A Method of Analysis for Unequal Numbers of Replicates in a Factorial Experiment

9 pages, 1 article*A Method of Analysis for Unequal Numbers of Replicates in a Factorial Experiment* (Paik, U. B.) 9 page

A Generalized Procedure for Constructing Fractional Replicates

39 pages, 1 article*A Generalized Procedure for Constructing Fractional Replicates* (Paik, U. B.; Federer, W. T.) 39 page

On the Construction of Fractional Replicates with Special Reference to Saturated Designs

33 pages, 1 article*On the Construction of Fractional Replicates with Special Reference to Saturated Designs* (Paik, U. B.; Federer, W. T.) 33 page

Decoherence in dc SQUID phase qubits

We report measurements of Rabi oscillations and spectroscopic coherence times in an Al/AlOx/Al and three Nb/AlOx/Nb dc SQUID phase qubits. One junction of the SQUID acts as a phase qubit and the other junction acts as a current-controlled nonlinear isolating inductor, allowing us to change the coupling to the current bias leads in situ by an order of magnitude. We found that for the Al qubit a spectroscopic coherence time T2* varied from 3 to 7 ns and the decay envelope of Rabi oscillations had a time constant T' = 25 ns on average at 80 mK. The three Nb devices also showed T2* in the range of 4 to 6 ns, but T' was 9 to 15 ns, just about 1/2 the value we found in the Al device. For all the devices, the time constants were roughly independent of the isolation from the bias lines, implying that noise and dissipation from the bias leads were not the principal sources of dephasing and inhomogeneous broadening.Comment: 5 figures. Accepted to Physical Review

Unsupervised joint PoS tagging and stemming for agglutinative languages

This is an accepted manuscript of an article published by Association for Computing Machinery (ACM) in ACM Transactions on Asian and Low-Resource Language Information Processing on 25/01/2019, available online: https://doi.org/10.1145/3292398 The accepted version of the publication may differ from the final published version.The number of possible word forms is theoretically infinite in agglutinative languages. This brings up the out-of-vocabulary (OOV) issue for part-of-speech (PoS) tagging in agglutinative languages. Since inflectional morphology does not change the PoS tag of a word, we propose to learn stems along with PoS tags simultaneously. Therefore, we aim to overcome the sparsity problem by reducing word forms into their stems. We adopt a Bayesian model that is fully unsupervised. We build a Hidden Markov Model for PoS tagging where the stems are emitted through hidden states. Several versions of the model are introduced in order to observe the effects of different dependencies throughout the corpus, such as the dependency between stems and PoS tags or between PoS tags and affixes. Additionally, we use neural word embeddings to estimate the semantic similarity between the word form and stem. We use the semantic similarity as prior information to discover the actual stem of a word since inflection does not change the meaning of a word. We compare our models with other unsupervised stemming and PoS tagging models on Turkish, Hungarian, Finnish, Basque, and English. The results show that a joint model for PoS tagging and stemming improves on an independent PoS tagger and stemmer in agglutinative languages.This research is supported by the Scientific and Technological Research Council of Turkey (TUBITAK) with the project number EEEAG-115E464.Published versio

Immunohistochemical evaluation of human epidermal growth factor receptor 2 and estrogen and progesterone receptors in breast carcinoma in Jordan

INTRODUCTION: Although breast carcinoma (BC) is the most common malignancy affecting Jordanian females and the affected population in Jordan is younger than that in the West, no information is available on its biological characteristics. Our aims in this study are to evaluate the expression of estrogen receptor (ER) and progesterone receptor (PR) and Her-2/neu overexpression in BC in Jordan, and to compare the expression of these with other prognostic parameters for BC such as histological type, histological grade, tumor size, patients' age, and number of lymph node metastases. METHOD: This is a retrospective study conducted in the Department of Pathology at Jordan University of Science and Technology. A confirmed 91 cases of BC diagnosed in the period 1995 to 1998 were reviewed and graded. We used immunohistochemistry to evaluate the expression of ER, PR, and Her-2. Immunohistochemical findings were correlated with age, tumor size, grade and axillary lymph node status. RESULTS: Her-2 was overexpressed in 24% of the cases. The mean age of Her-2 positive cases was 42 years as opposed to 53 years among Her-2 negative cases (p = 0.0001). Her-2 expression was inversely related to ER and PR expression. Her-2 positive tumors tended to be larger than Her-2 negative tumors with 35% overexpression among T3 tumors as opposed to 22% among T2 tumors (p = 0.13). Her-2 positive cases tended to have higher rates of axillary metastases, but this did not reach statistical significance. ER and PR positive cases were seen in older patients with smaller tumor sizes. CONCLUSION: Her-2 overexpression was seen in 24% of BC affecting Jordanian females. Her-2 overexpression was associated with young age at presentation, larger tumor size, and was inversely related to ER and PR expression. One-fifth of the carcinomas were Her-2 positive and ER negative. This group appears to represent an aggressive form of BC presenting at a young age with large primary tumors and a high rate of four or more axillary lymph node metastases

The Interspersed Spin Boson Lattice Model

We describe a family of lattice models that support a new class of quantum magnetism characterized by correlated spin and bosonic ordering [Phys. Rev. Lett. 112, 180405 (2014)]. We explore the full phase diagram of the model using Matrix-Product-State methods. Guided by these numerical results, we describe a modified variational ansatz to improve our analytic description of the groundstate at low boson frequencies. Additionally, we introduce an experimental protocol capable of inferring the low-energy excitations of the system by means of Fano scattering spectroscopy. Finally, we discuss the implementation and characterization of this model with current circuit-QED technology.Comment: Submitted to EPJ ST issue on "Novel Quantum Phases and Mesoscopic Physics in Quantum Gases

Genetic Predisposition of Donors Affects the Allograft Outcome in Kidney Transplantation; Polymorphisms of Stromal-Derived Factor-1 and CXC Receptor 4

Genetic interaction between donor and recipient may dictate the impending responses after transplantation. In this study, we evaluated the role of the genetic predispositions of stromal-derived factor-1 (SDF1) [rs1801157 (G>A)] and CXC receptor 4 (CXCR4) [rs2228014 (C>T)] on renal allograft outcomes. A total of 335 pairs of recipients and donors were enrolled. Biopsy-proven acute rejection (BPAR) and long-term graft survival were traced. Despite similar allele frequencies between donors and recipients, minor allele of SDF1 rs1801157 (GA+AA) from donor, not from recipients, has a protective effect on the development of BPAR compared to wild type donor (GG) (P = 0.005). Adjustment for multiple covariates did not affect this result (odds ratio 0.39, 95% C.I 0.20–0.76, P = 0.006). CXCR4 rs2228014 polymorphisms from donor or recipient did not affect the incidence of acute rejection. SDF1 was differentially expressed in renal tubular epithelium with acute rejection according to genetic variations of donor rs1801157 showing higher expressions in the grafts from GG donors. Contrary to the development of BPAR, the presence of minor allele rs1801157 A, especially homozygocity, predisposed poor graft survival (P = 0.001). This association was significant after adjusting for several risk factors (hazard ratio 3.01; 95% C.I = 1.19–7.60; P = 0.020). The allelic variation of recipients, however, was not associated with graft loss. A donor-derived genetic polymorphism of SDF1 has influenced the graft outcome. Thus, the genetic predisposition of donor should be carefully considered in transplantation

Tumor markers in breast cancer - European Group on Tumor Markers recommendations

Recommendations are presented for the routine clinical use of serum and tissue-based markers in the diagnosis and management of patients with breast cancer. Their low sensitivity and specificity preclude the use of serum markers such as the MUC-1 mucin glycoproteins ( CA 15.3, BR 27.29) and carcinoembryonic antigen in the diagnosis of early breast cancer. However, serial measurement of these markers can result in the early detection of recurrent disease as well as indicate the efficacy of therapy. Of the tissue-based markers, measurement of estrogen and progesterone receptors is mandatory in the selection of patients for treatment with hormone therapy, while HER-2 is essential in selecting patients with advanced breast cancer for treatment with Herceptin ( trastuzumab). Urokinase plasminogen activator and plasminogen activator inhibitor 1 are recently validated prognostic markers for lymph node-negative breast cancer patients and thus may be of value in selecting node-negative patients that do not require adjuvant chemotherapy. Copyright (C) 2005 S. Karger AG, Basel