Miracle-dz/UniFAR-FTUs huggingface dataset:
Communication-Efficient False Discovery Rate Control via Knockoff Aggregation

The false discovery rate (FDR)---the expected fraction of spurious discoveries among all the discoveries---provides a popular statistical assessment of the reproducibility of scientific studies in various disciplines. In this work, we introduce a new method for controlling the FDR in meta-analysis of many decentralized linear models. Our method targets the scenario where many research groups---possibly the number of which is random---are independently testing a common set of hypotheses and then sending summary statistics to a coordinating center in an online manner. Built on the knockoffs framework introduced by Barber and Candes (2015), our procedure starts by applying the knockoff filter to each linear model and then aggregates the summary statistics via one-shot communication in a novel way. This method gives exact FDR control non-asymptotically without any knowledge of the noise variances or making any assumption about sparsity of the signal. In certain settings, it has a communication complexity that is optimal up to a logarithmic factor.
No clinical evidence for performing trough plasma and intracellular imatinib concentrations monitoring in patients with chronic myelogenous leukaemia

This multicentre study focused on monitoring imatinib mesylate (IMA) trough plasma (Ctrough) and intracellular (IMA Cintrac) concentrations in 228 chronic myelogenous leukaemia patients. The median of measured IMA Ctrough in our patient group was 905.8 ng ml (range: 27.7–4628.1 ng/ml). We found a correlation between IMA Ctrough and alpha 1‐acid glycoprotein plasma concentrations (rS = 0.42; p < 0.001). All other analysed parameters revealed only weak (gender, dose of IMA per kg) or not significant (age, albumin, creatinine plasma concentration or body mass index) impact on measured IMA Ctrough. The IMA Ctrough decreased during the first 6 months and significantly increased later during treatment. The IMA Ctrough at the first month of therapy did not differ between patients with and without an optimal response at the 12th (p = 0.724) and 18th month (p = 0.135) of therapy. There were no significant differences in medians of IMA Ctrough between both groups measured during the first year of treatment. The IMA Cintrac during the first month were not different between patients with and without an optimal response at the 6th (p = 0.273) and the 12th month (p = 0.193) of therapy. Our data obtained from real life clinical practice did not find a benefit of routine and regular IMA Ctrough nor IMA Cintrac therapeutic drug monitoring in chronic myelogenous leukaemia patients or for subsequent adjustments of the IMA dose based on these results. Moreover, actual alpha 1‐acid glycoprotein plasma concentration should be used for proper interpretation of IMA Ctrough results. Copyright © 2013 John Wiley & Sons, Ltd.
The transcriptomes of cave and surface populations of Gammarus minus (Crustacea: Amphipoda) provide evidence for positive selection on cave downregulated transcripts

Gammarus minus, a freshwater amphipod living in the cave and surface streams in the eastern USA, is an excellent model for investigating evolutionary adaptation to the subterranean environment. RNA-Seq was conducted on one pair of morphologically distinct sister populations inhabiting surface and cave habitats to identify genes that were differentially expressed in the two populations, as well as to compare levels and patterns of genetic variation within and between populations. Of the 104,630 transcripts identified in the transcriptome assembly, 57% had higher average levels of expression in the cave population. After Benjamini-Hochberg correction for multiple tests, 1517 and 551 transcripts were significantly upregulated or downregulated, respectively, in the cave population, indicating an almost three-fold enrichment of cave-upregulated genes. The average level of nucleotide diversity across all transcripts was significantly lower in the cave population. Within the cave population, where the average nucleotide diversity of cave-downregulated transcripts was 75% that of the cave-upregulated transcripts, a highly significant difference, whereas within the spring population the nucleotide diversities of cave-downregulated and cave-upregulated transcripts was virtually identical. Three lines of evidence suggest that the reduced variation in cave downregulated transcripts is due to positive selection in the cave population: 1) the average neutrality index of cave-downregulated genes was < 1, consistent with positive selection, and significantly less than that of cave-upregulated genes; 2) Tajima’s D was positively correlated with the cave:surface expression ratio, and 3) cave-downregulated transcripts were significantly more likely to be highly diverged from their surface homologs than cave-upregulated transcripts. Five transcripts had fixed premature termination codons in the cave population. The expression patterns and sequence variation in one such transcript, encoding the DNA repair protein photolyase, were examined in more detail and provide the first evidence for the relaxation of functional constraint in this light-dependent protein in a subterranean population.
Evaluation of trehalose-mannitol broth for differentiation of Staphylococcus epidermidis from other coagulase-negative staphylococcal species

Trehalose-mannitol agar and various broth formulations thereof were evaluated for the differentiation of Staphylococcus epidermidis from other common coagulase-negative staphylococcal species isolated from human blood cultures. While this differentiation was accurately made on trehalose-mannitol agar in 18 h, modification of the medium to a broth formulation containing 2% each trehalose and mannitol in 0.2 ml of purple broth base provided greater than 95% accuracy when a heavy inoculum was incubated on a rotary shaker for at least 4 h.
Problems in the production and use of 5 nm avidin‐gold colloids

Over the past 5 years we have encountered several problems in the production and use of 5 nm avidin‐gold colloids for markers in electron microscopy. These problems include flocculation of colloids during reduction of chloroauric acid, insoluble gold pellets following ultracentrifugation, and non‐specific binding of avidin‐gold colloids to biological membranes. We are able to avoid these problems by: (1) avoiding the use of crystalline chloroauric acid; (2) succinoylating egg white avidin prior to adsorption on the gold sols; (3) resuspending the pellets following ultracentrifugation in 5 mM phosphate buffer, pH 7.5; and (4) using the avidin‐gold colloids within 4 weeks of production.
A 1-Kbit EEPROM in SIMOX technology for high-temperature applications up to 250/spl deg/C

A 1-Kbit high-temperature EEPROM memory module has been developed in a 1.6-/spl mu/m thin-film SIMOX technology. The memory array is based on single-poly EEPROM cells, which are erased and programmed by Fowler-Nordheim tunneling. Operation at elevated temperatures is achieved by a special array design, suitable for elimination of cell-disturb problems caused by temperature-induced leakage currents of the select transistors. High-voltage switching is done without PMOS transistors in order to avoid leakage currents due to the backgate effect. The memory module is designed for 5-V only operation and offers an access time of 260 ns at an operating temperature of 250/spl deg/C. At 250/spl deg/C, data retention of 3000 h and an endurance of 10000 erase/program cycles has been achieved. The area of the 1-Kbit memory module is 0.89/spl times/2.71 mm/sup 2/.
An effective class-centroid-based dimension reduction method for text classification

Motivated by the effectiveness of centroid-based text classification techniques, we propose a classification-oriented class-centroid-based dimension reduction (DR) method, called CentroidDR. Basically, CentroidDR projects high-dimensional documents into a low-dimensional space spanned by class centroids. On this class-centroid-based space, the centroid-based classifier essentially becomes CentroidDR plus a simple linear classifier. Other classification techniques, such as K-Nearest Neighbor (KNN) classifiers, can be used to replace the simple linear classifier to form much more effective text classification algorithms. Though CentroidDR is simple, non-parametric and runs in linear time, preliminary experimental results show that it can improve the accuracy of the classifiers and perform better than general DR methods such as Latent Semantic Indexing (LSI).
The Validity of Value-added Estimates from Low-Stakes Testing Contexts: The Impact of Change in Test-Taking Motivation and Test Consequences

Accountability mandates often prompt assessment of student learning gains (e.g., value-added estimates) via achievement tests. The validity of these estimates have been questioned when performance on tests is low stakes for students. To assess the effects of motivation on value-added estimates, we assigned students to one of three test consequence conditions: (a) an aggregate of test scores is used solely for institutional effectiveness purposes, (b) personal test score is reported to the student, or (c) personal test score is reported to faculty. Value-added estimates, operationalized as change in performance between two testing occasions for the same individuals where educational programming was experienced between testing occasions, were examined across conditions, in addition to the effects of test-taking motivation. Test consequences did not impact value-added estimates. Change in test-taking motivation, however, had a substantial effect on value-added estimates. In short, value-added estimates were attenuated due to decreased motivation from pretest to posttest.
Preservice Secondary Teachers’ Sense of Efficacy in Teaching Character Education

Character education is one of the most controversial domains of academic instruction in the United States. At the present time, many states and individual schools are considering the question of their responsibility for educating students about democratic principles and moral values as a vital part of a teacher's role. This study investigated the personal teaching efficacy and general teaching efficacy beliefs of 130 preservice secondary teachers at a large university in Florida. The subjects were in one teacher education program preparing to teach language arts, science, social studies, and mathematics. The teacher education program had no formal courses dedicated to character education, but the topic was included in some of the content coursework. The study utilized the Character Education Efficacy Belief Instrument (CEEBI), which was developed and validated by Milson and Mehlig (2002). The results of this survey add to the literature on character education and teacher education by taking a closer look at the specific beliefs of secondary preservice teachers regarding their Personal Teaching Efficacy (PTE) and General Teaching Efficacy (GTE) for character education. This study provides insight into the efficacy beliefs of secondary preservice teachers in a teacher preparation program in a state that mandates character education.
Trade-offs in the Configuration of a Network on Chip for Multiple Use-Cases

Systems on chip (SoC) are becoming increasingly complex, with a large number of applications integrated on the same chip. Such a system often supports a large number of use-cases and is dynamically reconfigured when platform conditions or user requirements change. Networks on chip (NoC) offer the designer unsurpassed runtime flexibility. This flexibility stems from the programmability of the individual routers and network interfaces. When a change in use-case occurs, the application task graph and the network connections change. To mitigate the complexity in programming the many registers controlling the NoC, an abstraction in the form of a configuration library is needed. In addition, such a library must leave the modified system in a consistent state, from which normal operation can continue. In this paper we present the facilities for controlling change in a reconfigurable NoC. We show the architectural additions and the many trade-offs in the design of a run-time library for NoC reconfiguration. We qualitatively and quantitatively evaluate the performance, memory requirements, predictability and reusability of the different implementations
Multiresolution Cache Management for Distributed Satellite Image Databases Using NACSIS-Thai International Link

This paper deals with the network technology that will be useful for the development of distributed satellite image databases. In particular, the author proposes a new caching mechanism by combining multiresolution image representation into cache management mechanism. The author first analyzes access pattern to a satellite image database and demonstrates that many kinds of access skew can be well characterized by Zipf-like laws. These statistical properties will be integrated into the cache server specially designed for satellite images. The author then deals with multiresolution image representation, which enables flexible access to huge satellite data; a client can access to any part of the image with many resolution. Finally the author addresses some of the preliminary results on wavelet-based image representation based on multiresolution representation.
SDBD: A Hierarchical Region-of-Interest Detection Approach in Large-Scale Remote Sensing Image

Region-of-interest (ROI) detection techniques are of great importance in the analysis of remote sensing images, especially in target detection, since the size of the image to be dealt with grows substantially with the improvement of spatial resolution. Most of current studies are not aiming at the specific type of object area detection, and the processed images are rather small compared to the size of the raw data acquired by high-resolution satellite. In this letter, a hierarchical task-driven ROI detection method, based on saliency and density, is proposed to address the detection of the potential object areas in large-scale remote sensing images. The proposed saliency and density-based detection method (SDBD) integrates bottom–up and top–down strategies, where the saliency-based multilevel histogram contrast is presented in the bottom–up phase to obtain the preliminary regions, while the centroid density distribution index (CDDI) is defined in the top–down scheme to refine the previous results. Specifically, superpixel segmentation is introduced in this letter to narrow down the ROI candidates. SDBD is capable of extracting ROI of different objects by adjusting the threshold of CDDI. The experiments are conducted on two data sets to extract ROIs of storage tanks and residence. Experimental results demonstrate that the proposed method is effective in identifying ROI in large-scale data.
SorLA in Interleukin-6 Signaling and Turnover

ABSTRACT Interleukin-6 (IL-6) is a multifunctional cytokine with important functions in various physiologic processes. Mice lacking IL-6 exhibit multiple phenotypic abnormalities, such as an inadequate immune and acute-phase response, and elevated levels of circulating IL-6 have been found to accompany several pathological conditions. IL-6 binds the nonsignaling IL-6 receptor (IL-6R), which is expressed as a transmembrane, as well as a secreted circulating protein, before it engages homodimeric gp130 for signaling. Complex formation between IL-6 and the membrane-bound IL-6 receptor gives rise to classic cis signaling, whereas complex formation between IL-6 and the soluble IL-6R results in trans signaling. Here, we report that the endocytic receptor SorLA targets IL-6 and IL-6R. We present evidence that SorLA mediates efficient cellular uptake of both IL-6 and the circulating IL-6R in astrocytes. We further show that SorLA interacts with the membrane-bound IL-6R at the cell surface and thereby downregulates IL-6 cis signaling. Finally, we find that the SorLA ectodomain, released from the cell membrane upon enzymatic cleavage of full-length SorLA, may act as an IL-6 carrier protein that stabilizes IL-6 and its capacity for trans signaling.
Adverse effects associated with persistent stimulation of Leydig cells with hCG in vitro

The detrimental effects of persistent stimulation with hCG were investigated in rat Leydig cells in vitro. Significant rise in lipid peroxidation and reactive oxygen species (ROS) with concomitant attenuation in the activities of antioxidant enzymes: superoxide dismutase, catalase, and glutathione‐S‐transferase was observed. Transcripts for catalase and superoxide dismutase were also depleted. Subsequent to each hCG challenge, the total antioxidant capacity in the target cells also declined significantly (P < 0.05). There was an increase in cell apoptosis (23%), which was associated with a rise in caspase‐3 activity, PARP cleavage, and Fas, FasL, caspase‐8 expression. While Bax and Caspase‐9 expression remained unchanged, Bcl‐2 demonstrated a marked decline. Taken together, the above data indicate that persistent hCG stimulation of Leydig cells induced adverse effects leading to oxidative stress and apoptosis which was channeled primarily through the extrinsic pathway. Mol. Reprod. Dev. 76: 1076–1083, 2009. © 2009 Wiley‐Liss, Inc.
Machine learning for constituency test of coordinating conjunctions in requirements specifications

Coordinating conjunctions have been a major source of ambiguity in Natural Language statements and the concern has been a major research focus in English Linguistics. Natural Language is also the most common form of expressing the requirements for an envisioned software system. These requirement documents also suffer from similar concern of coordination ambiguity. Presence of nocuous coordination ambiguity is a major concern for the requirements analysts. In this paper, we explore the applicability of constituency test for identifying coordinating conjunction instances in the requirements documents. We show through our study how identification of nocuous and innocuous coordinating conjunctions can be improved using semantic similarity heuristics and machine learning. Our study indicates that Naïve Bayes classifier outperforms other machine learning algorithms.
Second order optimality conditions for bang-bang control problems

Second order necessary and sufficient optimality conditions for bang–bang control problems have been studied in Milyutin, Osmolovskii (1998). These conditions amount to testing the positive (semi–)definiteness of a quadratic form on a critical cone. The assumptions are appropriate for numerical verification only in some special cases. In this paper, we study various transformations of the quadratic form and the critical cone which will be tailored to different types of control problems in practice. In particular, by means of a solution to a linear matrix differential equation, the quadratic form can be converted to perfect squares. We demonstrate by three practical examples that the conditions obtained can be verified numerically.
Probabilistic-based neural network implementation

This paper addresses a simple way for neural network hardware implementation based on probabilistic methodologies. We propose a new codification scheme that can be considered as an extension of stochastic computing (unipolar and bipolar codification formats), extending its representation range to any real number by using the ratio between two bipolar coded pulsed signals as codification method. Based on this codification, we propose the implementation of different linear and non-linear stochastic computational elements to be employed in artificial neural networks. Also this paper presents the accuracy associated to the proposed processing. The validation of the presented approach has been done with a sample application, (a spatial pattern classification example). The low cost in terms of hardware of the proposed methodology, along with the complexity of the mathematical expressions that can be implemented allows its use for massive parallel computing.
An Algebra for combining MPEG-4 compliant Facial Animations

$%675$&7 In this paper we discuss an extension of the Algebra of Expressions, an algebraic structure introduced in an earlier paper, consisting of a set of operators and related properties defined over a set that is a generalization of the MPEG-4’s Facial Animation Parameters. In particular, we extend the definition of the operators acting on whole animations, i.e. sequences of frames representing facial dynamics, instead of still facial displays. A set of examples of algebraic expressions combining animations of a facial model is then presented, showing that the algebra of expressions may be used: a) to describe, manipulate, and generate in a compact way facial dynamics; b) as a tool to further study and better understand the role of emotions conveyed by facial expressions and their relationships; c) as a basis to define an animation algorithm for MPEG-4 compliant facial models.
The effect of topical analgesics on ex vivo skin growth and human keratinocyte and fibroblast behavior

The application of topical analgesics to the donor site of split thickness skin grafts has been proven to be an effective method of pain management but little is known about their effects on wound reepithelialization. This study compares the effect of four analgesics on human keratinocytes and fibroblasts and whole skin explants in vitro to determine whether epithelial cell behavior is affected by topical analgesics. The effect of diclofenac, bupivacaine, lidocaine, and ketorolac was studied at concentrations between 10 mM and 1 nM. The effect on epithelial growth was measured using an ex vivo skin explant model. In addition, cell proliferation, and cytotoxicity were measured in cultured primary human keratinocytes and fibroblasts. Epithelial growth from the explant model was most inhibited by diclofenac with a significant reduction at 100 μM (p=>0.001). Diclofenac also exhibited the strongest inhibitory effect on cell proliferation especially in keratinocytes. Ketorolac was the most cytotoxic. Bupivacaine showed cytotoxicity in a dose‐dependent manner with only the very highest concentrations having a significant inhibitory effect. Lidocaine showed no evidence of cytotoxicity at the concentrations tested in either the in vitro cell studies or the ex vivo explant model. Topical analgesics alter keratinocyte and fibroblast behavior and such inhibition may affect wound healing.
Endometrial Cancer and the Role of Lymphadenectomy

Importance The role of lymph node dissection in early-stage endometrial cancer is highly debated, but staging and prognosis are dependent on knowledge of lymph node metastasis. Objective We sought to review the available data on the use of lymph node assessment in presumed early-stage endometrial cancer. Evidence Acquisition A comprehensive literature review was performed using MEDLINE, the Cochrane Collaborative Database, and PubMed. Results There is limited retrospective data that suggest a therapeutic benefit to lymphadenectomy. Prospective randomized trials have not shown a benefit to lymphadenectomy in low-risk patients, but found significant morbidity in patients undergoing lymphadenectomy. Selective lymph node assessment should be used in low-risk endometrial cancer. Sentinel lymph node assessment is emerging as a potential strategy for lymph node assessment. Conclusions and Relevance Selective use of lymphadenectomy in early-stage endometrial cancer can reduce the morbidity associated with lymph node dissection without compromising clinical outcomes. Multiple strategies are available including sentinel lymph nodes and risk factor based lymphadenectomy. Target Audience Gynecologic Oncologists. Learning Objectives After participating in this activity, physicians should be better able to describe the risk factors for lymph node metastasis in endometrial cancer; discuss the modalities of lymph node evaluation available; and describe the incidence of lymphedema after lymphadenectomy.