Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational Analyses of Packaging Signals in Influenza Virus PA, PB1, and PB2 Genomic RNA Segments

ABSTRACT The influenza A virus genome consists of eight negative-sense RNA segments that must each be packaged to produce an infectious virion. We have previously mapped the minimal cis-acting regions necessary for efficient packaging of the PA, PB1, and PB2 segments, which encode the three protein subunits of the viral RNA polymerase. The packaging signals in each of these RNAs lie within two separate regions at the 3′ and 5′ termini, each encompassing the untranslated region and extending up to 80 bases into the adjacent coding sequence. In this study, we introduced scanning mutations across the coding regions in each of these RNA segments in order to finely define the packaging signals. We found that mutations producing the most severe defects were confined to a few discrete 5′ sites in the PA or PB1 coding regions but extended across the entire (80-base) 5′ coding region of PB2. In sequence comparisons among more than 580 influenza A strains from diverse hosts, these highly deleterious mutations were each found to affect one or more conserved bases, though they did not all lie within the most broadly conserved portions of the regions that we interrogated. We have introduced silent and conserved mutations to the critical packaging sites, which did not affect protein function but impaired viral replication at levels roughly similar to those of their defects in RNA packaging. Interestingly, certain mutations showed strong tendencies to revert to wild-type sequences, which implies that these putative packaging signals are critical for the influenza life cycle.
National Cyber Security Policy and Strategy of Nigeria: A Qualitative Analysis

With advancements in modernization came the infiltration of information and communication technologies across the world, Nigeria inclusive. Several benefits are obtainable from these but also prevalent are some associated risks. Communication exists massively in cyberspace and as such poses a myriad of threats to a nation. This can be addressed on a national spectrum by the implementation of cyber security policies and strategies. This research involves making a qualitative analysis of the current Nigerian National Cyber Security Policy and Strategy. The documents were analyzed in the light of selected harmonized strategy developmental frameworks and subsequently comparatively evaluated with similar documents of selected countries. After the analysis, the national documents were found to have met majority of the requirements in terms of content, but failed to address certain elements of concern to cyber security in the Nigerian environment.
Complete Derandomization of Identity Testing and Reconstruction of Read-Once Formulas

In this article, we study the identity testing problem of arithmetic read-once formulas (ROFs) and some related models. An ROF is a formula (a circuit whose underlying graph is a tree) in which the operations are { +, × } and such that every input variable labels at most one leaf. We obtain the first polynomial-time deterministic identity testing algorithm that operates in the black-box setting for ROFs, as well as some other related models. As an application, we obtain the first polynomial-time deterministic reconstruction algorithm for such formulas. Our results are obtained by improving and extending the analysis of the algorithm of Shpilka and Yolkovich [51].
Determination of trace heavy Metals by Sequential Injection-anodic Stripping Voltammetry using Bismuth Film Screen-printed Carbon Electrode

A sequential injection-square-wave anodic stripping voltammetry (SIA-SWASV) is proposed for the simultaneous determination of Pb(II), Cd(II) and Zn(II), employing an in situ plated bismuth film screen-printed carbon electrode (Bi-SPCE) as a working electrode and hydrochloric acid as a supporting electrolyte. Bi(III) and analyte metal ions were on-line deposited onto a SPCE at −1.4 V vs. Ag/AgCl for 180 s. At a stopped flow, a square-wave voltammogram was recorded from–1.3 to 0 V vs. Ag/AgCl. The experimental conditions were optimized. Under the optimum conditions, the linear ranges were 0–70 mg L^−1 for Pb(II) and Cd(II), and 75–200 mg L^−1 for Zn(II). The limits of detection ( S / N = 3) were obtained at concentrations as low as 0.89 mg L^−1 for Pb(II) and 0.69 mg L^−1 for Cd(II) for a 180-s deposition time. The proposed method was applied to the determination of Pb(II), Cd(II) and Zn(II) in water samples with satisfactory results.
DRFx

The most intuitive memory model for shared-memory multi-threaded programming is sequential consistency (SC), but it disallows the use of many compiler and hardware optimizations and thus affects performance. Data-race-free (DRF) models, such as the C++11 memory model, guarantee SC execution for data-race-free programs. But these models provide no guarantee at all for racy programs, compromising the safety and debuggability of such programs. To address the safety issue, the Java memory model, which is also based on the DRF model, provides a weak semantics for racy executions. However, this semantics is subtle and complex, making it difficult for programmers to reason about their programs and for compiler writers to ensure the correctness of compiler optimizations. We present the drfx memory model, which is simple for programmers to understand and use while still supporting many common optimizations. We introduce a memory model (MM) exception that can be signaled to halt execution. If a program executes without throwing this exception, then drfx guarantees that the execution is SC. If a program throws an MM exception during an execution, then drfx guarantees that the program has a data race. We observe that SC violations can be detected in hardware through a lightweight form of conflict detection. Furthermore, our model safely allows aggressive compiler and hardware optimizations within compiler-designated program regions. We formalize our memory model, prove several properties of this model, describe a compiler and hardware design suitable for drfx, and evaluate the performance overhead due to our compiler and hardware requirements.
Hard thresholding with norm constraints

We introduce a new sparse recovery paradigm, called NORMED PURSUITS, where efficient algorithms from combinatorial and convex optimization interface for interpretable and model-based solutions. Synthetic and real data experiments illustrate that NORMED PURSUITS can significantly enhance the performance of both hard thresholding methods and convex solvers in sparse recovery.
Individual- and Neighborhood-Level Predictors of Mortality in Florida Colorectal Cancer Patients

Purpose We examined individual-level and neighborhood-level predictors of mortality in CRC patients diagnosed in Florida to identify high-risk groups for targeted interventions. Methods Demographic and clinical data from the Florida Cancer Data System registry (2007–2011) were linked with Agency for Health Care Administration and US Census data (n = 47,872). Cox hazard regression models were fitted with candidate predictors of CRC survival and stratified by age group (18–49, 50–64, 65+). Results Stratified by age group, higher mortality risk per comorbidity was found among youngest (21%), followed by middle (19%), and then oldest (14%) age groups. The two younger age groups had higher mortality risk with proximal compared to those with distal cancer. Compared with private insurance, those in the middle age group were at higher death risk if not insured (HR = 1.35), or received healthcare through Medicare (HR = 1.44), Medicaid (HR = 1.53), or the Veteran’s Administration (HR = 1.26). Only Medicaid in the youngest (52% higher risk) and those not insured in the oldest group (24% lower risk) were significantly different from their privately insured counterparts. Among 18–49 and 50–64 age groups there was a higher mortality risk among the lowest SES (1.17- and 1.23-fold higher in the middle age and 1.12- and 1.17-fold higher in the older age group, respectively) compared to highest SES. Married patients were significantly better off than divorced/separated (HR = 1.22), single (HR = 1.29), or widowed (HR = 1.19) patients. Conclusion Factors associated with increased risk for mortality among individuals with CRC included being older, uninsured, unmarried, more comorbidities, living in lower SES neighborhoods, and diagnosed at later disease stage. Higher risk among younger patients was attributed to proximal cancer site, Medicaid, and distant disease; however, lower SES and being unmarried were not risk factors in this age group. Targeted interventions to improve survivorship and greater social support while considering age classification may assist these high-risk groups.
Self-Monitoring and Status Motivation: An Implicit Cognition Perspective

Prior research has highlighted the role of self-monitoring as a key individual trait impacting consumer behavior. In an extensive review, Gangestad and Snyder (2000) identified a need for research investigating the role of status motivation in self-monitoring. This research constitutes an answer to their call from an implicit cognition perspective. To do this, we rely on the motivation and opportunity as determinants of attitude-behavior processes model (MODE, Fazio and Towles-Schwen 1999). Results indicate that both low- and high self-monitors share positive automatic attitudes about status. However, low self-monitors seem to rely on these automatic associations to make explicit status judgments whereas high self-monitors do less so. These results integrate prior findings in consumer research and open up avenues for future inquiry.
Recognition of driver eyes' states based on variance projections function

The detection of drivers' eyes states is a key part in detecting drivers' vigilance states based on vision analysis. The present methods were not in real-time due to complex algorithm, or were very sensitive to the variety of illumination, and they are not suit to drivers work condition. We presented a new method which is based on variance projections function. Variance projection reflects the variance of intensity along projection direction mainly. The intensity of eyes area changes orderly under any illumination. So the eyes' feature can be extracted through variance projection at any illumination. A lot of eyes area variance projections under different illumination have been studied and we find out there were distinct differences between the projections when the eyes were open and when the eyes were close, so we can recognize the two states of the eyes using these features. The experiments result that the method is Robust to different illumination condition.
Development of multidrug resistance due to multiple factors including P‐glycoprotein overexpression under K‐selection after MYC and HRAS oncogene activation

Multistep tumorigenesis is a form of microevolution consisting of mutation and selection. To clarify the role of selection modalities in tumor development, we examined two alternative evolutionary conditions, r‐selection in sparse culture, which allows cells to proliferate rapidly, and K‐selection in confluent culture, in which overcrowding constrains cell proliferation. Using MYC‐ and EJ‐RAS‐transformed rat embryo fibroblasts, we found that K‐selected cells acquired and stably maintained multidrug resistance (MDR) to DOX, VCR, MTX and Ara‐C. Then, we examined the involvement of a number of factors potentially causal of the development of MDR, that is, ploidy, Tp53 mutation, doubling time and the expression levels of genes related to drug resistance. Although ploidy status and Tp53 mutations did not correlate with MDR, we found that Abcb1/Mdr1, encoding P‐glycoprotein (Pgp), was significantly upregulated after K‐selection. Cyclosporin A, a competitive inhibitor of Pgp, increased the intracellular accumulation of DOX and reduced the resistance to it. Indeed, the population of Pgp‐transfected cells significantly expanded under K‐, but not under r‐selection. In addition to Pgp upregulation, altered expression of other genes such as Cda/cytidine deaminase and Slc29a1/equilibrative nucleoside transporter 1 and prolonged doubling times were associated with MDR. This system reproduces events associated with MDR in vivo and would be useful for analysis of MDR development. © 2005 Wiley‐Liss, Inc.
Neoadjuvant versus adjuvant systemic treatment in breast cancer: a meta-analysis.

BACKGROUND Interest in the use of preoperative systemic treatment in the management of breast cancer has increased because such neoadjuvant therapy appears to reduce the extent of local surgery required. We compared the clinical end points of patients with breast cancer treated preoperatively with systemic therapy (neoadjuvant therapy) and of those treated postoperatively with the same regimen (adjuvant therapy) in a meta-analysis of randomized trials. METHODS We evaluated nine randomized studies, including a total of 3946 patients with breast cancer, that compared neoadjuvant therapy with adjuvant therapy regardless of what additional surgery and/or radiation treatment was used. Fixed and random effects methods were used to combine data. Primary outcomes were death, disease progression, distant disease recurrence, and loco-regional disease recurrence. Secondary outcomes were local response and conservative local treatment. All statistical tests were two-sided. RESULTS We found no statistically or clinically significant difference between neoadjuvant therapy and adjuvant therapy arms associated with death (summary risk ratio [RR] = 1.00, 95% confidence interval [CI] = 0.90 to 1.12), disease progression (summary RR = 0.99, 95% CI = 0.91 to 1.07), or distant disease recurrence (summary RR = 0.94, 95% CI = 0.83 to 1.06). However, neoadjuvant therapy was statistically significantly associated with an increased risk of loco-regional disease recurrences (RR = 1.22, 95% CI = 1.04 to 1.43), compared with adjuvant therapy, especially in trials where more patients in the neoadjuvant, than the adjuvant, arm received radiation therapy without surgery (RR = 1.53, 95% CI = 1.11 to 2.10). Across trials, we observed heterogeneity in the rates of complete clinical response (range = 7%-65%; P for heterogeneity of <.001), pathologic response (range = 4%-29%; P for heterogeneity of <.001), and adoption of conservative local treatment (range = 28%-89% in neoadjuvant arms, P for heterogeneity of <.001). CONCLUSIONS Neoadjuvant therapy was apparently equivalent to adjuvant therapy in terms of survival and overall disease progression. Neoadjuvant therapy, compared with adjuvant therapy, was associated with a statistically significant increased risk of loco-regional recurrence when radiotherapy without surgery was adopted.
COMPARATIVE ANALYSIS OF MODULATION SCHEMES USING ADAPTIVE EQUALIZATION AS FADING MITIGATION TECHNIQUE

Inter-symbol interference (ISI) due to multipath fading is a vital problem in high-speed wireless communication which restricts communication quality and capacity. Therefore, in addition to choosing a fading mitigation technique, it is also important to strategically select a modulation scheme for effective data transmission. Recent literature review on wireless standards, such as 3G and 4G indicates that QAM and QPSK are suitable choices for data transmission. In this paper, a comparative analysis on selected modulation schemes is performed in a fading environment. The mitigation of fading is done using adaptive equalization technique. Also, we show that the signal to noise ratio (SNR) is an important parameter to choose. It is observed that, even when an adaptive equalizer is used at the receiver, a very low SNR gives very high symbol error rate (SER). We derive some important conclusions from our simulation result: QPSK shows minimum SER, whereas 256-PSK and 256-PAM perform worse. Given its spectral efficiency and a low SER, the best choice is 256- QAM.
Variability of the mc1r Gene in Melanic and Non-Melanic Podarcis lilfordi and Podarcis pityusensis from the Balearic Archipelago

The association between polymorphism at the mc1r locus and colour variation was studied in two wall lizard species (Podarcis lilfordi and P. pityusensis) from the Balearic archipelago. Podarcis lilfordi comprises several deep mitochondrial lineages, the oldest of which originated in the Pliocene, while much shallower mitochondrial lineages are found in P. pityusensis. Here, we examined whether specific substitutions were associated with the melanic colouration found in islet populations of these species. Homologous nuclear sequences covering most of the mc1r gene were obtained from 73 individuals from melanic and non-melanic Podarcis from different populations (the entire gene was also sequenced in six selected individuals). MtDNA gene trees were also constructed and used as a framework to assess mc1r diversity. Mc1r showed greater polymorphism in P. lilfordi than in P. pityusensis. However, we observed no substitutions that were common to all melanic individuals across the two species. Only one significant association was detected in the mc1r partial sequence, but this was a synonymous A/G mutation with A alleles being more abundant in melanic populations. In addition, there were no associations between the main dominant phenotypes (green and brown, blue and yellow spots and ventral colour) and synonymous or non-synonymous substitutions in the mc1r gene. There was no statistical evidence of selection on mc1r. This study suggests no relationship between mc1r polymorphism and colour variation in Balearic Podarcis.
Affinity Purification of an Archaeal DNA Replication Protein Network

ABSTRACT Nineteen Thermococcus kodakarensis strains have been constructed, each of which synthesizes a different His6-tagged protein known or predicted to be a component of the archaeal DNA replication machinery. Using the His6-tagged proteins, stable complexes assembled in vivo have been isolated directly from clarified cell lysates and the T. kodakarensis proteins present have been identified by mass spectrometry. Based on the results obtained, a network of interactions among the archaeal replication proteins has been established that confirms previously documented and predicted interactions, provides experimental evidence for previously unrecognized interactions between proteins with known functions and with unknown functions, and establishes a firm experimental foundation for archaeal replication research. The proteins identified and their participation in archaeal DNA replication are discussed and related to their bacterial and eukaryotic counterparts. IMPORTANCE DNA replication is a central and essential event in all cell cycles. Historically, the biological world was divided into prokaryotes and eukaryotes, based on the absence or presence of a nuclear membrane, and many components of the DNA replication machinery have been identified and characterized as conserved or nonconserved in prokaryotic versus eukaryotic organisms. However, it is now known that there are two evolutionarily distinct prokaryotic domains, Bacteria and Archaea, and to date, most prokaryotic replication research has investigated bacterial replication. Here, we have taken advantage of recently developed genetic techniques to isolate and identify many proteins likely to be components of the archaeal DNA replication machinery. The results confirm and extend predictions from genome sequencing that the archaeal replication system is less complex but more closely related to a eukaryotic than to a bacterial replication system. DNA replication is a central and essential event in all cell cycles. Historically, the biological world was divided into prokaryotes and eukaryotes, based on the absence or presence of a nuclear membrane, and many components of the DNA replication machinery have been identified and characterized as conserved or nonconserved in prokaryotic versus eukaryotic organisms. However, it is now known that there are two evolutionarily distinct prokaryotic domains, Bacteria and Archaea, and to date, most prokaryotic replication research has investigated bacterial replication. Here, we have taken advantage of recently developed genetic techniques to isolate and identify many proteins likely to be components of the archaeal DNA replication machinery. The results confirm and extend predictions from genome sequencing that the archaeal replication system is less complex but more closely related to a eukaryotic than to a bacterial replication system.
Application of constructive learning algorithms to the inverse problem

A constructive learning algorithm is used to generate networks that learn to approximate the functional of the magnetotelluric inverse problem. Based on synthetic data, several experiments are performed in order to generate and test the neural networks. Rather than producing, at the present time, a practical algorithm using this approach, the object of the paper is to explore the possibilities offered by the new tools. The generated networks can be used as an internal module in a more general inversion program, or their predicted models can be used by themselves or simply as inputs to an optimization program.
The preparation, characterization, and pharmacokinetic studies of chitosan nanoparticles loaded with paclitaxel/dimethyl-β-cyclodextrin inclusion complexes

A novel biocompatible and biodegradable drug-delivery nanoparticle (NP) has been developed to minimize the severe side effects of the poorly water-soluble anticancer drug paclitaxel (PTX) for clinical use. PTX was loaded into the hydrophobic cavity of a hydrophilic cyclodextrin derivative, heptakis (2,6-di-O-methyl)-β-cyclodextrin (DM-β-CD), using an aqueous solution-stirring method followed by lyophilization. The resulting PTX/DM-β-CD inclusion complex dramatically enhanced the solubility of PTX in water and was directly incorporated into chitosan (CS) to form NPs (with a size of 323.9–407.8 nm in diameter) using an ionic gelation method. The formed NPs had a zeta potential of +15.9–23.3 mV and showed high colloidal stability. With the same weight ratio of PTX to CS of 0.7, the loading efficiency of the PTX/DM-β-CD inclusion complex-loaded CS NPs was 30.3-fold higher than that of the PTX-loaded CS NPs. Moreover, it is notable that PTX was released from the DM-β-CD/CS NPs in a sustained-release manner. The pharmacokinetic studies revealed that, compared with reference formulation (Taxol®), the PTX/DM-β-CD inclusion complex-loaded CS NPs exhibited a significant increase in AUC0→24h (the area under the plasma drug concentration–time curve over the period of 24 hours) and mean residence time by 2.7-fold and 1.4-fold, respectively. Therefore, the novel drug/DM-β-CD inclusion complex-loaded CS NPs have promising applications for the significantly improved delivery and controlled release of the poorly water-soluble drug PTX or its derivatives, thus possibly leading to enhanced therapeutic efficacy and less severe side effects.