Miracle-dz/UniFAR-FTUs huggingface dataset:
Expanding the Roles for Pregnane X Receptor in Cancer: Proliferation and Drug Resistance in Ovarian Cancer

Purpose: We examined the presence of the pregnane X receptor (PXR) and its effects on ovarian cancer cells after activation by its cognate ligand. Experimental Design: SKOV-3 and OVCAR-8 ovarian carcinoma cells were analyzed for expression of PXR by quantitative reverse transcription-PCR and Western blot. Human ovarian cancer tissue was also analyzed for PXR expression by immunochemistry. Ligand (agonist)–induced PXR target genes were analyzed in SKOV-3 cells by quantitative reverse transcription-PCR. SKOV-3 cell proliferation was assessed by MTT assay. In vivo confirmation of in vitro effects of PXR ligands were done in NOD.SCID mice carrying SKOV-3 xenografts. Results: PXR is expressed in ovarian cancer cells. In SKOV-3 cells, PXR is functional and its activation by cognate ligands induces PXR target genes (CYP2B6, CYP3A4, and UGT1A1) but not MDR1 and MRP2. PXR activation in SKOV-3 cells induces cell proliferation and drug resistance. In mice harboring SKOV-3 xenografts, rifampicin (PXR agonist) induces cell proliferation and tumor growth. Conclusion: PXR activation, regardless of the type of ligand agonist present, promotes the “malignant” phenotype of cancer cells. These data serve as the basis for finding novel nontoxic inhibitors of PXR activation as a method to control cell growth and prevent induction of drug resistance.
Tunnel detection in protein structures using sampling-based motion planning

Proteins are involved in many biochemical processes. The behavior of proteins is influenced by internal void space such as tunnels or cavities. Tunnels are paths leading from an inner protein active site to its surface. The knowledge about tunnels and their evolution over time provides an insight into protein properties (e.g., stability). Sampling-based motion planning techniques like Rapidly Exploring Random Tree (RRT) can be used to find tunnels by sampling the corresponding configuration space. These methods can be easily adapted to operate with protein dynamics. The inner void space of proteins is very limited, which may decrease the ability of RRT to find a solution due to the narrow passage problem. In this paper, we propose to generate random samples using a Voronoi Diagram of the atoms. A subset of Voronoi vertices is dynamically maintained to support the generation of samples in promising regions inside the protein.
Models and methods for analyzing DCE-MRI: a review.

PURPOSE To present a review of most commonly used techniques to analyze dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), discusses their strengths and weaknesses, and outlines recent clinical applications of findings from these approaches. METHODS DCE-MRI allows for noninvasive quantitative analysis of contrast agent (CA) transient in soft tissues. Thus, it is an important and well-established tool to reveal microvasculature and perfusion in various clinical applications. In the last three decades, a host of nonparametric and parametric models and methods have been developed in order to quantify the CA's perfusion into tissue and estimate perfusion-related parameters (indexes) from signal- or concentration-time curves. These indexes are widely used in various clinical applications for the detection, characterization, and therapy monitoring of different diseases. RESULTS Promising theoretical findings and experimental results for the reviewed models and techniques in a variety of clinical applications suggest that DCE-MRI is a clinically relevant imaging modality, which can be used for early diagnosis of different diseases, such as breast and prostate cancer, renal rejection, and liver tumors. CONCLUSIONS Both nonparametric and parametric approaches for DCE-MRI analysis possess the ability to quantify tissue perfusion.
tRNA Derived smallRNAs: smallRNAs Repertoire Has Yet to Be Decoded in Plants

Among several smallRNAs classes, microRNAs play an important role in controlling the post-transcriptional events. Next generation sequencing has played a major role in extending the landscape of miRNAs and revealing their spatio-temporal roles in development and abiotic stress. Lateral evolution of these smallRNAs classes have widely been seen with the recently emerging knowledge on tRNA derived smallRNAs. In the present perspective, we discussed classification, identification and roles of tRNA derived smallRNAs across plants and their potential involvement in abiotic and biotic stresses.
One-step nucleic acid amplification (OSNA) fits better with lower cost in breast cancer axillary management

50 Abstract Introduction: One-Step Nucleic Acid Amplification (OSNA) has been already validated for Analysis of Sentinel Node (SLN) in breast cancer. We investigated benefits of OSNA beyond accuracy, with a focus on cost-effectiveness. Methods: 253 consecutive breast cancer patients were reviewed: SLN was analyzed by OSNA in 114 cases and by standard histopathology in 139 cases. Nodal involvement detection, reintervention rate, time between surgery and adjuvant therapy were assessed. A cost analysis of OSNA vs. standard histopathology was performed. Results: With OSNA the re-intervention rate significantly decreased (10.79% vs. 0%, p = 0.0003), and adjuvant therapy started earlier (38.5 days vs. 23.8 days, p < 0.0001). Total cost per patient was 5,990.8€ for histopathology vs. 4,308€ with OSNA (p < 0.0001) if positive SLN. In case of negative SLN costs were similar (2,419.6€ vs. 2,425.2€, p = 0.947). Conclusions: OSNA reduces re-interventions, allows to start earlier adjuvant therapy and is more cost-effective than histopathology.
A Sequence Identification Measurement Model to Investigate the Implicit Learning of Metrical Temporal Patterns

Implicit learning (IL) occurs unconsciously and without intention. Perceptual fluency is the ease of processing elicited by previous exposure to a stimulus. It has been assumed that perceptual fluency is associated with IL. However, the role of perceptual fluency following IL has not been investigated in temporal pattern learning. Two experiments by Schultz, Stevens, Keller, and Tillmann demonstrated the IL of auditory temporal patterns using a serial reaction-time task and a generation task based on the process dissociation procedure. The generation task demonstrated that learning was implicit in both experiments via motor fluency, that is, the inability to suppress learned information. With the aim to disentangle conscious and unconscious processes, we analyze unreported recognition data associated with the Schultz et al. experiments using the sequence identification measurement model. The model assumes that perceptual fluency reflects unconscious processes and IL. For Experiment 1, the model indicated that conscious and unconscious processes contributed to recognition of temporal patterns, but that unconscious processes had a greater influence on recognition than conscious processes. In the model implementation of Experiment 2, there was equal contribution of conscious and unconscious processes in the recognition of temporal patterns. As Schultz et al. demonstrated IL in both experiments using a generation task, and the conditions reported here in Experiments 1 and 2 were identical, two explanations are offered for the discrepancy in model and behavioral results based on the two tasks: 1) perceptual fluency may not be necessary to infer IL, or 2) conscious control over implicitly learned information may vary as a function of perceptual fluency and motor fluency.
Within-Subject and Between-Subject Biological Variation of Prothrombin Time and Activated Partial Thromboplastin Time

The within-subject and between-subject biological variation of prothrombin time (PT) and activated partial thromboplastin time (APTT) have been studied in a group of 19 women and 20 men over a period of 9 months. All measurements were performed with a mechanical coagulometer. The between-subject coefficients of variation were 6·8% for PT and 8·9% for APTT. The medians and the 90th percentiles of within-subject coefficients of variation were 1·7% and 5·9%, respectively, for PT, and 0·0% and 6·1% for APTT. These data were used to calculate the critical difference for significant change detection and the desirable between-day imprecision.
Verifiable and Redactable Medical Documents

This paper considers how to verify provenance and integrity of data in medical documents that are exchanged in a distributed system of health IT services. Provenance refers to the sources of health information within the document and integrity means that the information was not modified after generation by the source. Our approach allows intermediate parties to redact the document by removing information that they do not wish to reveal. For example, patients can store verifiable health information and provide subsets of it to third parties, while redacting sensitive information that they do not wish employers, insurers, or others to receive. Our method uses a cryptographic primitive known as a redactable signature. We study practical issues and performance impacts of building, redacting, and verifying Continuity of Care Documents (CCDs) that are protected with redactable signatures. Results show that manipulating redactable CCDs provides superior security and privacy with little computational overhead.
COMPUTERIZED POLYGRAPH SCORING SYSTEM

Digitized polygraph data were collected during criminal investigations to develop a computerized algorithm for evaluating zone comparison polygraph examinations. The algorithm was incorporated in a software system and provides consistent and objective examination interpretation. The software system evaluates the data using methods that are fundamentally different than those used by examiners. It is currently in use in more than 40 of the United States and in other countries around the world.
Evaluating the Overhead of Data Preparation for Heterogeneous Multicore System

As processor design has been transiting from homogeneous multicore processor to heterogeneous multicore processor, traditional Amdahl’s law can not meet the new challenges for heterogeneous computer architecture. In order to further investigate the impact factors related to the Overhead of Data Preparation (ODP) for Heterogeneous multicore systems, we evaluate a heterogeneous multicore system built with CPUGPU by measuring the overheads of memory transfer, computing kernel, cache missing and synchronization. This paper demonstrates that decreasing the overhead of data preparation is a promising approach to improve the whole performance of heterogeneous system. Keywords— overhead of data preparation; homogeneous multicore; Amdahl’s law; power consumption
Comparison of 6 automated assays for total and free prostate-specific antigen with special reference to their reactivity toward the WHO 96/670 reference preparation.

BACKGROUND Prostate-specific antigen (PSA) assays have historically produced different results. Our aim was to investigate the comparability of assay results of selected commercially available assay methods designed to measure total, free, or complexed PSA (tPSA, fPSA, and cPSA). METHODS We measured tPSA, fPSA, and cPSA in 70 samples and in the WHO PSA 96/670 reference preparation with 6 assays (Beckman-Coulter Access, Abbott ARCHITECT and AxSYM, Bayer Advia Centaur, DPC IMMULITE 2000, and Roche Modular Analytics E170). We also calculated the fPSA/tPSA ratio. RESULTS The mean deviations from the expected tPSA and fPSA values for the WHO 96/670 reference preparation were 0.37 (range, 0.01-1.32) and 0.19 (range, 0.05-0.49) microg/L, respectively. When plotted against the expected WHO 96/670 reference preparation value, regression slopes varied from 0.99 to 1.22 and r2 from 0.9996 to 1.000. When total PSA was measured in mixtures of sera with high and low tPSA concentrations, the mean (SD) slope of regression of different assays against an in-house method was 1.04 (0.09). In these specimens, the fPSA/tPSA ratio was 0.11-0.14 with different methods. The tPSA and fPSA values in patient samples measured in different assays and plotted against ARCHITECT gave regression slopes from 0.88 to 0.97. The results of the studied assays for tPSA in serum samples agreed within 15%, from each other, and all results for the WHO 96/670 reference preparation were within 6.8% (confidence interval, 1.7%-15.2%) of the expected value. The results for fPSA were more diverse. CONCLUSIONS Differences among PSA assays appear to have decreased since introduction of the WHO 96/670 reference preparation, but further efforts are needed to harmonize fPSA assays.
Probabilistic Framework for the Characterization of Surfaces and Edges in Range Images, with Application to Edge Detection

We develop a powerful probabilistic framework for the local characterization of surfaces and edges in range images. We use the geometrical nature of the data to derive an analytic expression for the joint probability density function (pdf) for the random variables used to model the ranges of a set of pixels in a local neighborhood of an image. We decompose this joint pdf by considering independently the cases where two real world points corresponding to two neighboring pixels are locally on the same real world surface or not. In particular, we show that this joint pdf is linked to the Voigt pdf and not to the Gaussian pdf as it is assumed in some applications. We apply our framework to edge detection and develop a locally adaptive algorithm that is based on a probabilistic decision rule. We show in an objective evaluation that this new edge detector performs better than prior art edge detectors. This proves the benefits of the probabilistic characterization of the local neighborhood as a tool to improve applications that involve range images.
Retinoic acid counteracts developmental defects in the substantia nigra caused by Pitx3 deficiency

Selective neuronal loss in the substantia nigra (SNc), as described for Parkinson's disease (PD) in humans and for Pitx3 deficiency in mice, highlights the existence of neuronal subpopulations. As yet unknown subset-specific gene cascades might underlie the observed differences in neuronal vulnerability. We identified a developmental cascade in mice in which Ahd2 (Aldh1a1) is under the transcriptional control of Pitx3. Interestingly, Ahd2 distribution is restricted to a subpopulation of the meso-diencephalic dopaminergic (mdDA) neurons that is affected by Pitx3 deficiency. Ahd2 is involved in the synthesis of retinoic acid (RA), which has a crucial role in neuronal patterning, differentiation and survival in the brain. Most intriguingly, restoring RA signaling in the embryonic mdDA area counteracts the developmental defects caused by Pitx3 deficiency. The number of tyrosine hydroxylase-positive (TH+) neurons was significantly increased after RA treatment in the rostral mdDA region of Pitx3-/- embryos. This effect was specific for the rostral part of the developing mdDA area, and was observed exclusively in Pitx3-/- embryos. The effect of RA treatment during the critical phase was preserved until later in development, and our data suggest that RA is required for the establishment of proper mdDA neuronal identity. This positions Pitx3 centrally in a mdDA developmental cascade linked to RA signaling. Here, we propose a novel mechanism in which RA is involved in mdDA neuronal development and maintenance, providing new insights into subset-specific vulnerability in PD.
Medroxyprogesterone acetate increases HIV-1 infection of unstimulated peripheral blood mononuclear cells in vitro

Objective:Several observational studies suggest that medroxyprogesterone acetate (MPA) injectable contraceptives may increase a woman's risk of sexual HIV-1 acquisition. In-vitro studies are conflicting, mainly due to differences in the type of progestin studied or activation status of the primary cells. We sought to determine whether MPA increases infection of unstimulated peripheral blood mononuclear cells (PBMCs). Methods:Freshly isolated PBMCs from normal blood donors were treated with physiologic MPA concentrations ranging from 0.003 to 5 ng/ml and infected with GFP-tagged R5-tropic or X4-tropic HIV-1 pseudoviruses by spinoculation. The infection was limited to a single cycle. Cells were stained with CD3, CD8 and CD14. Infection was quantified as the percentage of GFP+ cells by flow cytometry. Results:Absolute infection was greater among unstimulated MPA-treated CD3+CD8− T cells vs. untreated cells across MPA concentrations of 0.003–3 ng/ml using R5 (P < 0.003) and 0.03–0.3 ng/ml using X4 (P < 0.005) pseudovirus. There was increased relative infection of CD3+CD8− T cells in MPA-treated whole PBMC cultures but not after monocytes were depleted (P < 0.02). HIV-1 infection of stimulated PBMC showed no differences in R5 or X4 infection across all MPA concentrations (P > 0.5). Conclusion:The CD3+CD8− T-cell population of MPA-treated unstimulated PBMCs were more susceptible to HIV-1 infection than untreated cells. The increased infection was partly due to monocytes and was lost when PBMC were exogenously stimulated. These data provide confirmation of a biological association between MPA exposure and increased susceptibility to HIV-1 infection, particularly among women who inject drugs.
Identification and Characterization of the Regions Involved in the Nuclear Translocation of the Heterodimeric Leishmanial DNA Topoisomerase IB

Leishmania donovani, the causative organism for visceral leishmaniasis, contains a unique heterodimeric DNA-topoisomerase IB (LdTopIB). LdTopIB is a heterodimer made up of a large subunit and a small subunit that must interact with each other to build an active enzyme able to solve the topological tensions on the DNA. As LdTopIB is located within the nucleus, one or more nuclear localization signals (NLS) should exist to ensure its nuclear translocation. In this report three novel NLS have been identified through a sequential deletion study of the genes encoding of both subunits fused to that encoding the green fluorescent protein (GFP). NLS1 is a highly basic sequence of 43 amino acids in the C-terminal extension of the large protomer. We found two well-defined sequences in the small protomer: NLS2 is a 10-amino acid motif located in the N-terminal extension of the protein; NLS3 consists of a complex region of 28 amino acids placed in the vicinity of the catalytic Tyr-222 included at the conserved SKINY signature within the C-terminal. Furthermore, by means of yeast cell viability assays, conducted with several LdTopIB chimeras lacking any of the NLS motives, we have revealed that both subunits are transported independently to the nucleus. There was no evidence of LdTopIB accumulation in mitochondria or association to the kinetoplast DNA network. The results rule out the former hypothesis, which attributes nucleocytoplasmic transport of LdTopIB entirely to the large subunit. The LdTopIB is localized to the nucleus only.
Classifying articles in English and German Wikipedia

Named Entity (NE) information is critical for Information Extraction (IE) tasks. However, the cost of manually annotating sufficient data for training purposes, especially for multiple languages, is prohibitive, meaning automated methods for developing resources are crucial. We investigate the automatic generation of NE annotated data in German from Wikipedia. By incorporating structural features of Wikipedia, we can develop a German corpus which accurately classifies Wikipedia articles into NE categories to within 1% F -score of the state-of-the-art process in English.
Identification and localization of integrin subunits in oocytes and eggs of the mouse

Results of a recent study have implicated egg integrins in sperm binding to the egg plasma membrane (Blobel et al., 1991: Nature 356:248–252). In this report, immunoprecipitation was used to identify, and confocal immunofluorescence microscopy was used to localize, several different integrin subunits in mouse eggs. Antibodies to α2, α5, αv, and β1 subunits, as well as antibodies to the fibronectin receptor (FNR; α5β1 and/or α3β1) and vitronectin receptor (VNR; αvβ3 and/or αvβ5), detect polypeptides of the appropriate molecular weights following immunoprecipitation. β1 is localized preferentially to either the microvillar or amicrovillar membrane/cortical regions of eggs, and these asymmetric localizations depend on the antibody used. Proteins recognized by anti‐FNR antibodies are localized preferentially to the amicrovillar membrane/cortical region. Germinal vesicle‐intact oocytes display a symmetric plasma membrane distribution using β and FNR antibodies, and the asymmetric distribution develops as a consequence of oocyte maturation and is clearly observed by metaphase I. In contrast to the membrane localization of these integrin subunits, α2, α5, and VNR are predominantly localized in the cytoplasm of both oocytes and eggs. In the oocyte, each of these integrin subunits is uniformly distributed throughout the cytoplasm. Oocyte maturation is associated with a redistribution of α5 and VNR, leading to an asymmetric cytoplasmic distribution with an increased localization towards the spindle. αv, which is localized in the plasma membrane/cortex of both oocytes and eggs, does not show such a change during oocyte maturation. Results of these experiments are discussed in the context of a role for integrins in mediating sperm plasma membrane‐egg plasma membrane interactions leading to egg activation. © 1995 Wiley‐Liss, Inc.
A joint detection, localization and respiratory rate estimation of multiple static persons using UWB radar

In the past period, great efforts have been made to develop methods for the people detection based on monitoring their respiratory motion using ultrawideband (UWB) radar. The basic principle of the respiratory motion detection consists in the identification of sensor signal components possessing a significant power in the frequency band 0.1–0.7 Hz (frequency band of human respiratory rate) corresponding to a constant range between the target and radar antennas. However, the problem of person localization associated with the estimation of their breathing rate has not been studied deeply. In order to fill this gap, an approach for a joint localization and breathing rate estimation of persons will be introduced in the paper. For that purpose, a radar signal processing proceure for multiple static person localization along with their breathing frequency estimation will be introduced in this paper. The performance of the proposed procedure will be evaluated for the experimental scenario intent on through-the-wall localization and respiratory rate estimation of two static persons using single UWB radar employing one transmitting and two receiving antennas.