Miracle-dz/UniFAR-FTUs huggingface dataset:
Lack of Agreement Between Cervicography and Cytology and the Effect of Human Papillomavirus Infection and Viral Load

Objective. Cohort studies of the natural history of human papillomavirus (HPV) infection and cervical squamous intraepithelial lesions with repeated screening allow the comparison of different macroscopic and microscopic diagnostic methods. Materials and Methods. Concurrent visual inspection using cervicography and conventional Pap cytology tests were performed during multiple visits in a cohort of women attending a maternal and child health clinic in São Paulo, Brazil. HPV infection status at the same visits was determined by polymerase chain reaction followed by typing with specific oligonucleotide probing and viral load quantification. Information on reproductive health and hygiene habits was also collected at each visit. Results. Overall agreement between cervicography and cytology was low (&kgr; = 0.046), which increased only slightly when high oncogenic-risk HPV types (&kgr; = 0.120) or high viral burden (>100 copies/cell) (&kgr; = 0.170) was present. Analysis of reproductive health and hygiene habits revealed somewhat different risk factors for cervical lesions detected by these tests. However, presence of oncogenic HPV DNA (odds ratio = 36.0, 95% CI = 16.6-77.8) and high viral burden (odds ratio = 67.34; 95% CI = 27.1-167.0) were strongly associated with lesions detected by cytology but not by cervicography. Conclusions. Although changes in the cervix (because of age, gravidity, or hormonal effects) may influence the performance of morphology-based screening tests, the lack of agreement and the different degrees of association with HPV infection measures indicate that a visual inspection method such as cervicography may detect different cervical abnormalities relative to cytology.
Genome-wide analysis of DNA methylation patterns

Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests.
The regional vulnerability to hypoglycemia-induced neurotoxicity in organotypic hippocampal culture: protection by early tetrodotoxin or delayed MK-801

Profound hypoglycemia selectively damages CA1 and the dentate gyrus of the hippocampus. We have examined the time course of hippocampal neuronal injury in organotypic cultures following in vitro “hypoglycemia,” using the fluorescent vital dye propidium iodide to observe directly the regional distribution of early neuronal membrane injury in living cultures. The in vivo hippocampal pattern of hypoglycemic injury was reproduced by a 2 hr exposure to glucose-free media, which resulted in simultaneous, selective propidium staining of CA1 and the dentate gyrus starting by 4 hr after exposure. After 24 hr of recovery, CA3 remained spared. A similar pattern of propidium staining was produced by incubation of cultures for briefer periods in glucose-free medium containing 5 mM 2-deoxyglucose (2-DG) to inhibit glycolysis. This “hypoglycemic” pattern and time course of neuronal injury was mimicked by 300 microM aspartate but not by glutamate. The NMDA receptor antagonists MK-801 and CPP, but not the relatively selective non-NMDA receptor antagonist 6-cyano-7-dinitroquinoxaline-2,3- dione, prevented the development of propidium staining. MK-801 protected against injury even if added to the recovery media 30 min after the insult, while TTX (10 microM) protected only if added by the end of the exposure. The appearance of propidium staining after 4–6 hr of recovery was well correlated with histological observation of pyknotic neuronal nuclei in the injured regions. The characteristic hippocampal regional vulnerability of CA1 and the dentate gyrus to injury following profound hypoglycemia can be reproduced in organotypic hippocampal culture and appears to be mediated both by an early TTX- sensitive component and by a more prolonged period of toxic NMDA receptor activation, extending for at least 30 min into the recovery period.
Relative-entropy based beamforming for secret key transmission

In the context of the MISO flat-fading channel, we deal with the transmission of a secret key. More precisely, we seek to find the transmit beamformer to minimize the error probability of the legitimate receivers while maintaining a high (close to one) error probability for the eavesdroppers. To reach this goal, we exploit the popular “artificial noise” strategy which allows to confuse the eavesdroppers while the legitimate receivers are not affected. Under the low noise regime assumption for the eavesdroppers, we first derive the balancing coefficient to reach the constraint of high error probability for the eavesdroppers. Given this value, we find the optimal beamformer which minimizes the error probability of the legitimate receivers. We finally study the behavior of the error probability of the legitimate receivers with respect to the Signal To Noise Ratio and to the number of antennas at the transmission.
The Dynamics of Reorganization in Matching Markets: A Laboratory Experiment Motivated by a Natural Experiment

We create an environment in which congestion forces agents to match inefficiently early. We then introduce one of two centralized clearinghouse mechanisms. One of these has been successfully used to halt this kind of unraveling in a number of labor markets, while the other has failed. When it is costly for firms and workers to be mismatched compared with the costs of matching early, the experimental observations reproduce the field observations. Furthermore, the experiment permits us to observe the transition between a decentralized and a centralized market, both when the centralized market fails to control unraveling and when it succeeds, at a level of detail unavailable in field data.
beta-adrenergic receptor/cAMP-mediated signaling and apoptosis of S49 lymphoma cells.

beta-Adrenergic receptor (betaAR) activation and/or increases in cAMP regulate growth and proliferation of a variety of cells and, in some cells, promote cell death. In the current studies we addressed the mechanism of this growth reduction by examining betaAR-mediated effects in the murine T-lymphoma cell line S49. Wild-type S49 cells, derived from immature thymocytes (CD4(+)/CD8(+)) undergo growth arrest and subsequent death when treated with agents that increase cAMP levels (e.g., betaAR agonists, 8-bromo-cAMP, cholera toxin, forskolin). Morphological and biochemical criteria indicate that this cell death is a result of apoptosis. In cyc(-) and kin(-) S49 cells, which lack G(s)alpha and functional protein kinase A (PKA), respectively, betaAR activation of G(s)alpha and cAMP action via PKA are critical steps in this apoptotic pathway. S49 cells that overexpress Bcl-2 are resistant to cAMP-induced apoptosis. We conclude that betaAR activation induces apoptosis in immature T lymphocytes via G(s)alpha and PKA, while overexpression of Bcl-2 prevents cell death. betaAR/cAMP/PKA-mediated apoptosis may provide a means to control proliferation of immature T cells in vivo.
A Literature Review on Heating of Ventilation Air with Large Diameter Earth Tubes in Cold Climates

Earth-air heat exchange (EAHE) systems offer the possibility of reducing use of nonrenewable energy for heating ventilation air in cold climates. The number of installations of large diameter (greater than 900 mm) EAHE systems reported for cold climates is small. Even less has been reported on their heating performance, but the available information suggests that further rigorous assessment is warranted to determine whether the reported better than expected temperature rise is supported and, if so, the reasons for this. Another concern is the possibility of long-term heat depletion in the surrounding soil, which would affect performance. Only a couple of short-term experimental studies of ground temperature effects of heating with EAHE were found for cool climates. Four articles that addressed ground temperature effects with horizontal ground source heat pump exchangers had conflicting findings regarding heat depletion in the soil.
Tutorial: Advances and challenges in healthcare simulation modeling

Simulation has been used for modeling healthcare systems for over forty years. In many respects it is the ideal approach for addressing healthcare issues, yet the relatively small number of successful implementations would suggest that (outside academia) it has been underused in the health sector, compared with manufacturing industry or defense. In this paper we present a review of applications of simulation in healthcare, focusing on successful implementations, and we discuss some possible reasons why simulation has arguably failed to fulfill its potential. We describe recent advances in the area and identify opportunities for further research and new developments.
Globalisation and the decline of national identity?: An exploration across sixty-three countries

The relationship between globalisation and national identity is puzzling. While some observers have found that globalisation reduces people's identification with their nation, others have reached the opposite conclusion. This article explores this conundrum by examining the relationship between globalisation and people's feelings towards national identity. Using data from the International Social Survey Program National Identity II (2003) and the World Values Survey (2005), it analyses these relations across sixty-three countries. Employing a multilevel approach, it investigates how a country's level of globalisation is related to its public perceptions towards different dimensions of national identity. The results suggest that a country's level of globalisation is not related to national identification or nationalism but it is related negatively to patriotism, the willingness to fight for the country and ethnic conceptions of membership in the nation. An examination of alternative explanations indicates that globalisation has a distinct impact on national identity.
An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets

Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal reproduction. Dozens of such tests have been described, but many are hampered by long running times, confounding of selection and recombination, and/or inability to isolate the mosaic-producing event. We introduce a test that is exact, nonparametric, rapidly computable, free of the infinite-sites assumption, able to distinguish between recombination and variation in mutation/fixation rates, and able to identify the breakpoints and sequences involved in the mosaic-producing event. Our test considers three sequences at a time: two parent sequences that may have recombined, with one or two breakpoints, to form the third sequence (the child sequence). Excess similarity of the child sequence to a candidate recombinant of the parents is a sign of recombination; we take the maximum value of this excess similarity as our test statistic Δm,n,b. We present a method for rapidly calculating the distribution of Δm,n,b and demonstrate that it has comparable power to and a much improved running time over previous methods, especially in detecting recombination in large data sets.
Preclinical Testing of PI3K/AKT/mTOR Signaling Inhibitors in a Mouse Model of Ovarian Endometrioid Adenocarcinoma

Purpose: Genetically engineered mouse (GEM) models of ovarian cancer that closely recapitulate their human tumor counterparts may be invaluable tools for preclinical testing of novel therapeutics. We studied murine ovarian endometrioid adenocarcinomas (OEA) arising from conditional dysregulation of canonical WNT and PI3K/AKT/mTOR pathway signaling to investigate their response to conventional chemotherapeutic drugs and mTOR or AKT inhibitors. Experimental Design: OEAs were induced by injection of adenovirus expressing Cre recombinase (AdCre) into the ovarian bursae of Apcflox/flox; Ptenflox/flox mice. Tumor-bearing mice or murine OEA-derived cell lines were treated with cisplatin and paclitaxel, mTOR inhibitor rapamycin, or AKT inhibitors API-2 or perifosine. Treatment effects were monitored in vivo by tumor volume and bioluminescence imaging, in vitro by WST-1 proliferation assays, and in OEA tissues and cells by immunoblotting and immunostaining for levels and phosphorylation status of PI3K/AKT/mTOR signaling pathway components. Results: Murine OEAs developed within 3 weeks of AdCre injection and were not preceded by endometriosis. OEAs responded to cisplatin + paclitaxel, rapamycin, and AKT inhibitors in vivo. In vitro studies showed that response to mTOR and AKT inhibitors, but not conventional cytotoxic drugs, was dependent on the status of PI3K/AKT/mTOR signaling. AKT inhibition in APC−/Pten− tumor cells resulted in compensatory upregulation of ERK signaling. Conclusions: The studies show the utility of this GEM model of ovarian cancer for preclinical testing of novel PI3K/AKT/mTOR signaling inhibitors and provide evidence for compensatory signaling, suggesting that multiple rather than single agent targeted therapy will be more efficacious for treating ovarian cancers with activated PI3K/AKT/mTOR signaling. Clin Cancer Res; 17(23); 7359–72. ©2011 AACR.
Predicting Microsurgical Aptitude

Objective Microscopic techniques are an essential part of otolaryngologic practice. These procedures demand advanced psychomotor and visuospatial skills, and trainees possess these abilities to varying degrees. No method currently exists to predict who will possess an aptitude for microscopic surgery. Our goal was to determine whether performance can be predicted by background experiences or skills. Study Design Retrospective cohort study. Setting Tertiary academic hospital. Subjects Students with no previous surgical experience. Interventions Subjects were surveyed on a wide range characteristics thought to affect surgical aptitude, with a primary focus on video gaming and musical training. Main Outcome Measure Subjects performed a microsurgical task using a novel simulator and their performance was assessed by blinded investigators. Results Forty-six students were assessed. There was no correlation between video gaming and improved microsurgical performance. Rather, video gamers obtained worse scores, although this difference did not reach significance. The majority of students played a musical instrument. Within this group, musicians who began playing at younger ages obtained higher scores, with the highest scores obtained by musicians who began playing before age 6. However, musicians did not obtain higher scores than non-musicians, regardless of their age of initiation. Conclusions No improvement in microsurgical aptitude was seen in subjects who had a history of video gaming or musical instrument playing.
Level of categorisation effect: A novel effect in the picture-word interference paradigm

In four experiments we explored the effects of two variables in the picture-word interference paradigm: semantic relatedness and the level of categorisation of distractors relative to pictures' names. Experiment 1 addressed whether the contrasting effects of semantically related distractors in category- and basic-level naming have a methodological origin (i.e., differences in the number of responses and the number of repetitions of responses between experiments). Experiments 2, 3 and 4 explored the effect of the level of categorisation of distractor words relative to the level of categorisation of the response, independent of semantic relatedness. Two main results are reported. First, the effect of semantically related distractors depends on the level of categorisation at which the response has to be given. Second, semantically unrelated distractors at the same level of categorisation as that of the response interfere more than unrelated distractors at a different level of categorisation. The implications of these results for the interpretation of picture-word interference effects and their implications for models of lexical access in speech production are discussed.
Methods for fast blind identification and equalization of communication channels

We propose new methods for fast blind identification and equalization of communication channels based on channel outputs sampled at symbol rate. These methods exploit the FA property of the transmitted sequence as well as the algebraic structures and relationships of the symbol and channel parameter matrices to achieve blind equalization. The block based methods proposed herein are fast converging and data efficient. Simulated studies have illustrated the proposed methods capable of achieving reliable blind equalization with a sequence length as short as 20 samples over a wide-range of SNR.
Fiscal Issues in the New EU Member Countries - Prospects and Challenges Paper prepared for the IMF's Fiscal Affairs Department

This paper examines the fiscal challenges that the new EU member states in Central and Eastern Europe (NEW-8) are facing that arise from both EU membership and from developments that are essentially independent of EU membership. While the direct fiscal strains caused by EU membership may appear to be only short term and of minor importance, they are more challenging when regarded in the context of the impact on the NEW-8 of globalization (locational competition) and country-specific structural characteristics. It is argued that there is an urgent need for fiscal reforms in these countries that requires both determination with respect to restructuring the budget and innovativeness in regard of increasing the efficiency of public spending and collecting tax revenues. Several reform options are discussed.
The effect of size on structure and stress in grained films

ABSTRACT Molecular dynamics simulations are carried out to study the evolution of stress during deposition of atoms on the (001) plane of an FCC crystal, using rectangular simulation box with x–y periodic boundary conditions. The system consists of grains and boundaries. In the current study, we consider different values of the grain-to-grain distances and different relative sizes of deposited atoms. The structure was determined by the kinematical scattering theory. The main factors influencing the stress in thin film systems are creating of dislocation and changing the crystalline structure in grains. The deposited atoms can significantly contribute to the total stress. Depending on their size, atoms contribute compressive or tensile stresses to the total stress. This paper is part of a Thematic Issue on The Crystallographic Aspects of Metallic Alloys.
Query-driven Repairing of Inconsistent DL-Lite Knowledge Bases (Extended Abstract)

We consider the problem of query-driven repairing of inconsistent DL-Lite knowledge bases: query answers are computed under inconsistency-tolerant semantics, and the user provides feedback about which answers are erroneous or missing. The aim is to find a set of ABox modifications (deletions and additions), called a repair plan, that addresses as many of the defects as possible. After formalizing this problem and introducing different notions of optimality, we investigate the computational complexity of reasoning about optimal repair plans and propose interactive algorithms for computing such plans. For deletion-only repair plans, we also present a prototype implementation of the core components of the algorithm.
Standardized But Flexible I/O for Self-Virtualizing Devices

Moving device virtualization from the virtual machine monitor (VMM) to the devices improves virtual-machine performance significantly, but it requires support from the devices. PCI and PCI Express (PCIe) devices can provide VMs with direct and secure I/O through the use of multiple functions per card, but at significant cost and inflexibility. One solution to help reduce the costs is the PCIe SR-IOV standard, which introduces lightweight, virtual PCIe functions. We are currently developing a highly configurable and programmable PCIe networking device which can change its behavior at runtime and which can provide a number of different types of device functions to the host system (e.g., standard NIC, specialized packet capturing devices, or crypto offload engines). We have found the PCIe SR-IOV standard to be too inflexible to support these types of devices, primarily due to its mechanism for configuring virtual functions. In this paper we propose an alternative approach which does not require additional silicon and provides significantly higher flexibility than SR-IOV. We achieve this by delegating enumeration and configuration of "software configurable virtual functions" to the main device driver for the device. Our solution is compatible with the higher layers of the PCI device stack of modern operating systems and hypervisors so that we can leverage all the existing mechanisms for hot-plugging, discovering devices, loading device drivers, and assigning PCI devices to virtual machines (including providing DMA isolation with IO-MMUs). We present details of a prototype implementation for Linux and Xen.
First Record of Culicoides oxystoma Kieffer and Diversity of Species within the Schultzei Group of Culicoides Latreille (Diptera: Ceratopogonidae) Biting Midges in Senegal

The Schultzei group of Culicoides Latreille (Diptera: Ceratopogonidae) is distributed throughout Africa to northern Asia and Australasia and includes several potential vector species of livestock pathogens. The taxonomy of the species belonging to this species group is confounded by the wide geographical distribution and morphological variation exhibited by many species. In this work, morphological and molecular approaches were combined to assess the taxonomic validity of the species and morphological variants of the Schultzei group found in Senegal by comparing their genetic diversity with that of specimens from other geographical regions. The species list for Senegal was updated with four species: Culicoides kingi, C. oxystoma, C. enderleini and C. nevilli being recorded. This is the first record of C. oxystoma from Africa south of Sahara, and its genetic relationship with samples from Israel, Japan and Australia is presented. This work provides a basis for ecological studies of the seasonal and spatial dynamics of species of this species group that will contribute to better understanding of the epidemiology of the viruses they transmit.