Miracle-dz/UniFAR-FTUs huggingface dataset:
An artificially induced follicle stimulating hormone surge at the time of human chorionic gonadotrophin administration in controlled ovarian stimulation cycles has no effect on cumulus expansion, fertilization rate, embryo quality and implantation rate.

In the spontaneous menstrual cycle, the mid-cycle gonadotrophin surge causes maturation of the cumulus-oocyte complex, mucification of cumulus cells and expansion of the cumulus oophorus, resumption of meiosis and maturation of the cytoplasm of the oocyte. Whether this is an effect purely of luteinizing hormone (LH) or whether follicle stimulating hormone (FSH) also plays a role is unknown. The effect of an artificially induced FSH surge at the time of human chorionic gonadotrophin (HCG) injection on maturation of the cumulus-oocyte complex was investigated in a prospective randomized double-blind trial. Twelve patients underwent controlled ovarian hyperstimulation [long gonadotrophin-releasing hormone agonist (GnRHa)/human menopausal gonadotrophin (HMG) protocol] for in-vitro fertilization (IVF) treatment. At the time of HCG administration, six patients received a bolus injection of FSH (450 IU i.m.); the other six patients received a placebo. The peak plasma concentrations of FSH of the experimental group were compared with the peak values of FSH obtained at the mid-cycle gonadotrophin surge of the natural cycle of a group of 12 volunteers to validate the bolus injection of FSH. Maturation of the cumulus-oocyte complex was quantified by measuring the expansion of the cumulus, by the fertilization rate and the implantation rate. The quality of the embryos was scored according the average morphology score. The bolus injection of FSH mimicked the mid-cycle gonadotrophin surge. The mean peak value of FSH (12.9 IU/l) in the experimental group was fully comparable with the mean peak value of FSH (10.0 IU/l) of the mid-cycle gonadotrophin surge in the natural cycle. No effect of a bolus injection of FSH on the maturation of the cumulus-oocyte complex or any other outcome variable was found. It is not advantageous to combine the final HCG injection with a bolus injection of FSH in GnRHa/HMG stimulated cycles.
Multiple Alignment Using Hidden Markov Models

A simulated annealing method is described for training hidden Markov models and producing multiple sequence alignments from initially unaligned protein or DNA sequences. Simulated annealing in turn uses a dynamic programming algorithm for correctly sampling suboptimal multiple alignments according to their probability and a Boltzmann temperature factor. The quality of simulated annealing alignments is evaluated on structural alignments of ten different protein families, and compared to the performance of other HMM training methods and the ClustalW program. Simulated annealing is better able to find near-global optima in the multiple alignment probability landscape than the other tested HMM training methods. Neither ClustalW nor simulated annealing produce consistently better alignments compared to each other. Examination of the specific cases in which ClustalW outperforms simulated annealing, and vice versa, provides insight into the strengths and weaknesses of current hidden Markov model approaches.
Constant Factor Approximation for Capacitated k-Center with Outliers

The $k$-center problem is a classic facility location problem, where given an edge-weighted graph $G = (V,E)$ one is to find a subset of $k$ vertices $S$, such that each vertex in $V$ is "close" to some vertex in $S$. The approximation status of this basic problem is well understood, as a simple 2-approximation algorithm is known to be tight. Consequently different extensions were studied. In the capacitated version of the problem each vertex is assigned a capacity, which is a strict upper bound on the number of clients a facility can serve, when located at this vertex. A constant factor approximation for the capacitated $k$-center was obtained last year by Cygan, Hajiaghayi and Khuller [FOCS'12], which was recently improved to a 9-approximation by An, Bhaskara and Svensson [arXiv'13]. In a different generalization of the problem some clients (denoted as outliers) may be disregarded. Here we are additionally given an integer $p$ and the goal is to serve exactly $p$ clients, which the algorithm is free to choose. In 2001 Charikar et al. [SODA'01] presented a 3-approximation for the $k$-center problem with outliers. In this paper we consider a common generalization of the two extensions previously studied separately, i.e. we work with the capacitated $k$-center with outliers. We present the first constant factor approximation algorithm with approximation ratio of 25 even for the case of non-uniform hard capacities.
An Analysis of Galileo E 5 Signal Acquisition Strategies

Nagaraj C Shivaramaiah is currently a doctoral student within the GNSS receiver design group in the School of Surveying and Spatial Information Systems at the University of New South Wales, Australia. He obtained his Masters degree from the Centre for Electronics Design and Technology at Indian Institute of Science, Bangalore, India. His research interests include base band signal processing and FPGA based receiver design for GNSS.
Output consensus control for heterogeneous multi-agent systems

We study distributed output feedback control of a heterogeneous multi-agent system (MAS), consisting of N different continuous-time dynamic systems. Conditions on the existence of distributed output feedback control protocols are derived and a solution is proposed to synthesize the stabilizing and consensus control protocols over directed graphs. The results in this paper complement the existing ones, and are illustrated by a numerical example.
Algorithms for Wireless Capacity

In this paper, we address two basic questions in wireless communication. First, how long does it take to schedule an arbitrary set of communication requests? Second, given a set of communication requests, how many of them can be scheduled concurrently? Our results are derived in the signal-to-interference-plus-noise ratio (SINR) interference model with geometric path loss and consist of efficient algorithms that find a constant approximation for the second problem and a logarithmic approximation for the first problem. In addition, we show that the interference model is robust to various factors that can influence the signal attenuation. More specifically, we prove that as long as influences on the signal attenuation are constant, they affect the capacity only by a constant factor.
Serial-omics characterization of equine urine

Horse urine is easily collected and contains molecules readily measurable using mass spectrometry that can be used as biomarkers representative of health, disease or drug tampering. This study aimed at analyzing microliter levels of horse urine to purify, identify and quantify proteins, polar metabolites and non-polar lipids. Urine from a healthy 12 year old quarter horse mare on a diet of grass hay and vitamin/mineral supplements with limited pasture access was collected for serial-omics characterization. The urine was treated with methyl tert-butyl ether (MTBE) and methanol to partition into three distinct layers for protein, non-polar lipid and polar metabolite content from a single liquid-liquid extraction and was repeated two times. Each layer was analyzed by high performance liquid chromatography—high resolution tandem mass spectrometry (LC-MS/MS) to obtain protein sequence and relative protein levels as well as identify and quantify small polar metabolites and lipids. The results show 46 urine proteins, many related to normal kidney function, structural and circulatory proteins as well as 474 small polar metabolites but only 10 lipid molecules. Metabolites were mostly related to urea cycle and ammonia recycling as well as amino acid related pathways, plant diet specific molecules, etc. The few lipids represented triglycerides and phospholipids. These data show a complete mass spectrometry based—omics characterization of equine urine from a single 333 μL mid-stream urine aliquot. These omics data help serve as a baseline for healthy mare urine composition and the analyses can be used to monitor disease progression, health status, monitor drug use, etc.
Molecular Characterization of the Ankle-Link Complex in Cochlear Hair Cells and Its Role in the Hair Bundle Functioning

Several lines of evidence indicate that very large G-protein-coupled receptor 1 (Vlgr1) makes up the ankle links that connect the stereocilia of hair cells at their base. Here, we show that the transmembrane protein usherin, the putative transmembrane protein vezatin, and the PDZ (postsynaptic density-95/Discs large/zona occludens-1) domain-containing submembrane protein whirlin are colocalized with Vlgr1 at the stereocilia base in developing cochlear hair cells and are absent in Vlgr1−/− mice that lack the ankle links. Direct in vitro interactions between these four proteins further support their involvement in a molecular complex associated with the ankle links and scaffolded by whirlin. In addition, the delocalization of these proteins in myosin VIIa defective mutant mice as well as the myosin VIIa tail direct interactions with vezatin, whirlin, and, we show, Vlgr1 and usherin, suggest that myosin VIIa conveys proteins of the ankle-link complex to the stereocilia. Adenylyl cyclase 6, which was found at the base of stereocilia, was both overexpressed and mislocated in Vlgr1−/− mice. In postnatal day 7 Vlgr1−/− mice, mechanoelectrical transduction currents evoked by displacements of the hair bundle toward the tallest stereocilia (i.e., in the excitatory direction) were reduced in outer but not inner hair cells. In both cell types, stimulation of the hair bundle in the opposite direction paradoxically resulted in significant transduction currents. The absence of ankle-link-mediated cohesive forces within hair bundles lacking Vlgr1 may account for the electrophysiological results. However, because some long cadherin-23 isoforms could no longer be detected in Vlgr1−/− mice shortly after birth, the loss of some apical links could be involved too. The premature disappearance of these cadherin isoforms in the Vlgr1−/− mutant argues in favor of a signaling function of the ankle links in hair bundle differentiation.
Analysis of Non-Rectangular Laminated Anisotropic Plates by Chebyshev Collocation Method

The purpose of this work is to solve the governing differential equations of arbitrarily non-rectangular laminated anisotropic plates by using the Chebyshev collocation method. The four sides of the plate herein are not restricted to be straight lines, and they can be curves as well. Meanwhile, these four sides can be expressed in four mathematical functions. The transformation from non-rectangular boundary into rectangular type is the key point to the solution of this kind of problems. In general, the research on laminated anisotropic plates is almost focused on the case of rectangular plate. It is difficult to handle the laminated anisotropic plate problems with non-rectangular borders, any kind of stacking sequence and the variety of boundary conditions. However, through the merits of Chebyshev collocation method, such problems can be overcome as stated as follows. Two cases in EXAMPLES section are illustrated to highlight the displacements, stress resultants and moment resultants of our proposed work. The preciseness is also found in comparison with the numerical results by using finite element method incorporated with the software of NASTRAN.
From Objects to Landmarks: The Function of Visual Location Information in Spatial Navigation

Landmarks play an important role in guiding navigational behavior. A host of studies in the last 15 years has demonstrated that environmental objects can act as landmarks for navigation in different ways. In this review, we propose a parsimonious four-part taxonomy for conceptualizing object location information during navigation. We begin by outlining object properties that appear to be important for a landmark to attain salience. We then systematically examine the different functions of objects as navigational landmarks based on previous behavioral and neuroanatomical findings in rodents and humans. Evidence is presented showing that single environmental objects can function as navigational beacons, or act as associative or orientation cues. In addition, we argue that extended surfaces or boundaries can act as landmarks by providing a frame of reference for encoding spatial information. The present review provides a concise taxonomy of the use of visual objects as landmarks in navigation and should serve as a useful reference for future research into landmark-based spatial navigation.
Automatic Verb Classification Using a General Feature Space

Automatic Verb Classification Using a General Feature Space Eric Joanis Master of Science Graduate Department of Computer Science University of Toronto 2002 We develop a general feature space that can be used for the semantic classification of English verbs. We design a technique to extract these features from a large corpus of English, while trying to maintain portability to other languages—the only language-specific tools we use to extract our core features are a part-of-speech tagger and a partial parser. We show that our general feature space reduces the chance error rate by 40% or more in ten experiments involving from two to thirteen verb classes. We also show that it usually performs as well as features that are selected using specific linguistic expertise, and that it is therefore unnecessary to manually do linguistic analysis for each class distinction of interest. Finally, we consider the use of an automatic feature selection technique, stepwise feature selection, and show that it does not work well with our feature space.
* on Jackknifing Kernel Regression Function Estimators

"Estimation of the value of a regression function at a point of continuity using a kernel-type estimator is discussed and improvements of the technique by a generalized jackknife estimator are presented. It is shown that the generalized jackknife technique produces estimators with faster bias rates. In a small example it is investigated, if the generalized jackknife method works for all choices of bandwidths. It turns out that an improper choice of this parameter may inflate the mean square error of the generalized jackknife estimator. AMS Subject Classifications: Primary 62G05, Secondary 62J02.
Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naïve vs. Formal

Applications exploiting the hierarchical relations recorded in the Unified Medical Language System (UMLS) Metathesaurus suffer from the presence of inconsistencies in these relations. A formal approach to identifying and eliminating circular hierarchical relations has been proposed in previous work, leading to the creation of a directed acyclic Metathesaurus graph. However, this approach is at best semi-automatic and its implementation is far from trivial. A simpler, alternative approach consists in avoiding loops while traversing the Metathesaurus graph by preventing nodes from being visited twice. Our objective is to evaluate the benefit of the formal approach to eliminating cycles over a naïve approach to avoiding them. To this end, we compared the size and semantic coherence of sets of descendants obtained by both approaches. 12% of the concepts with descendants exhibit some differences. The formal approach significantly reduces the number of descendants in these cases. The benefits in terms of semantic coherence are more subtle.
Topical Key Concept Extraction from Folksonomy

Concept extraction is a primary subtask of ontology construction. It is difficult to extract new concepts from traditional text corpus. Moreover, building a single ontology for multiple-topic corpus may lead to misconception. To deal with these problems, this paper proposes a novel framework to extract topical key concepts from folksonomy. Folksonomy is a valuable data source due to real-time update and rich user-generated contents. We first identify topics from folksonomy using topic models. Next the tags are ranked according to their importance for a certain topic by applying topic-specific random walk methods. The top-ranking tags are extracted as topical key concepts. Especially, a novel link weight function which combines the local structure information and global semantic similarity is proposed in importance score propagation. From the perspectives of qualitative and quantitative investigation, our method is feasible and effective.
Differential growth kinetics are exhibited by human immunodeficiency virus type 1 TAR mutants

The human immunodeficiency virus type 1 (HIV-1) TAR element is critical for the activation of gene expression by the transactivator protein, Tat. Mutagenesis has demonstrated that a stable stem-loop RNA structure containing both loop and bulge structures transcribed from TAR is the major target for tat activation. Though transient assays have defined elements critical for TAR function, no studies have yet determined the role of TAR in viral replication because of the inability to generate viral stocks containing mutations in TAR. In the current study, we developed a strategy which enabled us to generate stable 293 cell lines which were capable of producing high titers of different viruses containing TAR mutations. Viruses generated from these cell lines were used to infect both T-lymphocyte cell lines and peripheral blood mononuclear cells. Viruses containing TAR mutations in either the upper stem, the bulge, or the loop exhibited dramatically decreased HIV-1 gene expression and replication in all cell lines tested. However, we were able to isolate lymphoid cell lines which stably expressed gene products from each of these TAR mutant viruses. Though the amounts of virus in these cell lines were roughly equivalent, cells containing TAR mutant viruses were extremely defective for gene expression compared with cell lines containing wild-type virus. The magnitude of this decrease in viral gene expression was much greater than previously seen in transient expression assays using HIV-1 long terminal repeat chloramphenicol acetyltransferase gene constructs. In contrast to the defects in viral growth found in T-lymphocyte cell lines, several of the viruses containing TAR mutations were much less defective for gene expression and replication in activated peripheral blood mononuclear cells. These results indicate that maintenance of the TAR element is critical for viral gene expression and replication in all cell lines tested, though the cell type which is infected is also a major determinant of the replication properties of TAR mutant viruses.
Clinical Prognostic Factors in 86 Chinese Patients with Primary Myelodysplastic Syndromes and Trisomy 8: A Single Institution Experience

Purpose The objective was to determine the characteristics and prognostic factors of 86 Chinese patients with trisomy 8 aberrations and compare the prognostic value of International Prognostic System (IPSS) and Revised IPSS (IPSS-R) in this cohort. Materials and Methods A total of 86 cases diagnosed with primary myelodysplastic syndromes (MDS) with isolated tr8 or with tr8 and other additional cytogenetic aberrations diagnosed and treated at the Union Hospital, Tongji Medical College of Huazhong University of Science and Technology between July 2002 and March 2013 were reviewed. Results The median survival of the entire group was 23.0 months, and acute myeloid leukemia (AML) developed in 43% (37/86) patients within the follow up time. The univariate analysis revealed that overall survival (OS) was correlated with age, thrombocytopenia, absolute neutrophil count, marrow blasts, cytogenetic status and red blood cell transfusion at diagnosis, and the multivariate analysis revealed that age, marrow blasts, cytogenetic status and transfusion dependence were independent parameters for the OS. The cytogenetic complexity and marrow blasts had the strongest impact on the AML transformation by multivariate analysis. Comparing the two prognostic systems, both two systems could successfully discriminate risk groups for survival. IPSS-R was more refined than IPSS for predicting OS, but had no advantage in predicting the risk of AML development. Conclusion This study confirmed the influence of clinical factors on the prognosis of 86 Chinese MDS patients with trisomy 8. In addition, IPSS-R can further refine prognostic discrimination in the IPSS risk categories.
Protective role of NK1.1+ cells in experimental Staphylococcus aureus arthritis

In a model of Staphylococcus aureus‐induced septic arthritis in C57Bl/6 mice we investigated the role of natural killer (NK) cells in the development of disease. Depletion of NK1.1+ cells was achieved by repeated injections of the PK136 antibody, whereas control mice received an irrelevant monoclonal antibody, O1C5.B2. Both groups of mice then received injections intravenously with 2 × 107 live S. aureus LS‐1 secreting toxic shock syndrome toxin‐1 (TSST‐1). The mice were evaluated for 16 days with regard to weight, mortality and arthritis. Nine days after bacterial injection, 9/19 mice depleted of NK cells had developed arthritis compared with 1/17 in the control group (P = 0.01). The experiment was repeated twice with the same outcome. NK cell‐depleted and control mice displayed the same degree of histopathological signs of arthritis at day 16. Depletion of NK cells did not affect uptake of bacteria by phagocytic cells in vitro, or bacterial clearance in vivo. In NK cell‐depleted mice there was a tendency to increased levels of antibodies to TSST‐1, whereas total immunoglobulin levels were similar to those in controls. NK cell depletion of non‐infected mice did not affect the magnitude of inflammatory response during the T cell‐dependent cutaneous DTH reaction to oxazolone, or during granulocyte‐mediated inflammation. However, specific antibody responses to oxazolone were greatly increased in depleted animals. In conclusion, our study demonstrates that NK cells protect against arthritis during S. aureus infection. This outcome does not seem to be due to an influence on bacterial clearance, but could be due to an interaction with the host anti‐inflammatory mechanisms.
Simulation 101 software: Workshop and beyond

The C source code associated with the Simulation 101 pre-conference workshop (offered at the 2006 and 2007 Winter Simulation Conferences) is presented here. This paper begins with general instructions for downloading, compiling, and executing the software. This is followed by sections on four groups of the software, categorized by functionality: libraries, Monte Carlo simulations, discrete-event simulations, and utilities. The libraries contain code to generate random numbers, code to generate random variates, and code to evaluate probability density functions, cumulative distribution functions, and inverse distribution functions. The Monte Carlo simulations consist of six programs that estimate various probabilities associated with simple probability problems, some with known analytic solutions and others without analytic solutions. The discrete-event simulations consist of various applications from queueing and inventory systems. Finally, the utilities are used to calculate various point and interval estimators from data sets.
The Clutterpalette: An Interactive Tool for Detailing Indoor Scenes

We introduce the Clutterpalette, an interactive tool for detailing indoor scenes with small-scale items. When the user points to a location in the scene, the Clutterpalette suggests detail items for that location. In order to present appropriate suggestions, the Clutterpalette is trained on a dataset of images of real-world scenes, annotated with support relations. Our experiments demonstrate that the adaptive suggestions presented by the Clutterpalette increase modeling speed and enhance the realism of indoor scenes.