interactions. An integrated drug-target bioactivity matrix across 52,498 chemical compounds and 467 kinase targets, including a total of 246,088 KIBA scores, has been made freely available.
Sequence and tissue distribution of a second protein of hepatic gap junctions, Cx26, as deduced from its cDNA

While a number of different gap junction proteins have now been identified, hepatic gap junctions are unique in being the first demonstrated case where two homologous, but distinct, proteins (28,000 and 21,000 Mr) are found within a single gap junctional plaque (Nicholson, B. J., R. Dermietzel, D. Teplow, O. Traub, K. Willecke, and J.-P. Revel. 1987. Nature [Lond.]. 329:732-734). The cDNA for the major 28,000-Mr component has been cloned (Paul, D. L. 1986. J. Cell Biol. 103:123-134) (Kumar, N. M., and N. B. Gilula. 1986. J. Cell Biol. 103:767-776) and, based on its deduced formula weight of 32,007, has been designated connexin 32 (or Cx32 as used here). We now report the selection and characterization of clones for the second 21,000-Mr protein using an oligonucleotide derived from the amino-terminal protein sequence. Together the cDNAs represent 2.4 kb of the single 2.5- kb message detected in Northern blots. An open reading frame of 678 bp coding for a protein with a calculated molecular mass of 26,453 D was identified. Overall sequence homology with Cx32 and Cx43 (64 and 51% amino acid identities, respectively) and a similar predicted tertiary structure confirm that this protein forms part of the connexin family and is consequently referred to as Cx26. Consistent with observations on Cx43 (Beyer, E. C., D. L. Paul, and D. A. Goodenough. 1987. J. Cell Biol. 105:2621-2629) the most marked divergence between Cx26 and other members of the family lies in the sequence of the cytoplasmic domains. The Cx26 gene is present as a single copy per haploid genome in rat and, based on Southern blots, appears to contain at least one intron outside the open reading frame. Northern blots indicate that Cx32 and Cx26 are typically coexpressed, messages for both having been identified in liver, kidney, intestine, lung, spleen, stomach, testes, and brain, but not heart and adult skeletal muscle. This raises the interesting prospect of having differential modes of regulating intercellular channels within a given tissue and, at least in the case of liver, a given cell.
Selecting Text Spans for Document Summaries: Heuristics and Metrics

Human-quality text summarization systems are difficult to design, and even more difficult to evaluate, in part because documents can differ along several dimensions, such as length, writing style and lexical usage. Nevertheless, certain cues can often help suggest the selection of sentences for inclusion in a summary. This paper presents an analysis of news-article summaries generated by sentence extraction. Sentences are ranked for potential inclusion in the summary using a weighted combination of linguistic features - derived from an analysis of news-wire summaries. This paper evaluates the relative effectiveness of these features. In order to do so, we discuss the construction of a large corpus of extraction-based summaries, and characterize the underlying degree of difficulty of summarization at different compression levels on articles in this corpus. Results on our feature set are presented after normalization by this degree of difficulty.
Molecular characterization and phylogenetic analysis of quinolone resistance-determining regions (QRDRs) of gyrA, gyrB, parC and parE gene loci in viridans group streptococci isolated from adult patients with cystic fibrosis.

OBJECTIVES Ciprofloxacin is the most frequently used member of the fluoroquinolones during initial eradication therapy of Pseudomonas aeruginosa, as well as during acute pulmonary exacerbations. However, its long-term effect on the susceptibility of the commensal flora within the cystic fibrosis (CF) airways has not yet been examined. The aim of this study was therefore to examine the consequence of oral ciprofloxacin usage on the resistance of the commensal viridans group streptococci (VGS), in terms of MICs and mutational analysis of the quinolone resistance-determining regions (QRDRs). METHODS The MICs of ciprofloxacin, efflux activities and amino acid substitutions in the QRDRs for 190 isolates of VGS, originating from the sputa of adult CF patients who had been exposed constantly to ciprofloxacin, were examined. VGS organisms included Streptococcus salivarius, Streptococcus mitis, Streptococcus sanguinis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus infantis, Streptococcus gordonii, Streptococcus anginosus, Streptococcus cristatus, Streptococcus australis and Streptococcus mutans. Ciprofloxacin susceptibility was determined by broth microdilution and QRDRs within the gyrA, gyrB, parC and parE gene loci were explored using sequence analysis. RESULTS Twenty-seven (14.2%) streptococcal isolates were resistant to ciprofloxacin (MICs ≥8 mg/L) and 21 (11.1%) had reduced susceptibility (MICs 4 mg/L). As a comparator, clinically non-significant and non-invasive VGS organisms were examined in 12 consecutive non-CF patients in the community, where no resistance to ciprofloxacin was observed. Five novel QRDR PCR assays were developed to elucidate mutations within the CF VGS population, where there were six positions, which corresponded to previously reported quinolone resistance responsible mutations, and eight novel potential QRDR resistance mutations. Double mutations in gyrA and parC/parE led to MICs of 16 to >64 mg/L, while single mutations in parC or parE resulted in MICs of 8-32 mg/L and 8 mg/L, respectively. The mean homologies of each species to Streptococcus pneumoniae R6 were: gyrA, 70.3%-95%; gyrB, 69.6%-96.2%; parC, 76.1%-94.8%; and parE, 70.7%-94.7%. The close relatives of S. pneumoniae, S. mitis and S. oralis, showed high similarity for all four genes (more than 86%). CONCLUSIONS Treatment of P. aeruginosa with oral ciprofloxacin in patients with CF may concurrently reduce antibiotic susceptibility in the commensal VGS flora, where these organisms may potentially act as a reservoir of fluoroquinolone resistance gene determinants for newly acquired and antibiotic-susceptible pathogens, particularly the Streptococcus milleri group.
Combining Content and Quality Indicators in Ranking Ambiguous Query Results On Flickr

When a user submits a text based query to content sharing sites like Flickr, a list of ranked result with limited refinement options are normally provided. Typical options would allow a user to rank the results in different ways such as relevancy, time, or quality respectively. The downside of such approach is that relevant results might not be of high quality while high quality results are often irrelevant. Possible ambiguity of query terms makes it even more difficult to get high quality and relevant results. In this paper we apply link based analysis to combine content and quality indicators for ranking query results in Flickr. Experiment show that our approach are able to identify high quality photos that match a query user's intention and put them at the top of the list. The precision is better than original quality based ranking and possible query expansion results. Our approach relies on a set of seed users representing content and quality preference. We prove experimentally that the ranking is not sensitive to seed user selection, which makes it very practical.
Entrez Gene: gene-centered information at NCBI

Entrez Gene () is NCBI's database for gene-specific information. Entrez Gene includes records from genomes that have been completely sequenced, that have an active research community to contribute gene-specific information or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of both curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases and from other databases within NCBI. Records in Entrez Gene are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is provided via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programing utilities (E-Utilities), and for bulk transfer by ftp.
Aquaporins: The Molecular Basis of Facilitated Water Movement Through Living Plant Cells?

Osmotic effects observed with living cells indicate that their plasma membranes are freely permeable to water while essentially creating a barrier to other molecules. The hydraulic conductivity of biological membranes is sometimes still ascribed to the simple diffusion of water molecules through the lipid bilayer. However, more than 30 years ago the idea was advanced that hydraulic water movement through living cells occurs by bulk flow of water through pores in the membrane (Sidel and Solomon, 1957). Certain membranes of animal cells are unusually permeable to water and there is now a substantial body of evidence for the existence of water transport channels in such membranes (reviewed by Finkelstein, 1987; Verkman, 1992). For example, membranes from red blood cells and renal proximal tubules are exceptionally permeable to water; the membranes of the convoluted dista1 tubules of the kidney are also highly water permeable, and water permeability can be modulated by hormones. The hydraulic conductivity of plant cells has been thoroughly investigated and numerous reviews on this subject have been published (for a recent review, see Steudle, 1992). Many observations on plants and animals support the recent discovery of proteins that form water channels (Preston et al., 1992; Fushimi et al., 1993; Maurel et al., 1993). We proposed to cal1 such proteins "aquaporins" (Agre et al., 1993). These water channel proteins belong to the MIP family, an ancient family of membrane proteins (see Reizer et al., 1993, for review). Aquaporins form water-selective channels, allowing water to pass freely while excluding ions and metabolites. In plants, aquaporins have been demonstrated in the tonoplast (vacuolar membrane) (Hofte et al., 1992), but they also may be present in the plasma membrane (Kammerloher and Schaffner, 1993). In animal cells, aquaporins are found in the plasma membranes of specific cell types. It is important to note that such channels permit or facilitate the movement of water through membranes and do not act as pumps. The driving forces behind water movement are hydraulic or osmotic in nature.