Miracle-dz/UniFAR-FTUs huggingface dataset:
Inhibition of interleukin 10 by rituximab results in down-regulation of bcl-2 and sensitization of B-cell non-Hodgkin's lymphoma to apoptosis.

Treatment of patients with non-Hodgkin's lymphoma (NHL) is frequently hampered by development of chemoresistance. Rituximab is a chimeric mouse antihuman CD20 antibody that offers an alternative; however, its mechanism of action is not clearly understood. Treatment of lymphoma cell lines with Rituximab sensitizes the cells to the cytotoxic and apoptotic effects of therapeutic drugs, e.g., cisplatin, fludarabine, vinblastine, and Adriamycin. This study investigated the mechanism(s) involved in the reversal of drug resistance by Rituximab therapy. NHL cells synthesize and secrete antiapoptotic cytokines implicated in drug resistance, including interleukin (IL)-6, IL-10, and tumor necrosis factor alpha. We hypothesized, therefore, that sensitization by Rituximab may be due in part to modification of cytokine production. In this study, examination of cytokine secretion by NHL 2F7 tumor cells revealed down-regulation of IL-10 by Rituximab treatment. Moreover, cytotoxicity assays using exogenous IL-10 and IL-10-neutralizing antibodies demonstrated that IL-10 serves as an antiapoptotic/protective factor in these tumor cells against cytotoxic drugs. Furthermore, expression in 2F7 cells of the protective factor, Bcl-2, was shown to be dependent on IL-10 levels and down-regulated by Rituximab. Other gene products such as Bax, Bcl-x, Bad, p53, c-myc, and latent membrane protein-1 (LMP) were not affected by Rituximab treatment. Drug sensitization, as well as down-regulation of both IL-10 and Bcl-2, was corroborated in experiments using the NHL cell line 10C9. The Ramos and Daudi NHL cell lines were not sensitizable, nor did their Bcl-2 or IL-10 levels change. These studies demonstrate that one mechanism by which Rituximab sensitizes NHL to chemotherapeutic drugs is mediated through down-regulation of antiapoptotic IL-10 autocrine/paracrine loops and Bcl-2. The clinical relevance of these findings is discussed.
AN OVERVIEW OF THE AT&T SPOKEN DOCUMENT RETRIEVAL

We present an overview of a spoken document retrieval system developed at AT&T Labs-Research for the HUB4 Broadcast News corpus. This overview includes a description of the intonational phrase boundary detection, classification, speech recognition, information retrieval and user interface components of the system, along with updated system assessments based on the 49-query task defined for the TREC-6 SDR track. Results from a comparative ranking study, based on queries taken from AP Newswire headlines from the same time period that the Broadcast News corpus was recorded, are presented. For the AP task, retrieval accuracy is assessed by comparing the documents retrieved from ASR generated transcriptions with those from human generated transcriptions.
Workload-aware database monitoring and consolidation

In most enterprises, databases are deployed on dedicated database servers. Often, these servers are underutilized much of the time. For example, in traces from almost 200 production servers from different organizations, we see an average CPU utilization of less than 4%. This unused capacity can be potentially harnessed to consolidate multiple databases on fewer machines, reducing hardware and operational costs. Virtual machine (VM) technology is one popular way to approach this problem. However, as we demonstrate in this paper, VMs fail to adequately support database consolidation, because databases place a unique and challenging set of demands on hardware resources, which are not well-suited to the assumptions made by VM-based consolidation. Instead, our system for database consolidation, named Kairos, uses novel techniques to measure the hardware requirements of database workloads, as well as models to predict the combined resource utilization of those workloads. We formalize the consolidation problem as a non-linear optimization program, aiming to minimize the number of servers and balance load, while achieving near-zero performance degradation. We compare Kairos against virtual machines, showing up to a factor of 12× higher throughput on a TPC-C-like benchmark. We also tested the effectiveness of our approach on real-world data collected from production servers at Wikia.com, Wikipedia, Second Life, and MIT CSAIL, showing absolute consolidation ratios ranging between 5.5:1 and 17:1.
Effect of beta2-adrenergic receptor functioning and increased norepinephrine on the hypercoagulable state with mental stress.

BACKGROUND Procoagulant stress responses may contribute to atherosclerosis development and acute coronary thrombosis. In the present study, we examined the role of beta2-adrenergic receptor function and plasma catecholamines in the stress-induced increase in the 2 hypercoagulability markers thrombin-antithrombin III (TAT) complex and fibrin D-dimer (DD). METHODS Lymphocyte beta2-adrenoreceptor sensitivity and density were assessed at rest, and plasma levels of TAT, DD, epinephrine, and norepinephrine were measured at rest and in response to a standardized mental stress task in 19 normotensive and mildly hypertensive nonmedicated subjects (mean age 38 years, age range 29 to 48 years). RESULTS The stressor elicited a significant increase in TAT (P =.024), DD (P =.026), and norepinephrine (P =.005). Resting beta2-adrenoreceptor sensitivity (isoproterenol-stimulated cyclic adenosine monophosphate production) plus the norepinephrine change scores (stress minus rest) accounted for 59% of the variance in the absolute TAT increase in response to stress (P =.001). Hypertension status and demographic variables such as sex did not influence the results. CONCLUSIONS Acute mental stress may trigger a hypercoagulable state evidenced by increased thrombin activity and increased fibrin turnover. Beta2-adrenergic receptor sensitivity and plasma catecholamine activity may mediate the procoagulant response to acute stressors. These mechanisms may help explain the adverse impact of mental stress on the cardiovascular system.
Detection of Wuchereria bancrofti L3 Larvae in Mosquitoes: A Reverse Transcriptase PCR Assay Evaluating Infection and Infectivity

Background Detection of filarial DNA in mosquitoes by PCR cannot differentiate infective mosquitoes from infected mosquitoes. In order to evaluate transmission risk an assay is needed that can specifically detect infective L3 stage parasites. We now report the development of an assay that specifically detects the infective stage of Wuchereria bancrofti in mosquitoes. The assay detects an L3-activated mRNA transcript by reverse-transcriptase PCR (RT-PCR). Methodology/Principal Findings W. bancrofti cuticle-related genes were selected using bioinformatics and screened as potential diagnostic target genes for L3 detection in mosquitoes. Expression profiles were determined using RT-PCR on RNA isolated from mosquitoes collected daily across a two-week period after feeding on infected blood. Conventional multiplex RT-PCR and real-time multiplex RT-PCR assays were developed using an L3-activated cuticlin transcript for L3 detection and a constitutively expressed transcript, tph-1, for ‘any-stage’ detection. Conclusions/Significance This assay can be used to simultaneously detect W. bancrofti infective stage larvae and ‘any-stage’ larvae in pooled vector mosquitoes. This test may be useful as a tool for assessing changes in transmission potential in the context of filariasis elimination programs.
Rapid Diagnosis of Histoplasma capsulatum Endocarditis Using the AccuProbe on an Excised Valve

ABSTRACT Histoplasma capsulatum is an infrequent but serious cause of endocarditis. The definitive diagnosis requires culture, which may require a long incubation. We demonstrated the ability of theHistoplasma capsulatum AccuProbe to accurately identify this organism when applied directly on an excised valve that contained abundant yeast forms consistent with H. capsulatum.
Preparation and characterization of celecoxib solid dispersions; comparison of poloxamer-188 and PVP-K30 as carriers

Objective(s): Solid dispersion formulation is the most promising strategy to improve oral bioavailability of poorly water soluble drugs. The aim of this study was to compare the effect of polyvinylpyrrolidone K30 (PVP) and poloxamer-188 (PLX) as carrier in solid dispersion formulations of celecoxib (CLX). Materials and Methods: Solid dispersions of CLX:PVP or CLX:PLX were prepared at different ratios (2:1, 1:1, 1:2, 1:4, 1:6) by solvent evaporation and melting methods, respectively. The characterization of samples was performed using differential scanning calorimetery (DSC), X-Ray powder diffraction (XRPD) and Fourier transform infrared spectroscopy (FT-IR). The Gordon-Taylor equation was used to estimate the Tg of solid dispersion systems and the possibility of the interaction between CLX and PVP. Also, the dissolution rate of all samples was determined. Results: DSC and XRPD analyses confirmed the presence of amorphous state of drug in solid dispersion systems. FT-IR studies showed CLX could participate in hydrogen bonding with PVP whilst no specific interaction between CLX and PLX was observed. Both PVP and PLX enhanced the dissolution rate of drug in solid dispersion samples. The dissolution rate was dependent on the ratio of drug: carrier. Interestingly, the solid dispersion samples of PLX at 2:1 and 1:1 drug: carrier showed slower dissolution rate than pure CLX, whilst these results were not observed for PVP. Conclusion: The effect of PVP on dissolution rate enhancement was more pronounced compared to the other carrier. Having a higher Tg and more effect on dissolution rate, PVP could be considered as a more suitable carrier compared to PLX in solid dispersion formulation of CLX.
TIMP-1 Inhibits Apoptosis in Lung Adenocarcinoma Cells via Interaction with Bcl-2

Tissue inhibitors of metalloproteinases (TIMPs) are multifaceted molecules that exhibit properties beyond their classical proteinase inhibitory function. Although TIMP-1 is a known inhibitor of apoptosis in mammalian cells, the mechanisms by which it exerts its effects are not well-established. Our earlier studies using H2009 lung adenocarcinoma cells, implanted in the CNS, showed that TIMP-1 overexpressing H2009 cells (HB-1), resulted in more aggressive tumor kinetics and increased vasculature. The present study was undertaken to elucidate the role of TIMP-1 in the context of apoptosis, using the same lung cancer cell lines. Overexpressing TIMP-1 in a lung adenocarcinoma cell line H2009 resulted in an approximately 3-fold increased expression of Bcl-2, with a marked reduction in apoptosis upon staurosporine treatment. This was an MMP-independent function as a clone expressing TIMP-1 mutant T2G, lacking MMP inhibition activity, inhibited apoptosis as strongly as TIMP1 overexpressing clones, as determined by inhibition of PARP cleavage. Immunoprecipitation of Bcl-2 from cell lysates also co-immunoprecipitated TIMP-1, indicative of an interaction between these two proteins. This interaction was specific for TIMP-1 as TIMP-2 was not present in the Bcl-2 pull-down. Additionally, we show a co-dependency of TIMP-1 and Bcl-2 RNA and protein levels, such that abrogating Bcl-2 causes a downregulation of TIMP-1 but not TIMP-2. Finally, we demonstrate that TIMP-1 dependent inhibition of apoptosis occurs through p90RSK, with phosphorylation of the pro-apoptotic protein BAD at serine 112, ultimately reducing Bax levels and increasing mitochondrial permeability. Together, these studies define TIMP-1 as an important cancer biomarker and demonstrate the potential TIMP-1 as a crucial therapeutic target.
NKp46+ Innate Lymphoid Cells Dampen Vaginal CD8 T Cell Responses following Local Immunization with a Cholera Toxin-Based Vaccine

Innate and adaptive immune cells work in concert to generate efficient protection at mucosal surface. Vaginal mucosa is an epithelial tissue that contains innate and adaptive immune effector cells. Our previous studies demonstrated that vaginal administration of Cholera toxin -based vaccines generate antigen-specific CD8 T cells through the stimulation of local dendritic cells (DC). Innate lymphoid cells (ILC) are a group of lymphocytes localized in epithelial tissues that have important immune functions against pathogens and in tissue homeostasis. Their contribution to vaccine-induced mucosal T cell responses is an important issue for the design of protective vaccines. We report here that the vaginal mucosa contains a heterogeneous population of NKp46+ ILC that includes conventional NK cells and ILC1-like cells. We show that vaginal NKp46+ ILC dampen vaccine-induced CD8 T cell responses generated after local immunization. Indeed, in vivo depletion of NKp46+ ILC with anti-NK1.1 antibody or NKG2D blockade increases the magnitude of vaginal OVA-specific CD8 T cells. Furthermore, such treatments also increase the number of DC in the vagina. NKG2D ligands being expressed by vaginal DC but not by CD8 T cells, these results support that NKp46+ ILC limit mucosal CD8 T cell responses indirectly through the NKG2D-dependent elimination of vaginal DC. Our data reveal an unappreciated role of NKp46+ ILC in the regulation of mucosal CD8 T cell responses.
Modelling diseases with relapse and nonlinear incidence of infection: a multi-group epidemic model

In this paper, we introduce a basic reproduction number for a multi-group SIR model with general relapse distribution and nonlinear incidence rate. We find that basic reproduction number plays the role of a key threshold in establishing the global dynamics of the model. By means of appropriate Lyapunov functionals, a subtle grouping technique in estimating the derivatives of Lyapunov functionals guided by graph-theoretical approach and LaSalle invariance principle, it is proven that if it is less than or equal to one, the disease-free equilibrium is globally stable and the disease dies out; whereas if it is larger than one, some sufficient condition is obtained in ensuring that there is a unique endemic equilibrium which is globally stable and thus the disease persists in the population. Furthermore, our results suggest that general relapse distribution are not the reason of sustained oscillations. Biologically, our model might be realistic for sexually transmitted diseases, such as Herpes, Condyloma acuminatum, etc.
NAD Kinase Levels Control the NADPH Concentration in Human Cells*

NAD kinases (NADKs) are vital, as they generate the cellular NADP pool. As opposed to three compartment-specific isoforms in plants and yeast, only a single NADK has been identified in mammals whose cytoplasmic localization we established by immunocytochemistry. To understand the physiological roles of the human enzyme, we generated and analyzed cell lines stably deficient in or overexpressing NADK. Short hairpin RNA-mediated down-regulation led to similar (about 70%) decrease of both NADK expression, activity, and the NADPH concentration and was accompanied by increased sensitivity toward H2O2. Overexpression of NADK resulted in a 4–5-fold increase in the NADPH, but not NADP+, concentration, although the recombinant enzyme phosphorylated preferentially NAD+. Surprisingly, NADK overexpression and the ensuing increase of the NADPH level only moderately enhanced protection against oxidant treatment. Apparently, to maintain the NADPH level for the regeneration of oxidative defense systems human cells depend primarily on NADP-dependent dehydrogenases (which re-reduce NADP+), rather than on a net increase of NADP. The stable shifts of the NADPH level in the generated cell lines were also accompanied by alterations in the expression of peroxiredoxin 5 and Nrf2. Because the basal oxygen radical level in the cell lines was only slightly changed, the redox state of NADP may be a major transmitter of oxidative stress.
[Expression of the selected adhesive molecules (cadherin E, CD44, LGAL3 and CA50) in papillary thyroid carcinoma].

INTRODUCTION The aim of the study was to determine the expression of selected adhesive molecules in papillary thyroid carcinoma. MATERIAL AND METHODS 47 papillary thyroid carcinoma cases and 11 nonmalignant goiter cases were analyzed by immunohistochemistry. RESULTS Galectin-3 (LGAL3) was a sensitive and specific marker, present in 91% of analyzed tumors and only in 5% of tumor margin. The presence of CA50 was 86% and 3% respectively with only 3% positive non-malignant cases. Cadherin E expression was noted in 91% of primary tumors, in 84% of the surrounding tissue and in 63% of non-malignant goiter. CD44 (DF1485) was observed in 89% of primary tumors and 48% of surrounding tissue; the reaction with BBA10 was more characteristic for metastases. CONCLUSIONS Our study confirms the high diagnostic value of galectin-3 in papillary thyroid carcinoma and reveals the similar efficiency of CA50. CD44 (DF1485) expression in primary tumor is more intensive than in surrounding tissue, but the diagnostical inportance is not high because it is often observed in benign lesions. Using of BBA10 is more sensitive, but less specific. High expression of cadherin E in benign lesions impairs its diagnostical application in papillary thyroid cancer.
A Review on the Interpretability-Accuracy Trade-Off in Evolutionary Multi-Objective Fuzzy Systems (EMOFS)

Interpretability and accuracy are two important features of fuzzy systems which are conflicting in their nature. One can be improved at the cost of the other and this situation is identified as “Interpretability-Accuracy Trade-Off”. To deal with this trade-off Multi-Objective Evolutionary Algorithms (MOEA) are frequently applied in the design of fuzzy systems. Several novel MOEA have been proposed and invented for this purpose, more specifically, Non-Dominated Sorting Genetic Algorithms (NSGA-II), Strength Pareto Evolutionary Algorithm 2 (SPEA2), Fuzzy Genetics-Based Machine Learning (FGBML), (2 + 2) Pareto Archived Evolutionary Strategy ((2 + 2) PAES), (2 + 2) Memetic- Pareto Archived Evolutionary Strategy ((2 + 2) M-PAES), etc. This paper introduces and reviews the approaches to the issue of developing fuzzy systems using Evolutionary Multi-Objective Optimization (EMO) algorithms considering ‘Interpretability-Accuracy Trade-off’ and mainly focusing on the work in the last decade. Different research issues and challenges are also discussed.
Renormalization Reductions for Systems with Delay

The renormalization method which is a type of perturbation method is extended to a tool to study weakly nonlinear time-delay systems. For systems with order-one delay, we show that the renormalization method leads to reduced systems without delay. For systems with order-one and large-delay, we propose an extended renormalization method which leads to reduced systems with delay. In some examples, the validities of our perturbative results are confirmed analytically and numerically. We also compare our reduced equations with reduced ones obtained by another perturbation method.
Linear receivers for the DS-CDMA downlink exploiting orthogonality of spreading sequences

We address the problem of downlink interference rejection in a DS-CDMA system. Periodic orthogonal Walsh-Hadamard sequences spread different users' symbols followed by scrambling by a symbol aperiodic base-station specific overlay sequence. This corresponds to the downlink of the European UMTS wideband CDMA proposal. The point to point propagation channel from the cell-site to a certain mobile station is the same for all downlink signals (desired user as well as the interference). The composite channel is shorter than a symbol period for some user signals, while other users can have significant ISI owing to a faster transmission rate. In any case, orthogonality of the underlying Walsh-Hadamard sequences is destroyed by multipath propagation, resulting in multiuser interference if a coherent combiner (the RAKE receiver) is employed. We propose linear zero-forcing (ZF) and minimum mean-squared-error (MMSE) receivers which equalize for the estimated channel, thus rendering the user signals orthogonal again. A simple code matched filter subsequently suffices to cancel the multiple access interference (MAI) from intracell users.
Parallel Banding Algorithm to compute exact distance transform with the GPU

We propose a Parallel Banding Algorithm (PBA) on the GPU to compute the exact Euclidean Distance Transform (EDT) for a binary image in 2D and higher dimensions. Partitioning the image into small bands to process and then merging them concurrently, PBA computes the exact EDT with optimal linear total work, high level of parallelism and a good memory access pattern. This work is the first attempt to exploit the enormous power of the GPU in computing the exact EDT, while prior works are only on approximation. Compared to these other algorithms in our experiments, our exact algorithm is still a few times faster in 2D and 3D for most input sizes. We illustrate the use of our algorithm in applications such as computing the Euclidean skeleton using the integer medial axis transform, performing morphological operations of 3D volumetric data, and constructing 2D weighted centroidal Voronoi diagrams.
Multi-organ plant identification with multi-column deep convolutional neural networks

Automatically identifying plants from images is a hot research topic due to its importance in production and science popularization. This process attempts to automatically identify the name of a plant with a known taxon from a given image. The majority of existing studies on automatic plant identification focus on identifying plants with a single organ, such as flower, leaf, or fruits. Plant identification using a single organ is not sufficiently reliable because different plants many have similar organs. To overcome this problem, this paper is devoted to automatically identifying plants by combining multiple organs of plants. Specifically, we propose a multi-column deep convolutional neural networks (MCDCNN) model to combine multiple organs for efficient plant identification. Extensive experiments demonstrate the effectiveness of our model, and the plant identification performance is greatly improved.
Camazotz: Multimodal activity-based GPS sampling

Long-term outdoor localisation with battery-powered devices remains an unsolved challenge, mainly due to the high energy consumption of GPS modules. The use of inertial sensors and short-range radio can reduce reliance on GPS to prolong the operational lifetime of tracking devices, but they only provide coarse-grained control over GPS activity. In this paper, we introduce our feature-rich lightweight Camazotz platform as an enabler of Multimodal Activity-based Localisation (MAL), which detects activities of interest by combining multiple sensor streams for fine-grained control of GPS sampling times. Using the case study of long-term flying fox tracking, we characterise the tracking, connectivity, energy, and activity recognition performance of our module under both static and 3-D mobile scenarios. We use Camazotz to collect empirical flying fox data and illustrate the utility of individual and composite sensor modalities in classifying activity. We evaluate MAL for flying foxes through simulations based on retrospective empirical data. The results show that multimodal activity-based localisation reduces the power consumption over periodic GPS and single sensor-triggered GPS by up to 77% and 14% respectively, and provides a richer event type dissociation for fine-grained control of GPS sampling.