Miracle-dz/UniFAR-FTUs huggingface dataset:
Abacavir-lamivudine versus tenofovir-emtricitabine for initial HIV-1 therapy.

BACKGROUND The use of fixed-dose combination nucleoside reverse-transcriptase inhibitors (NRTIs) with a nonnucleoside reverse-transcriptase inhibitor or a ritonavir-boosted protease inhibitor is recommended as initial therapy in patients with human immunodeficiency virus type 1 (HIV-1) infection, but which NRTI combination has greater efficacy and safety is not known. METHODS In a randomized, blinded equivalence study involving 1858 eligible patients, we compared four once-daily antiretroviral regimens as initial therapy for HIV-1 infection: abacavir-lamivudine or tenofovir disoproxil fumarate (DF)-emtricitabine plus efavirenz or ritonavir-boosted atazanavir. The primary efficacy end point was the time from randomization to virologic failure (defined as a confirmed HIV-1 RNA level > or = 1000 copies per milliliter at or after 16 weeks and before 24 weeks, or > or = 200 copies per milliliter at or after 24 weeks). RESULTS A scheduled interim review by an independent data and safety monitoring board showed significant differences in virologic efficacy, according to the NRTI combination, among patients with screening HIV-1 RNA levels of 100,000 copies per milliliter or more. At a median follow-up of 60 weeks, among the 797 patients with screening HIV-1 RNA levels of 100,000 copies per milliliter or more, the time to virologic failure was significantly shorter in the abacavir-lamivudine group than in the tenofovir DF-emtricitabine group (hazard ratio, 2.33; 95% confidence interval, 1.46 to 3.72; P<0.001), with 57 virologic failures (14%) in the abacavir-lamivudine group versus 26 (7%) in the tenofovir DF-emtricitabine group. The time to the first adverse event was also shorter in the abacavir-lamivudine group (P<0.001). There was no significant difference between the study groups in the change from the baseline CD4 cell count at week 48. CONCLUSIONS In patients with screening HIV-1 RNA levels of 100,000 copies per milliliter or more, the times to virologic failure and the first adverse event were both significantly shorter in patients randomly assigned to abacavir-lamivudine than in those assigned to tenofovir DF-emtricitabine. (ClinicalTrials.gov number, NCT00118898.)
Retrospect of Machine Learning Techniques for Designing Secure System

Security is the latest research which is of essential concern for many researchers. As the data is generated every second both in host and network so it’s necessary to ensure the preservation of their integrity. So, this paper is retrospection of various security measures which are necessary to protect the system from harmful threats/attacks. Machine learning is one of the best technique by which we can apply to get the best results and in turn build an efficient Intrusion Detection System. General Terms Intrusion Detection System
Kinetochore-independent chromosome segregation driven by lateral microtubule bundles

During cell division, chromosomes attach to spindle microtubules at sites called kinetochores, and force generated at the kinetochore-microtubule interface is the main driver of chromosome movement. Surprisingly, kinetochores are not required for chromosome segregation on acentrosomal spindles in Caenorhabditis elegans oocytes, but the mechanism driving chromosomes apart in their absence is not understood. In this study, we show that lateral microtubule–chromosome associations established during prometaphase remain intact during anaphase to facilitate separation, defining a novel form of kinetochore-independent segregation. Chromosome dynamics during congression and segregation are controlled by opposing forces; plus-end directed forces are mediated by a protein complex that forms a ring around the chromosome center and dynein on chromosome arms provides a minus-end force. At anaphase onset, ring removal shifts the balance between these forces, triggering poleward movement along lateral microtubule bundles. This represents an elegant strategy for controlling chromosomal movements during cell division distinct from the canonical kinetochore-driven mechanism. DOI: http://dx.doi. org/10.7554/eLife.06462. 001
ELECTRONIC STRUCTURE CALCULATIONS IN PLANE-WAVE CODES WITHOUT DIAGONALIZATION

We present an algorithm to reduce the computational complexity for plane-wave codes used in electronic structure calculations. Our proposed algorithm avoids the diagonalization of large Hermitian matrices arising in such problems. The computational time for the diagonalization procedure typically grows as the cube of the number of atoms, or the number of eigenvalues required. To reduce this computational demand, we approximate directly in a certain subspace the occupation operator corresponding to the eigenvectors associated with the occupied states, without actually computing these eigenvectors. A smoothed Chebyshev-Jackson expansion of the Heaviside function of the Hamiltonian matrix is used to represent the occupation operator. This procedure requires only matrix-vector products and is intrinsically parallelizable.
Nanotechnology Public Funding and Impact Analysis: A Tale of Two Decades (1991-2010)

Nanotechnology's economic and societal benefits have continued to attract significant research and development (R&D) attention from governments and industries worldwide. Over the past two decades, nanotechnology has seen quasi-exponential growth in the numbers of scientific papers and patent publications produced. New research topics and application areas are continually emerging, and investment from government, industry, and academia [1], [2] has expanded at substantial levels. But what is the impact of public funding on nanotechnology? How important is its role in driving innovation, invention, and knowledge transfer?
Transcriptional pulsing of a nucleolar transgene

The pulsatile nature of transcription has recently emerged as an important property of gene expression. Here we report on the characterization of a RNA polymerase II transgene that is transcribed in the nucleolus. Using the MS2-GFP reporter system and live cell imaging, we found that the synthesis of a MS2-tagged transcript in the nucleolus was discontinuous in all of the cells that were observed, with periods of activity lasting from 15 minutes to 21 hours. The frequency of pulse lengths could be fitted with an exponential function, from which we determined that transcription occurs on average for periods of 20 minutes. These ON periods alternate with periods of inactivity which last on average 29 minutes. The post-mitotic reactivation of transcription was found to be asynchronous in daughter cell pairs. Our observation of discontinuous transcriptional activity in the nucleolus may reflect cycling in the assembly and disassembly of active chromatin structure in and/or around the rDNA genes.
Good Seeds Grow in Strong Cultures.

Regardless of the focus of particular change efforts, schools need to nurture and build on the cultural norms that contribute to growth. School improvement emerges from the confluence of four elements: The strengthening of teachers skills, the systematic renovation of curriculum, the improvement of the organization, and the involvement of parents and citizens in responsible school-community partnerships. Underlying all four strands, however, is a school culture that either energized or undermines them. Essentially, the culture of the school is the foundation for school improvement, a view summarized by Purkey and Smith (1982):
Cross-Situational Learning: An Experimental Study of Word-Learning Mechanisms

Cross-situational learning is a mechanism for learning the meaning of words across multiple exposures, despite exposure-by-exposure uncertainty as to the word’s true meaning. We present experimental evidence showing that humans learn words effectively using cross-situational learning, even at high levels of referential uncertainty. Both overall success rates and the time taken to learn words are affected by the degree of referential uncertainty, with greater referential uncertainty leading to less reliable, slower learning. Words are also learned less successfully and more slowly if they are presented interleaved with occurrences of other words, although this effect is relatively weak. We present additional analyses of participants’ trial-by-trial behavior showing that participants make use of various cross-situational learning strategies, depending on the difficulty of the word-learning task. When referential uncertainty is low, participants generally apply a rigorous eliminative approach to cross-situational learning. When referential uncertainty is high, or exposures to different words are interleaved, participants apply a frequentist approximation to this eliminative approach. We further suggest that these two ways of exploiting cross-situational information reside on a continuum of learning strategies, underpinned by a single simple associative learning mechanism.
Lifting the Curtain : Using Topology to Probe the Hidden Action of Enzymes

ne of the important issues in molecular biology is the three-dimensional structure (shape) of proteins and deoxyribonucleic acid (DNA) in solution in the cell and the relationship between structure and function. Ordinarily, protein and DNA structure is determined by X-ray crystallography or electron microscopy. Because of the close packing needed for crystallization and the manipulation required to prepare a specimen for electron microscopy, these methods provide little direct evidence for molecular shape in solution. Topology can shed light on this key issue. The topological approach to enzymology is an experimental protocol in which the descriptive and analytical powers of topology and geometry are employed in an indirect effort to determine the enzyme mechanism and the structure of active enzyme-DNA complexes in vitro (in a test tube). We describe how recent results in 3-dimensional topology [3, 5, 9, 10, 11] have proven to be of use in the description and quantization of the action of cellular enzymes on DNA.
A long isoform of the epithelial sodium channel alpha subunit forms a highly active channel

A long isoform of the human Epithelial Sodium Channel (ENaC) α subunit has been identified, but little data exist regarding the properties or regulation of channels formed by α728. The baseline whole cell conductance of oocytes expressing trimeric α728βγ channels was 898.1 ± 277.2 and 49.59 ± 13.2 µS in low and high sodium solutions, respectively, and was 11 and 2 fold higher than the conductances of α669βγ in same solutions. α728βγ channels were also 2 to 5 fold less sensitive to activation by the serine proteases subtilisin and trypsin than α669βγ in low and high Na+ conditions. The long isoform exhibited lower levels of full length and cleaved protein at the plasma membrane and a rightward shifted sensitivity to inhibition by increases of [Na+]i. Both channels displayed similar single channel conductances of 4 pS, and both were activated to a similar extent by reducing temperature, altogether indicating that activation of baseline conductance of α728βγ was likely mediated by enhanced channel activity or open probability. Expression of α728 in native kidneys was validated in human urinary exosomes. These data demonstrate that the long isoform of αENaC forms the structural basis of a channel with different activity and regulation, which may not be easily distinguishable in native tissue, but may underlie sodium hyperabsorption and salt sensitive differences in humans.
Identification and Characterization of Single-Chain Antibodies that Specifically Bind GI Noroviruses

Norovirus infections commonly lead to outbreaks of acute gastroenteritis and spread quickly, resulting in many health and economic challenges prior to diagnosis. Rapid and reliable diagnostic tests are therefore essential to identify infections and to guide the appropriate clinical responses at the point-of-care. Existing tools, including RT-PCR and enzyme immunoassays, pose several limitations based on the significant time, equipment and expertise required to elicit results. Immunochromatographic assays available for use at the point-of-care have poor sensitivity and specificity, especially for genogroup I noroviruses, thus requiring confirmation of results with more sensitive testing methods. Therefore, there is a clear need for novel reagents to help achieve quick and reliable results. In this study, we have identified two novel single-chain antibodies (scFvs)—named NJT-R3-A2 and NJT-R3-A3—that effectively detect GI.1 and GI.7 virus-like particles (VLPs) through selection of a phage display library against the P-domain of the GI.1 major capsid protein. The limits of detection by each scFv for GI.1 and GI.7 are 0.1 and 0.2 ng, and 6.25 and 25 ng, respectively. They detect VLPs with strong specificity in multiple diagnostic formats, including ELISAs and membrane-based dot blots, and in the context of norovirus-negative stool suspensions. The scFvs also detect native virions effectively in norovirus-positive clinical stool samples. Purified scFvs bind to GI.1 and GI.7 VLPs with equilibrium constant (KD) values of 27 nM and 49 nM, respectively. Overall, the phage-based scFv reagents identified and characterized here show utility for detecting GI.1 and GI.7 noroviruses in multiple diagnostic assay formats with strong specificity and sensitivity, indicating promise for integration into existing point-of-care tests to improve future diagnostics.
Temporal Annotation: A Proposal for Guidelines and an Experiment with Inter-annotator Agreement

This article presents work carried out within the framework of the ongoing ANR (French National Research Agency) project Chronolines, which focuses on the temporal processing of large news-wire corpora in English and French. The aim of the project is to create new and innovative interfaces for visualizing textual content according to temporal criteria. Extracting and normalizing the temporal information in texts through linguistic annotation is an essential step towards attaining this objective. With this goal in mind, we developed a set of guidelines for the annotation of temporal and event expressions that is intended to be compatible with the TimeML markup language, while addressing some of its pitfalls. We provide results of an initial application of these guidelines to real news-wire texts in French over several iterations of the annotation process. These results include inter-annotator agreement figures and an error analysis. Our final inter-annotator agreement figures compare favorably with those reported for the TimeBank 1.2 annotation project.
Vestibular Hearing and Speech Processing

Vestibular hearing in human is evoked as a result of the auditory sensitivity of the saccule to low-frequency high-intensity tone. The objective was to investigate the relationship between vestibular hearing using cervical vestibular-evoked myogenic potentials (cVEMPs) and speech processing via word recognition scores in white noise (WRSs in wn). Intervention comprised of audiologic examinations, cVEMPs, and WRS in wn. All healthy subjects had detectable cVEMPs (safe vestibular hearing). WRSs in wn were obtained for them (66.9 ± 9.3% in the right ears and 67.5 ± 11.8% in the left ears). Dizzy patients in the affected ears, had the cVEMPs abnormalities (insecure vestibular hearing) and decreased the WRS in wn (51.4 ± 3.8% in the right ears and 52.2 ± 3.5% in the left ears). The comparison of the cVEMPs between the subjects revealed significant differences (P < 0.05). Therefore, the vestibular hearing can improve the speech processing in the competing noisy conditions.
Yield of primary and repeat induced sputum testing for Pneumocystis jiroveci in human immunodeficiency virus-positive and -negative patients.

CONTEXT Induced sputum sampling has an approximate 70% sensitivity for detection of Pneumocystis jiroveci in human immunodeficiency virus (HIV) patients. Bronchoalveolar lavage sampling has greater than 90% sensitivity but is a far more invasive procedure. Therefore, bronchoalveolar lavage testing is often recommended as a follow-up after a negative induced sputum. In HIV-negative patients, the utility of induced sputum testing is still not well defined. OBJECTIVE To determine whether repeat induced sputum sampling increases diagnostic yield and might thereby reduce the need for follow-up bronchoalveolar lavage sampling. To determine the utility of induced sputum sampling in HIV-negative patients. DESIGN A 2-year retrospective review of the utility of repeat induced sputa testing in patients with previous first and/or second negative induced sputa. Retrospective review of induced sputa detection in HIV-negative patients. RESULTS Repeat testing of induced sputa for Pneumocystic jirovecii did not significantly increase diagnostic yield. Furthermore, in HIV-negative patients, induced sputum testing was diagnostically insensitive. CONCLUSIONS Bronchoalveolar lavage testing should be performed initially in HIV-negative patients and after a first negative induced sputum in HIV-positive patients.
A Chemical Marker Proposal for the Lantana genus: Composition of the Essential Oils from the Leaves of Lantana radula and L. canescens

Essential oil extracts from the leaves of two Lantana species (L. radula Sw. and L. canescens Kunth), for which no prior analysis has been reported, were analyzed by GC-MS. This information was utilized to propose chemical markers for Lantana species so that identification between physically similar plant species can be achieved through chemical analysis. Results showed 33 constituents for L. canescens, among which β-caryophyllene (43.9%), β-cubebene (10.1%), elixene (8.6%), β-phellandrene (6.1%), α-caryophyllene (2.6%) and dehydro-aromadendrene (2.6%) were the principle components. L. radula revealed the presence of 21 compounds, the most abundant of which were β-cubebene (31.0%), β-caryophyllene (20.8%), elixene (10.0%), α-salinene (6.4%), β-phellandrene (6.1%), copaene (4.9%) cadinene (1.4%) and psi-limonene (1.4%). The high concentration of β-caryophyllene in the samples tested here and those in the literature make it a good candidate for a chemical marker for Lantana species, with β-cubebene, elixene and β-phellandrene following as minor compounds identified more sporadically in this genus. On the other hand, Lippia species, which are morphologically similar to those from the Lantana genus, would contain limonene, citral, carvacrol, β-myrcene, camphor and thymol as the main chemical markers. These chemical markers would be a powerful tool for maintaining quality control in the extraction of essential oils for use in medicinal applications, as well as in identification of plant specimens to a taxonomist.
Efficient Index Maintenance Under Dynamic Genome Modification

Efficient text indexing data structures have enabled large-scale genomic sequence analysis and are used to help solve problems ranging from assembly to read mapping. However, these data structures typically assume that the underlying reference text is static and will not change over the course of the queries being made. Some progress has been made in exploring how certain text indices, like the suffix array, may be updated, rather than rebuilt from scratch, when the underlying reference changes. Yet, these update operations can be complex in practice, difficult to implement, and give fairly pessimistic worst-case bounds. We present a novel data structure, SkipPatch, for maintaining a k-mer-based index over a dynamically changing genome. SkipPatch pairs a hash-based k-mer index with an indexable skip list that is used to efficiently maintain the set of edits that have been applied to the original genome. SkipPatch is practically fast, significantly outperforming the dynamic extended suffix array in terms of update and query speed.
Directed Safe Zones and the Dual Extent Algorithms for Efficient Grid Traversal during Ray Tracing

Ray tracing is inherently a very time consuming process There have been a variety of techniques de veloped for reducing the rendering time While using space subdivision techniques the object space is di vided into a set of disjoint voxels and only those ob jects are checked for intersection with the ray which pierce the voxels along the path of the ray As the grid size is increased in an attempt to reduce the number of objects encountered along the path of the ray more empty voxels are encountered along the path In other words considerable rendering time could be invested in moving from one empty voxel to another empty voxel The proximity clouds method uses distance transformations to identify the empty regions and combined with the DDA grid traver sal SEADS technique has been shown to be the fastest grid traversal technique available today In this paper we present two further improve ments to the proximity clouds method called the Directed Safe Zones DSZ and the Dual Extents DEs We have implemented four methods for our comparison SEADS DDA proximity clouds Di rected Safe Zones DSZs and Dual Extents DEs We present both the theoretical and statistical anal ysis of the four methods We show that DSZs and DEs surpass the performance of both the proxim ity clouds and SEADS implementations The DSZs method usually outperforms the Dual Extents im plementation except when the topology of the scene favors the Dual Extent method
Adaptive GPS duty cycling and radio ranging for energy-efficient localization

This paper addresses the tradeoff between energy consumption and localization performance in a mobile sensor network application. The focus is on augmenting GPS location with more energy-efficient location sensors to bound position estimate uncertainty in order to prolong node lifetime. We use empirical GPS and radio contact data from a large-scale animal tracking deployment to model node mobility, GPS and radio performance. These models are used to explore duty cycling strategies for maintaining position uncertainty within specified bounds. We then explore the benefits of using short-range radio contact logging alongside GPS as an energy-inexpensive means of lowering uncertainty while the GPS is off, and we propose a versatile contact logging strategy that relies on RSSI ranging and GPS lock back-offs for reducing the node energy consumption relative to GPS duty cycling. Results show that our strategy can cut the node energy consumption by half while meeting application-specific positioning criteria.