Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating EST Clustering with Simulated Data

Expressed sequence tags (ESTs) provide a rapid and inexpensive approach to gene sequencing, gene discovery, and the characterization of gene regulation and alternate splicings. The first step in using ESTs is to cluster them, that is, to group them according to the gene that produced them. In these applications, clustering performance and quality are the most critical issues. Most efforts in EST clustering have focused on biological data, but such data make assessment of clustering quality and robustness difficult. In this paper, we use the EST simulator of Hazelhurst and Bergheim, ESTSim, to study experimentally the accuracy and robustness of four different EST clustering tools, ESTate, N2tool, BlastClust, and simple hierarchical agglomerative clustering based on Smith-Waterman similarities, using the Rand index as a measure of clustering quality. Our results indicate that N2tool consistently dominates BlastClust and that, in turn, ESTate and clustering based on Smith-Waterman similarities greatly outperform N2tool, with the much slower Smith-Waterman-based clustering slightly outperforming ESTate. We also find that, of the various parameters affecting EST generation that can be set in the ESTSim simulator (EST length, indels and substitutions, polymerase decay, stutter, and ligation), polymerase decay has by far the largest effect on the quality of clustering—a finding that could lead to improved EST and assembly quality through the control of bench procedures.
Perceptions of medical sciences students towards probiotics.

BACKGROUND Regarding the importance of probiotics in prevention of different diseases, the knowledge of people particularly health-related professionals about the beneficial effects and availability of probiotic products is important. Considering the limited studies, the present study was conducted to assess the knowledge of medical sciences students as future provider of health information about probiotics in Tabriz, Iran. METHODS This cross-sectional study was carried out on 296 medical sciences students from different faculty majors with mean age of 22 ± 4 years. The students completed two self-administered questionnaires; the one was about the demographic characteristics and the other one with nine closed questions as for knowledge as well as probiotics and their health effects and 2 questions related to availability of probiotic products. Scoring of 9 knowledge questions was divided to three sections 0-3, 4-6, 7-9 and classified as poor, acceptable and good, respectively. The Chi-square test was used to examine the differences in knowledge of the students across different gender, major and degree groups. RESULTS Six percent of students had poor, 43% acceptable, and 51% good knowledge. Total mean±(SD) of knowledge was 6.25 ±1.6 . Answers of students about the availability of probiotic products were 36.9% low, 48.1% moderate, and 15% high. Comparison of knowledge result between different major and degree groups was statistically significant (P<0.05). CONCLUSION Although students had approximately acceptable level of knowledge about probiotics and their health effects, their awareness about common available form of probiotic products was low. The use of efficient co-educational materials such as teaching new findings for students may be beneficial.
Strange stars as persistent sources of gravitational waves

We investigate the relevance of the gravitational-wave driven r-mode instability for strange stars. We find that the unstable r-modes affect strange stars in a way that is quite distinct from the neutron star case. For accreting strange stars, we show that the onset of r-mode instability does not lead to the thermo-gravitational runaway that is likely to occur in neutron stars. Instead, the strange star evolves towards a quasi-equilibrium state on a time-scale of about a year. This mechanism could thus explain the clustering of spin frequencies inferred from kHz quasi-periodic oscillation data in low-mass X-ray binaries. For young strange stars, we show that the r-mode driven spin-evolution is also distinct from the neutron star case. In a young strange star, the r-mode undergoes short cycles of instability during the first few months. This is followed by a quasi-adiabatic phase where the r-mode remains at a small, roughly constant, amplitude for thousands of years. Another distinguishing feature from the neutron star case is that the r-modes in a strange star never grow to amplitudes of the order of unity. Our results suggest that the r-modes in a strange star emit a persistent gravitational-wave signal that should be detectable with large-scale interferometers given an observation time of a few months. If detected, these signals would provide unique evidence for the existence of strange stars, which would put useful constraints on the parameters of quantum chromodynamics.
Hierarchical Classifier Design Using Mutual Information

A nonparametric algorithm is presented for the hierarchical partitioning of the feature space. The algorithm is based on the concept of average mutual information, and is suitable for multifeature multicategory pattern recognition problems. The algorithm generates an efficient partitioning tree for specified probability of error by maximizing the amount of average mutual information gain at each partitioning step. A confidence bound expression is presented for the resulting classifier. Three examples, including one of handprinted numeral recognition, are presented to demonstrate the effectiveness of the algorithm.
Carbon Balance and Management

Background: Carbon plantations are introduced in climate change policy as an option to slow the build-up of atmospheric carbon dioxide (CO2) concentrations. Here we present a methodology to evaluate the potential effectiveness of carbon plantations. The methodology explicitly considers future long-term land-use change around the world and all relevant carbon (C) fluxes, including all natural fluxes. Both issues have generally been ignored in earlier studies. Results: Two different baseline scenarios up to 2100 indicate that uncertainties in future land-use change lead to a near 100% difference in estimates of carbon sequestration potentials. Moreover, social, economic and institutional barriers preventing carbon plantations in natural vegetation areas decrease the physical potential by 75–80% or more. Nevertheless, carbon plantations can still considerably contribute to slowing the increase in the atmospheric CO2 concentration but only in the long term. The most conservative set of assumptions lowers the increase of the atmospheric CO2 concentration in 2100 by a 27 ppm and compensates for 5–7% of the total energy-related CO2 emissions. The net sequestration up to 2020 is limited, given the short-term increased need for agricultural land in most regions and the long period needed to compensate for emissions through the establishment of the plantations. The potential is highest in the tropics, despite projections that most of the agricultural expansion will be in these regions. Plantations in high latitudes as Northern Europe and Northern Russia should only be established if the objective to sequester carbon is combined with other activities. Conclusion: Carbon sequestration in plantations can play an important role in mitigating the buildup of atmospheric CO2. The actual magnitude depends on natural and management factors, social barriers, and the time frame considered. In addition, there are a number of ancillary benefits for local communities and the environment. Carbon plantations are, however, particularly effective in the long term. Furthermore, plantations do not offer the ultimate solution towards stabilizing CO2 concentrations but should be part of a broader package of options with clear energy emission reduction measures. Published: 15 April 2008 Carbon Balance and Management 2008, 3:3 doi:10.1186/1750-0680-3-3 Received: 20 December 2007 Accepted: 15 April 2008 This article is available from: http://www.cbmjournal. com/content/3/1/3 © 2008 van Minnen 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.
Design of Hierarchical Fuzzy Logic Control for Mobile Robot System

This paper studies the problem of motion and control law design for a mobile robot that moves inside a partially unknown environment, under the assumption of parametric uncertainty in the model that describes the motion of the robot. This paper deals with a fuzzy-based intelligent mobile robotic system by hierarchical structure that requires various capabilities normally associated with intelligence. The proposed method is applied for a path planning problem of a mobile robot; the effectiveness of the method is illustrated through some experiment
Essays in industrial organisation

This thesis presents four largely independent essays on industrial organisation. The first three essays examine how search and switching costs distort competitive markets, whilst the fourth essay studies how firms themselves might eliminate competition by agreeing to fix the market price. The key insight from the first two essays is that by choosing to pay a search cost, a consumer reveals to a retailer some private information about their product valuations. In this context the first essay re-examines the well-known theoretical Diamond Paradox in which markets completely break down if firms sell only a single product. I demonstrate that multiproduct retailers offer an elegant and realistic way of overcoming this Paradox, and then apply the model to supermarkets. In particular, this essay provides new insights into why convenience stores charge high prices and why grocery stores use selected loss-leaders. The second essay looks at internet search and therefore focuses on the special case in which search frictions become very small. It seeks to explain why retailers pay so much for online advertising, when consumers can easily click on whichever links they like. I show that if consumers have prior information about products, their search behaviour is limited but very informative about their preferences. This places prominent firms in a privileged position, and makes them substantially more profitable. The third essay provides a simple model in which small switching costs are pro-competitive and beneficial to consumers. This challenges the conventional wisdom, but also argues that switching costs should be less of a policy priority than search costs. The final essay examines a game in which two firms bargain over a collusive price. It is shown that entry into such a market may make collusion easier, and may increase price.
Modulation of gonadotropin levels by peptides acting at the anterior pituitary gland.

There are several lines of evidence that point to peptides participating in the regulation of LH and/or FSH levels by action at the pituitary. This evidence includes altered secretion of gonadotropins from the anterior pituitary cells or tissue in vitro when exposed to the peptide. Additionally, modification of GnRH-stimulated LH/FSH secretion has been observed. Furthermore, there is potential for a separately modulated interaction with the primed response. Another potential of action is by interaction among non-GnRH peptides on gonadotropin-regulating processes, although there are no good data available on this aspect. Other observations, consistent with a pituitary role for the peptides in modulation of LH, include detection of the peptides in portal blood, detection of high-affinity receptors or receptor mRNA in the pituitary, and detection of intrapituitary peptide or peptide mRNA in the pituitary. The modulation by steroids of both concentrations and type of activities provides a further level of physiological refinement. There is, however, some confusion regarding the involvement of these peptides in gonadotropin control. The reasons can be seen by considering aspects of investigations. There are experimental variations such as 1) species studied, e.g., NPY has been reported to have an effect on LH secretion from rat cells (168) but not on sheep anterior pituitary tissue (64), and substance P inhibits GnRH-stimulated release from rat cells (182) but potentiates the response in prepubertal porcine cells (92); 2) the steroidal conditions under which the study is performed, e.g., NPY has opposite effects in certain endocrine environments, augmenting GnRH-stimulated LH release in proestrus-like conditions (168), and inhibiting in metestrus-like environment (66); 3) the type of cell preparation, e.g., responsiveness to substance P might depend on whether cells in overnight culture were in separated or clustered state (91); 4) the time course considered, e.g., oxytocin that might induce marked LH release from pituitary cells after a longer length of incubation than GnRH requires (68); 5) length of exposure to peptide, e.g., endothelin that augmented or inhibited GnRH-stimulated LH release (50); 6) In addition, it is possible that the traditional endpoint selected in such studies, namely, observation of gonadotropin secretion, is not necessarily the most important for these peptides (56, 81, 117). Unfortunately, at this stage a definitive answer to the question "What do the peptides actually do? " cannot be provided and we remain tantalized by the glimpses of potential roles. Perhaps in a few years an updated review will be able to include a more complete answer. It is necessary for the full understanding of LH control that not only the properties of the peptides in isolation be characterized but also their interactions.
The Simple Clinical Score predicts mortality for 30 days after admission to an acute medical unit.

BACKGROUND Predictive scores such as APACHE II and SAPS II have been used to assess patients in intensive care units, but only the modified early warning (MEW) score has been used to assess acutely ill general medical patients. DESIGN Observational study of predictors of mortality. SETTING Small Irish rural hospital. METHODS From 17 February 2000 to 29 January 2004, 9,964 consecutive patients admitted as acute medical emergencies were divided into a derivation cohort of 6,736 patients and a validation cohort of 3,228 patients. RESULTS In the derivation cohort, 316 patients (4.7%) died within 30 days of hospital admission. Under univariate analysis, age, vital signs and 18 categorical variables were associated with increased risk of death, and nine with reduced risk. Logistic regression identified 16 independent predictors of 30-day mortality, from which the Simple Clinical Score was derived, stratifying patients into five risk classes. In each class, mortality was not significantly different between the derivation and validation cohorts: 0-0.1% for very low risk, 1.5-1.6% for low risk, 3.8-3.9% for average risk, 9.0-10.3% for high risk, and 29.2-34.4% for very high risk. DISCUSSION The Simple Clinical Score quickly and accurately identifies patients at both a low and high risk of death from the first to the 30th day after admission, enabling prompt triage and placement within a health-care facility.
Stemming and similarity measures for Arabic Documents Clustering

Arabic Documents Clustering is an important task for obtaining good results with the traditional Information Retrieval (TR) systems especially with the rapid growth of the number of online documents present in Arabic language. Document clustering aims to automatically group similar documents in one cluster using different similarity/distance measures. In this paper, we evaluate the impact of the stemming on the Arabic Text Document Clustering with five similarity/distance measures: Euclidean Distance, Cosine Similarity, Jaccard Coefficient, Pearson Correlation Coefficient and Averaged Kullback-Leibler Divergence, for the testing dataset. Our experiments on this latter show that the use of the stemming will not yield good results, but makes the representation of the document smaller and the clustering faster.
Triangle groups and Jacobians of CM type

In the last years, two new tools have been developed for an approach to the question whether a given nonsingular projective algebraic curve over a number field has a Jacobian of CM type. First, such curves can be characterized by the existence of Belyi functions or Grothendieck’s dessins d’enfants ([Be], [Gr], [VS], [CIW], [JS3]) — for detailed definitions see Section 1. There is some reasonable hope that dessins also encode deeper properties of curves which has already been proved for places of bad reduction ([Fu], [Bec]), so one should try to read information about the endomorphism algebra of the Jacobian also from combinatorial properties of dessins. We will mainly consider regular dessins or equivalently, Riemann surfaces with many automorphisms. The reduction to this particular case is described in Section 2. Second, there has been considerable progress in transcendence. A classical criterion due to Th. Schneider says that an elliptic curve defined over Q̄ has complex multiplication if and only if the period quotient is algebraic. From Wüstholz’ analytic subgroup theorem follows a generalization to abelian varieties and their period quotients in the Siegel upper half space ([Coh], [SW], see Theorem 3) and has applications in particular to curves with many automorphisms (Sections 4 and 7). The key in joining both tools is the use of the canonical representation of the automorphism group G of the curve X on the space of holomorphic differentials. The Jacobian of X is isogenous to a direct product A1 1 × . × Am m
Total Laparoscopic Hysterectomy in Patients with Large Uteri: Comparison of Uterine Removal by Transvaginal and Uterine Morcellation Approaches

The aim of this study was to compare the clinical results of total laparoscopic hysterectomy (TLH) for large uterus with uterus size of 12 gestational weeks (g.w.) or greater through transvaginal or uterine morcellation approaches. We retrospectively collected the clinical data of those undergoing total laparoscopic hysterectomies between January 2004 and June 2012. Intraoperative and postoperative outcomes were compared between patients whose large uterus was removed through transvaginal or morcellation approaches. The morcellation group has significantly shorter mean operation time and uterus removal time and smaller incidence of intraoperative complications than the transvaginal group (all P < 0.05). No statistical significant difference regarding the mean blood loss, uterine weight, and length of hospital stay was noted in the morcellation and transvaginal groups (all P > 0.05). In two groups, there was one patient in each group who underwent conversion to laparotomy due to huge uterus size. With regard to postoperative complications, there was no statistical significant difference regarding the frequencies of pelvic hematoma, vaginal stump infection, and lower limb venous thrombosis in two groups (all P > 0.05). TLH through uterine morcellation can reduce the operation time, uterus removal time, and the intraoperative complications and provide comparable postoperative outcomes compared to that through the transvaginal approaches.
Effect of Intent Descriptions on Retrieval Evaluation

Test collections play an important role in adhoc and diversity retrieval evaluation. Constructing a test collection for adhoc evaluation involves (1) selecting a set of queries to be judged, (2) selecting an intent (topic) description for that query, and (3) obtaining relevance judgments with respect to the specific intent description for that particular query. Recent work showed that the selection of intents play an important role in the relative performance of retrieval systems for diversity evaluation. However, no previous work has analysed how the choice of a specific intent description may affect adhoc evaluation. We show that intent descriptions have a significant impact in adhoc evaluation and that special care should be given as to how the intent descriptions are selected. We further show that it is better to have very general intent descriptions or no intent descriptions at all when constructing test collections for adhoc evaluation. We then focus on diversity evaluation and identify the effect intent descriptions have on diversity based retrieval evaluation. We quantify this effect and discuss experimental design decisions for the optimal distribution of judgment effort across different intents for a query vs. different queries.
Non-host Resistance: DNA Damage Is Associated with SA Signaling for Induction of PR Genes and Contributes to the Growth Suppression of a Pea Pathogen on Pea Endocarp Tissue

Salicylic acid (SA) has been reported to induce plant defense responses. The transcriptions of defense genes that are responsible for a given plant’s resistance to an array of plant pathogens are activated in a process called non-host resistance. Biotic signals capable of carrying out the activation of pathogenesis-related (PR) genes in pea tissue include fungal DNase and chitosan, two components released from Fusarium solani spores that are known to target host DNA. Recent reports indicate that SA also has a physical affinity for DNA. Here, we report that SA-induced reactive oxygen species release results in fragment alterations in pea nuclear DNA and cytologically detectable diameter and structural changes in the pea host nuclei. Additionally, we examine the subsequent SA-related increase of resistance to the true pea pathogen F. solani f.sp. pisi and the accumulation of the phytoalexin pisatin. This is the first report showing that SA-induced PR gene activation may be attributed to the host pea genomic DNA damage and that at certain concentrations, SA can be temporally associated with subsequent increases in the defense response of this legume.
A Novel Path Loss Model for High-Speed Railway Viaduct Scenarios

This paper presents an empirical path loss model derived from the 930MHz measurements along "Zhengzhou-Xi'an" high-speed railway in China. All the measurements were taken on the viaduct with the height of 23 meters above the ground surface. It applies to distances and base station antenna effective heights h not well-covered by existing models. The Least Squares Method (LS) is utilized in the curve fitting. The path loss exponent n determined by the slop of the linear fitting curve is statistically modeled, with the considering of base station antenna effective height h. Based on the log-normal shadowing model, a novel path loss model was developed. The proposed path loss model applies to high-speed railway viaduct scenarios, with base antenna heights from 15 to 30 m, base-to-train distances from 0.5 to 4 km. Compared with Hata and Winner II models, it raises path loss prediction accuracy for 3～10 dB and reduces the standard deviation by 1～3 dB.
Calcium in the initiation, progression and as an effector of Alzheimer’s disease pathology

• Introduction ‐ Familial and sporadic AD ‐ APP processing and the amyloid cascade hypothesis • Calcium in the initiation of pathology ‐ Effects of calcium on APP processing and Aβ deposition/aggregation ‐ Genetic linkage in calcium related genes and AD ‐ Apoε4 and calcium ‐ Calcium and APP processing ‐ Synaptic regulation of Aβ production ‐ Normal age‐related changes in calcium homeostasis and AD pathology ‐ Age‐related reductions in autophagy • Calcium in disease progression ‐ Linking Aβ and τ ‐ Calcium, calpains and τ pathology • Calcium as a disease effector ‐ Synaptic calcium dyshomeostasis and AD – a focus on NMDA receptors ‐ Aβ elevates cytosolic intracellular calcium levels in vivo ‐ Aβ and mitochondrial calcium dyshomeostasis • Current therapeutics • Conclusions