Miracle-dz/UniFAR-FTUs huggingface dataset:
MODELLING OF THE BINARY INDEPENDENCE RETRIEVAL MODEL

The binary independence retrieval (BIR) model is a main pillar of information retrieval (IR); recently, the model even attracted the attention of database research on ranking tuples for SQL queries. One of the problems with the BIR model is that though it is referred to as a probabilistic model, the retrieval status value actually lacks a probabilistic interpretation since the BIR model is based on the odd (fraction) of the relevance probabilities. This makes it hard to implement the BIR model in a probabilistic reasoning framework that aggregates and generates sound probabilities. Because of the growing impact of the BIR model for database research, and because the aggregation of the BIR term weights lacks a probabilistic meaning, we investigate in this paper the probabilistic relational implementations of the BIR model. This investigation led to the following findings: The probabilistic variants of the BIR model perform at least as good as the genuine model, where slightly refined variants outperform the genuine model, but cannot achieve the performance of tf -idf -based retrieval.
GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays

There is an increasing interest in using single nucleotide polymorphism (SNP) genotyping arrays for profiling chromosomal rearrangements in tumors, as they allow simultaneous detection of copy number and loss of heterozygosity with high resolution. Critical issues such as signal baseline shift due to aneuploidy, normal cell contamination, and the presence of GC content bias have been reported to dramatically alter SNP array signals and complicate accurate identification of aberrations in cancer genomes. To address these issues, we propose a novel Global Parameter Hidden Markov Model (GPHMM) to unravel tangled genotyping data generated from tumor samples. In contrast to other HMM methods, a distinct feature of GPHMM is that the issues mentioned above are quantitatively modeled by global parameters and integrated within the statistical framework. We developed an efficient EM algorithm for parameter estimation. We evaluated performance on three data sets and show that GPHMM can correctly identify chromosomal aberrations in tumor samples containing as few as 10% cancer cells. Furthermore, we demonstrated that the estimation of global parameters in GPHMM provides information about the biological characteristics of tumor samples and the quality of genotyping signal from SNP array experiments, which is helpful for data quality control and outlier detection in cohort studies.
Web Page Evaluation based on Implicit User Reactions and Neural Networks

This paper proposes a method for evaluating web pages by considering implicit user reaction on web pages. Usually users spend more time and make more reactions, such as clicking, dragging and scrolling, while reading interesting pages. Based on this observation, a web page evaluation method by observing implicit user reaction is proposed. The system is designed with Ajax for observing user reactions, and neural networks for learning correlation between user reactions and usefulness of pages. The amounts of each type of user reactions are inputted to neural networks. Also the numbers of characters and images of pages are used as inputs because the amount of users’ behaviors has a tendency to increase as the length of pages increase. The experiment is conducted with 113 people and 74 pages. Each page is ranked by users with a questionnaire. The proposed method shows more close ranking results to the user ranks than Google. That is, our system evaluates web pages more closely to users’ viewpoint than Google. Although our experiment is limited, our result shows powerful potential of new element for web page evaluation. Some approaches evaluate web pages with their contents and some evaluate web pages with structural attributes, particularly links, of pages. Web page evaluation is for users, so the best evaluation can be done by users themselves. So, user feedback is one of the most important factors for web page evaluation. This paper proposes a new method which reflects user feedbacks on web pages.
Heat shock transcription factor activates yeast metallothionein gene expression in response to heat and glucose starvation via distinct signalling pathways

Metallothioneins constitute a class of low-molecular-weight, cysteine-rich metal-binding stress proteins which are biosynthetically regulated at the level of gene transcription in response to metals, hormones, cytokines, and other physiological and environmental stresses. In this report, we demonstrate that the Saccharomyces cerevisiae metallothionein gene, designated CUP1, is transcriptionally activated in response to heat shock and glucose starvation through the action of heat shock transcription factor (HSF) and a heat shock element located within the CUP1 promoter upstream regulatory region. CUP1 gene activation in response to both stresses occurs rapidly; however, heat shock activates CUP1 gene expression transiently, whereas glucose starvation activates CUP1 gene expression in a sustained manner for at least 2.5 h. Although a carboxyl-terminal HSF transcriptional activation domain is critical for the activation of CUP1 transcription in response to both heat shock stress and glucose starvation, this region is dispensable for transient heat shock activation of at least two genes encoding members of the S. cerevisiae hsp70 family. Furthermore, inactivation of the chromosomal SNF1 gene, encoding a serine-threonine protein kinase, or the SNF4 gene, encoding a SNF1 cofactor, abolishes CUP1 transcriptional activation in response to glucose starvation without altering heat shock-induced transcription. These studies demonstrate that the S. cerevisiae HSF responds to multiple, distinct stimuli to activate yeast metallothionein gene transcription and that these stimuli elicit responses through nonidentical, genetically separable signalling pathways.
The DACH/EYA/SIX gene network and its role in tumor initiation and progression

The functional abnormality of developmental genes is a common phenomenon in cancer initiation and progression. The retinal determination gene network (RDGN) is a key signal in Drosophila eye specification, and this conservative pathway is also required for the development of multiple organs in mammalian species. Recent studies demonstrated that aberrant expressions of RDGN components in vertebrates, mainly Dach, Six, and Eya, represent a novel tumor signal. RDGN regulates proliferation, apoptosis, tumor growth and metastasis through interactions with multiple signaling pathways in a co‐ordinated fashion; Dach acts as a tumor suppressor, whereas Six and Eya function as oncogenes. Clinical analyses demonstrated that the expression levels of RDGN correlate with tumor stage, metastasis and survival, suggesting that combinational detection of this pathway might be used as a promising biomarker for the stratification of therapy and for the prediction of the prognosis of cancer patients.
Word Pairs in Language Modeling for Information Retrieval

Previous language modeling approaches to information retrieval have focused primarily on single terms. The use of bigram models has been studied, but the restriction on word order and adjacency may not be justified for information retrieval. We propose a new language modeling approach to information retrieval that incorporates lexical affinities, or pairs of words that occur near each other, without a constraint on word order. The use of compound terms in the vector space model has been shown to outperform the vector model with only single terms (Nie & Dufort, 2002). We explore the use of compound terms in a language modeling approach, and compare our results with the vector space model, and unigram and bigram language model approaches.
Karyotype variability in tropical maize sister inbred lines and hybrids compared with KYS standard line

Maize karyotype variability has been extensively investigated. The identification of maize somatic and pachytene chromosomes has improved with the development of fluorescence in situ hybridization (FISH) using tandemly repeated DNA sequences as probes. We identified the somatic chromosomes of sister inbred lines that were derived from a tropical flint maize population (Jac Duro [JD]), and hybrids between them, using FISH probes for the 180-bp knob repeat, centromeric satellite (CentC), centromeric satellite 4 (Cent4), subtelomeric clone 4-12-1, 5S ribosomal DNA and nucleolus organizing region DNA sequences. The observations were integrated with data based on C-banded mitotic metaphases and conventional analysis of pachytene chromosomes. Heterochromatic knobs visible at pachynema were coincident with C-bands and 180-bp FISH signals on somatic chromosomes, and most of them were large. Variation in the presence of some knobs was observed among lines. Small 180-bp knob signals were invariant on the short arms of chromosomes 1, 6, and 9. The subtelomeric 4-12-1 signal was also invariant and useful for identifying some chromosomes. The centromere location of chromosomes 2 and 4 differed from previous reports on standard maize lines. Somatic chromosomes of a JD line and the commonly used KYS line were compared by FISH in a hybrid of these lines. The pairing behavior of chromosomes 2 and 4 at pachytene stage in this hybrid was investigated using FISH with chromosome-specific probes. The homologues were fully synapsed, including the 5S rDNA and CentC sites on chromosome 2, and Cent4 and subtelomeric 4-12-1 sites on chromosome 4. This suggests that homologous chromosomes could pair through differential degrees of chromatin packaging in homologous arms differing in size. The results contribute to current knowledge of maize global diversity and also raise questions concerning the meiotic pairing of homologous chromosomes possibly differing in their amounts of repetitive DNA.
Fundamentals for a Pragmatic MIMO Performance Evaluation

The user’s experience of a mobile communication system entirely depends on the performance of the bidirectional radio link between the base station (BS) and the handset. Each mobile network operator creates a system of linked BSs located to provide coverage of as large a physical area as possible. While the BS will typically be equipped with a relatively large high-gain antenna and a transmitter cable for delivering some tens of watts of radio frequency (RF) power, the handset relies on an antenna whose dimensions are severely constrained by those of the handset in which it is fitted, with typical maximum effective radiated power of 1 watt. With this said, the communication link quality, and hence the user’s experience, can mainly get as good as the handset antenna performance. Multiple Input Multiple Output (MIMO) has promised the potential for improved data rates and signal quality (Foschini, 1998). The promised improvement in the system’s performance comes at the expense of added challenges, especially from the perspective of handset antenna design. An important aspect in the process of designing a multi-antenna handset is the proper evaluation of its performance. Although the antenna itself can be seen as a deterministic element, its performance becomes random once operated in a realistic, random, environment and in the presence of the operating user. The key questions in ensuring performance are: What are the parameters that need attention when designing the multi-antenna system and how should the evaluation of this system be done? In this chapter the author discusses some aspects that are fundamental for a pragmatic evaluation of multi-antenna system. This becomes especially important to realize at the early stages of a design process when the multi-antenna system is evaluated entirely or partially through simulations.
Primary care access for new patients on the eve of health care reform.

IMPORTANCE Current measures of access to care have intrinsic limitations and may not accurately reflect the capacity of the primary care system to absorb new patients. OBJECTIVE To assess primary care appointment availability by state and insurance status. DESIGN, SETTING, AND PARTICIPANTS We conducted a simulated patient study. Trained field staff, randomly assigned to private insurance, Medicaid, or uninsured, called primary care offices requesting the first available appointment for either routine care or an urgent health concern. The study included a stratified random sample of primary care practices treating nonelderly adults within each of 10 states (Arkansas, Georgia, Illinois, Iowa, Massachusetts, Montana, New Jersey, Oregon, Pennsylvania, and Texas), selected for diversity along numerous dimensions. Collectively, these states comprise almost one-third of the US nonelderly, Medicaid, and currently uninsured populations. Sampling was based on enrollment by insurance type by county. Analyses were weighted to obtain population-based estimates for each state. MAIN OUTCOMES AND MEASURES The ability to schedule an appointment and number of days to the appointment. We also examined cost and payment required at the visit for the uninsured. RESULTS Between November 13, 2012, and April 4, 2013, we made 12,907 calls to 7788 primary care practices requesting new patient appointments. Across the 10 states, 84.7% (95% CI, 82.6%-86.8%) of privately insured and 57.9% (95% CI, 54.8%-61.0%) of Medicaid callers received an appointment. Appointment rates were 78.8% (95% CI, 75.6%-82.0%) for uninsured patients with full cash payment but only 15.4% (95% CI, 13.2%-17.6%) if payment required at the time of the visit was restricted to $75 or less. Conditional on getting an appointment, median wait times were typically less than 1 week (2 weeks in Massachusetts), with no differences by insurance status or urgency of health concern. CONCLUSIONS AND RELEVANCE Although most primary care physicians are accepting new patients, access varies widely across states and insurance status. Navigator programs are needed, not only to help patients enroll but also to identify practices accepting new patients within each plan's network. Tracking new patient appointment availability over time can inform policies designed to strengthen primary care capacity and enhance the effectiveness of the coverage expansions with the Patient Protection and Affordable Care Act.
Hi-Trees and Their Layout

We introduce hi-trees, a new visual representation for hierarchical data in which, depending on the kind of parent node, the child relationship is represented using either containment or links. We give a drawing convention for hi-trees based on the standard layered drawing convention for rooted trees, then show how to extend standard bottom-up tree layout algorithms to draw hi-trees in this convention. We also explore a number of other more compact layout styles for layout of larger hi-trees and give algorithms for computing these. Finally, we describe two applications of hi-trees: argument mapping and business decision support.
Structural Determinants and Mechanism of Action of a GluN2C-selective NMDA Receptor Positive Allosteric Modulator

NMDA receptors are tetrameric complexes of GluN1, GluN2A-D, and GluN3A-B subunits and are involved in normal brain function and neurologic disorders. We identified a novel class of stereoselective pyrrolidinone (PYD) positive allosteric modulators for GluN2C-containing NMDA receptors, exemplified by methyl 4-(3-acetyl-4-hydroxy-1-[2-(2-methyl-1H-indol-3-yl)ethyl]-5-oxo-2,5-dihydro-1H-pyrrol-2-yl)benzoate. Here we explore the site and mechanism of action of a prototypical analog, PYD-106, which at 30 μM does not alter responses of NMDA receptors containing GluN2A, GluN2B, and GluN2D and has no effect on AMPA [α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid] and kainate receptors. Coapplication of 50 μM PYD-106 with a maximally effective concentration of glutamate and glycine increases the response of GluN1/GluN2C NMDA receptors in HEK-293 cells to 221% of that obtained in the absence of PYD (taken as 100%). Evaluation of the concentration dependence of this enhancement revealed an EC50 value for PYD of 13 μM. PYD-106 increased opening frequency and open time of single channel currents activated by maximally effective concentrations of agonist but only had modest effects on glutamate and glycine EC50. PYD-106 selectively enhanced the responses of diheteromeric GluN1/GluN2C receptors but not triheteromeric GluN1/GluN2A/GluN2C receptors. Inclusion of residues encoded by GluN1-exon 5 attenuated the effects of PYD. Three GluN2C residues (Arg194, Ser470, Lys470), at which mutagenesis virtually eliminated PYD function, line a cavity at the interface of the ligand binding and the amino terminal domains in a homology model of GluN1/GluN2C built from crystallographic data on GluN1/GluN2B. We propose that this domain interface constitutes a new allosteric modulatory site on the NMDA receptor.
Issues in IC Implementation of High Level, Abstract Designs

With the exponential explosion in chip complexity there is a growing need for high level design aids. A preliminary experiment was conducted in mating a hierarchical, top-down DA system for data paths with an existing IC placement and router. Nine designs ranging in complexity from 7 to 150 register transfers were synthesized. Strong correlations were observed between high level, abstract measures and final placed and routed chip area. It was observed that use of logic primitives of a moderate level abstraction yielded a 50% savings in placed and routed chip area.
Preparation of novel solid lipid microparticles loaded with gentamicin and its evaluation in vitro and in vivo

Objective: To formulate and evaluate solid-reversed-micellar-solution (SRMS)-based solid lipid microparticles (SLMs) for intramuscular administration of gentamicin. Methods: SRMS formulated with Phospholipon® 90G and Softisan® 154 were used to prepare gentamicin-loaded SLMs. Characterizations based on size and morphology, stability and encapsulation efficiency (EE%) were carried out on the SLMs. In vitro release of gentamicin from the SLMs was performed in phosphate buffer while in vivo release studies were conducted in rats. Results: Maximum EE% of 90.0, 91.6 and 83.0% were obtained for SLMs formed with SRMS 1:1, 1:2 and 2:1, respectively. Stable, spherical and smooth SLMs of size range 9.80 ± 1.46 µm to 33.30 ± 6.42 µm were produced. The release of gentamicin in phosphate buffer varied widely with the lipid contents. Moreover, significant (p < 0.05) amount of gentamicin was released in vivo from the SLMs. Conclusion: SRMS-based SLMs would likely offer a reliable means of delivering gentamicin intramuscularly.
Aryl Hydrocarbon Receptor Antagonists Promote the Expansion of Human Hematopoietic Stem Cells

Stem Cell Expansion The ability to expand hematopoietic stem cells (HSCs) during ex-vivo culture has been an important goal for over 20 years. Using a high-throughput chemical screen, Boitano et al. (p. 1345, published online 5 August; see the Perspective by Sauvageau and Humphries) found that a purine derivative, StemRegenin1 (SR1), promoted the expansion of human HSCs. Treatment of HSCs with SR1 (which blocked the activity of the aryl hydrocarbon receptor) led to the expansion of CD34+ cells and a 12 to 17-fold increase in the number of HSCs that engraft immune deficient mice. The identification of a mechanism for ex vivo amplification may facilitate clinical application of hematopoietic stem cell therapies. Although practiced clinically for more than 40 years, the use of hematopoietic stem cell (HSC) transplants remains limited by the ability to expand these cells ex vivo. An unbiased screen with primary human HSCs identified a purine derivative, StemRegenin 1 (SR1), that promotes the ex vivo expansion of CD34+ cells. Culture of HSCs with SR1 led to a 50-fold increase in cells expressing CD34 and a 17-fold increase in cells that retain the ability to engraft immunodeficient mice. Mechanistic studies show that SR1 acts by antagonizing the aryl hydrocarbon receptor (AHR). The identification of SR1 and AHR modulation as a means to induce ex vivo HSC expansion should facilitate the clinical use of HSC therapy.
The Informed Decisions Toolbox: Tools for Knowledge Transfer and Performance Improvement

In recent years, spurred by developments in evidence-informed medicine, a movement to strengthen evidence-informed managerial decision making in healthcare organizations has emerged in the United States and in other countries. The drivers of this movement include demands by payers and consumer groups for improved quality of care, increased operational efficiency, and greater accountability from healthcare organizations. But numerous barriers to managers' use of evidence in decision making exist, including time pressures, perceived threats to autonomy, preference for colloquial knowledge based on individual experiences, difficulty accessing the relevant evidence base, reliance on external consultants (and others) to determine the quality of the information, and lack of resources. To help managers overcome these barriers, we developed the Informed Decisions Toolbox. It provides tools to help managers efficiently perform the six key steps in the evidence-informed approach to decision making: (1) framing the management question, (2) finding sources of information, (3) assessing the accuracy of the information, (4) assessing the applicability of the information, (5) assessing the actionability of the evidence, and (6) determining if the information is adequate. To build an organizational environment conducive to evidence-informed decision making, we suggest four leadership-driven strategies: (1) recognize and respond to the growing demand for accountability as a strategic issue, (2) establish organizational structures and processes for knowledge transfer, (3) build a questioning organizational culture, and (4) build organizational research capabilities. With organizational support, managers who use the tools presented in the Informed Decisions Toolbox will be able to take control of the decision-making process, will be less reliant on colloquial evidence and consultants, and will be better able to improve the performance of their organizations.
The C‐type lectin‐like domain superfamily

The superfamily of proteins containing C‐type lectin‐like domains (CTLDs) is a large group of extracellular Metazoan proteins with diverse functions. The CTLD structure has a characteristic double‐loop (‘loop‐in‐a‐loop’) stabilized by two highly conserved disulfide bridges located at the bases of the loops, as well as a set of conserved hydrophobic and polar interactions. The second loop, called the long loop region, is structurally and evolutionarily flexible, and is involved in Ca2+‐dependent carbohydrate binding and interaction with other ligands. This loop is completely absent in a subset of CTLDs, which we refer to as compact CTLDs; these include the Link/PTR domain and bacterial CTLDs. CTLD‐containing proteins (CTLDcps) were originally classified into seven groups based on their overall domain structure. Analyses of the superfamily representation in several completely sequenced genomes have added 10 new groups to the classification, and shown that it is applicable only to vertebrate CTLDcps; despite the abundance of CTLDcps in the invertebrate genomes studied, the domain architectures of these proteins do not match those of the vertebrate groups. Ca2+‐dependent carbohydrate binding is the most common CTLD function in vertebrates, and apparently the ancestral one, as suggested by the many humoral defense CTLDcps characterized in insects and other invertebrates. However, many CTLDs have evolved to specifically recognize protein, lipid and inorganic ligands, including the vertebrate clade‐specific snake venoms, and fish antifreeze and bird egg‐shell proteins. Recent studies highlight the functional versatility of this protein superfamily and the CTLD scaffold, and suggest further interesting discoveries have yet to be made.