Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotype and Genotype of Pancreatic Cancer Cell Lines

Abstract The dismal prognosis of pancreatic adenocarcinoma is due in part to a lack of molecular information regarding disease development. Established cell lines remain a useful tool for investigating these molecular events. Here we present a review of available information on commonly used pancreatic adenocarcinoma cell lines as a resource to help investigators select the cell lines most appropriate for their particular research needs. Information on clinical history; in vitro and in vivo growth characteristics; phenotypic characteristics, such as adhesion, invasion, migration, and tumorigenesis; and genotypic status of commonly altered genes (KRAS, p53, p16, and SMAD4) was evaluated. Identification of both consensus and discrepant information in the literature suggests careful evaluation before selection of cell lines and attention be given to cell line authentication.
Reactivity profiles of broadly neutralizing anti-HIV-1 antibodies are distinct from those of pathogenic autoantibodies

Objective:Broadly neutralizing antibodies (bNt Abs) against HIV-1 are rarely produced during natural infection, and efforts to induce such Abs by vaccination have been unsuccessful. Thus, elucidating the nature and cellular origins of bNt Abs is a high priority for vaccine research. As the bNt monoclonal Abs (MAbs) 2F5, 4E10 and 2G12 have been reported to bind select autoantigens, we investigated whether these MAbs display a broader range of autoreactivity and how their autoreactivity compares with that of pathogenic autoAbs. Methods:An autoantigen microarray comprising 106 connective tissue disease-related autoantigens and control antigens was developed and used, in combination with ELISAs, to compare the reactivity profiles of MAbs 4E10, 2F5 and 2G12 to those of four pathogenic autoAbs derived from patients with antiphospholipid-syndrome (APS), and to serum from a patient with systemic lupus erythematosus (SLE). Results:The APS MAbs and SLE serum reacted strongly with multiple autoantigens on the microarray, whereas anti-HIV-1 MAb reactivity was limited mainly to HIV-1-related antigens. The APS autoAbs reacted strongly with CL, yet only 4E10 bound CL at high concentrations; both 2F5 and 4E10 bound their HIV-1 epitopes with a 2–3-log higher apparent affinity than CL. Moreover, the polyreactivity of 4E10, but not CL15, could be blocked with dried milk. Conclusion:The reactivity profiles of bNt anti-HIV-1 MAbs are fundamentally distinct from those of pathogenic autoAbs that arise from dysregulated tolerance mechanisms. This suggests that the limited polyreactivity observed for the bNt MAbs, and for HIV-1-Nt Abs in general, may arise through alternative mechanisms, such as extensive somatic mutation due to persistent antigen selection during chronic infection.
Building Accurate Emulators for Stochastic Simulations via Quantile Kriging

Computer simulation has increasingly become popular for analysis of systems that cannot be feasibly changed because of costs or scale. This work proposes a method to construct an emulator for stochastic simulations by performing a designed experiment on the simulator and developing an emulative distribution. Existing emulators have focused on estimation of the mean of the simulation output, but this work presents an emulator for the distribution of the output. This construction provides both an explicit distribution and a fast sampling scheme. Beyond the emulator description, this work demonstrates the emulator’s efficiency, that is, its convergence rate is the asymptotically optimal among all possible emulators using the same sample size (under certain conditions). An example of its practical use is demonstrated using a stochastic simulation of fracture mechanics. Supplementary materials for this article are available online.
Sexual violence in armed conflict

Which armed groups have perpetrated sexual violence in recent conflicts? This article presents patterns from the new Sexual Violence in Armed Conflict (SVAC) dataset. The dataset, coded from the three most widely used sources in the quantitative human rights literature, covers 129 active conflicts, and the 625 armed actors involved in these conflicts, during the period 1989–2009. The unit of observation is the conflict-actor-year, allowing for detailed analysis of the patterns of perpetration of sexual violence for each conflict actor. The dataset captures six dimensions of sexual violence: prevalence, perpetrators, victims, forms, location, and timing. In addition to active conflict-years, the dataset also includes reports of sexual violence committed by conflict actors in the five years post-conflict. We use the data to trace variation in reported conflict-related sexual violence over time, space, and actor type, and outline the dataset's potential utility for scholars. Among the insights offered are that the prevalence of sexual violence varies dramatically by perpetrator group, suggesting that sexual violations are common – but not ubiquitous. In addition, we find that state militaries are more likely to be reported as perpetrators of sexual violence than either rebel groups or militias. Finally, reports of sexual violence continue into the post-conflict period, sometimes at very high levels. The data may be helpful both to scholars and policymakers for better understanding the patterns of sexual violence, its causes, and its consequences.
Protocol Complications with the IP Network Address Translator

Many internet applications can be adversely affected when end nodes are not in the same address realm and seek the assistance of an IP Network Address Translator (NAT) enroute to bridge the realms. The NAT device alone cannot provide the necessary application/protocol transparency in all cases and seeks the assistance of Application Level Gateways (ALGs) where possible, to provide transparency. The purpose of this document is to identify the protocols and applications that break with NAT enroute. The document also attempts to identify any known workarounds. It is not possible to capture all applications that break with NAT in a single document. This document attempts to capture as much information as possible, but is by no means a comprehensive coverage. We hope the coverage provides sufficient clues for applications not covered.
Peer Group Self-Identification in Samples of Russian and U.S. Adolescents

Most peer group self-identification research has been conducted in the United States. This article examined the generalizability of self-identified group name research among teens in Ufa, a city in the Russian Federation. A cross-sectional, anonymous collection of data on group self-identification, drug use, addiction concern, sensation seeking, and self-rated school performance was collected from 365 10th grade youth in Ufa and 965 10th grade youth in the United States. The results supported the existence of peer group self-identification by youth in both countries and, in general, replicated the findings that youth who self-identify as a High Risk Youth, are relatively likely to use drugs, show greater concern about becoming an addict, report a greater sensation seeking preference, higher levels of depression, and poorer school performance. Implications of these results are discussed.
Polymorphisms in the neuronal isoform of tryptophan hydroxylase 2 are associated with bipolar disorder in French Canadian pedigrees

Objective Tryptophan hydroxylase is the rate-limiting enzyme in the serotonin biosynthetic pathway and plays an important role in the regulation of serotonin levels. Recently, a brain-specific isoform, tryptophan hydroxylase 2 or n-tryptophan hydroxylase, has been discovered. Some studies reported genetic and functional associations between this isoform and bipolar disorder and/or major depressive disorder. The aim of this study was to investigate further association of genetic variants in French Canadian samples with bipolar disorders. Methods Genetic variants in the tryptophan hydroxylase 2 gene were genotyped in a case–control sample consisting of 225 affected individuals (191 bipolar I and 34 bipolar II) and 221 controls and in a collection of extended pedigrees and trios from the same population 357 nuclear families (201 bipolar I, 64 bipolar II, 79 recurrent major depressive disorder). Results We determined linkage disequilibrium structure in our isolated population and analyzed six tagged single nucleotide polymorphisms in the case–control sample. Whereas no single, single nucleotide polymorphism gave any significant result, a three single nucleotide polymorphism haplotype gave a global P=0.01. Family-based association showed significant association (P=0.004) of one polymorphism (rs4290270) with the major allele overtransmitted to affected offspring. Conclusions Case–control and family-based association studies further support the presence of a susceptibility locus for bipolar disorder in tryptophan hydroxylase 2 by showing statistically significant associations with both, single nucleotide polymorphism alone and haplotype of single nucleotide polymorphism markers.
Different components in human serum inhibit multiplication of Cryptococcus neoformans and enhance fluconazole activity

The inhibitory effect of human serum on the multiplication of Cryptococcus neoformans and the interaction with fluconazole were studied. Compared with cryptococcal multiplication in RPMI 1640 medium alone, 5% human serum in medium inhibited multiplication by 76% +/- 6% (n = 8). The inhibitory effect of human serum was donor independent, [corrected] heat stable (56 degrees C, 30 min), and not due to albumin or globulin. Bovine and murine sera were not inhibitory at that concentration. A fungistatic concentration of fluconazole (5.0 micrograms/ml) in medium plus 5% human serum resulted in 40% +/- 5% (n = 8) killing (reduction of inoculum CFU) in a 24-h assay. Bovine or murine sera did not have the enhancing effect, and this human serum activity was heat stable and donor independent. At 2.5 micrograms of fluconazole per ml, fungistasis by fluconazole plus human serum was significantly greater than with either alone. Higher serum concentrations [corrected] potentiated fluconazole more. At higher fluconazole concentrations (e.g., 20 micrograms/ml) fluconazole alone could kill, but serum potentiated this. A fluconazole-resistant isolate (MIC, 100 micrograms/ml) was not killed by fluconazole (5.0 micrograms/ml) in 5% human serum, but human serum potentiated the partial fluconazole inhibition. When human serum was dialyzed (molecular weight cutoff, 6,000 to 8,000) against phosphate-buffered saline, it lost the ability to synergize with fluconazole for killing Cryptococcus organisms but not the capacity to inhibit multiplication. Filtration of serum suggested the filtrate with a molecular weight of < 10,000 could interact synergistically with fluconazole for killing but could not inhibit cryptococcal multiplication. These findings indicate that human serum has two components, one (macromolecular) with a unique ability to inhibit C. neoformans and a low-molecular-weight component that enhances fluconazole anticryptococcal activity.
A fuzzy‐set‐theory‐based approach to analyse species membership in DNA barcoding

Reliable assignment of an unknown query sequence to its correct species remains a methodological problem for the growing field of DNA barcoding. While great advances have been achieved recently, species identification from barcodes can still be unreliable if the relevant biodiversity has been insufficiently sampled. We here propose a new notion of species membership for DNA barcoding—fuzzy membership, based on fuzzy set theory—and illustrate its successful application to four real data sets (bats, fishes, butterflies and flies) with more than 5000 random simulations. Two of the data sets comprise especially dense species/population‐level samples. In comparison with current DNA barcoding methods, the newly proposed minimum distance (MD) plus fuzzy set approach, and another computationally simple method, ‘best close match’, outperform two computationally sophisticated Bayesian and BootstrapNJ methods. The new method proposed here has great power in reducing false‐positive species identification compared with other methods when conspecifics of the query are absent from the reference database.
Estimating the impact of contextual variables on the productivity: An enhanced slack-based DEA model

The contextual variable is an important issue that makes an indispensable impact on the productivities of decision making units (DMUs). Analyzing the contribution of such factors to productivity differences is an intriguing area of research in data envelopment analysis (DEA). We first investigate whether and how contextual variables impact performances of the DMUs based on slack-based measurement. We extend the implicit assumption of prior studies and suggest that contextual variables can be a catalyst to increase the productivity. Impact and error factors, which are derived from regression analysis and stochastic frontier analysis (SFA), are defined to better represent the composition of two contradictory impacts, catalyst and depressant, of contextual variables. A statistical analysis is provided to identify the significance of such impacts and recognize multi-collinearity among contextual variables. The two factors are also moderated flexibly by decision makers in accordance with various production scenarios. Accordingly, original inputs and outputs are appropriately adjusted. Further, modified slack-based DEA models are proposed to incorporate DEA and regression analysis within an integrated framework. Several properties and propositions are presented to better describe the characteristics of the models. An empirical example is shown to verify the feasibility of the proposed approach.
Work engagement in female academics at an open distance learning and a contact university in South Africa - a review and critique

This research focused on the work engagement as represented by the sub-dimensions of vigour, absorption and dedication in female academics at two universities in South Africa. An open distance learning (ODL) university, as well as a traditional contact university were targeted. A positive psychological paradigm perspective guided the research. A cross-sectional survey design was used. In total 187 permanently employed female academics at the two universities completed the survey. The findings included that the work engagement scores of the female academics were just above average. It is recommended that universities introduce a management strategy to facilitate, nurture and encourage the experience of work engagement among female academics and that these academics take personal responsibility for their own wellness. Furthermore, they need to act on the initial signs of decreasing work engagement, rather than dismissing it as mere fatigue or lack of energy. DOI: 10.5901/mjss.2014. v5n7p324
Human Immunodeficiency Virus Type 1 Gag-Specific Mucosal Immunity after Oral Immunization with Papillomavirus Pseudoviruses Encoding Gag

ABSTRACT Mucosal surfaces are the primary portals for human immunodeficiency virus (HIV) transmission. Because systemic immunization, in general, does not induce effective mucosal immune responses, a mucosal HIV vaccine is urgently needed. For this study, we developed papillomavirus pseudoviruses that express HIV-1 Gag. The pseudoviruses are synthetic, nonreplicating viruses, yet they can produce antigens for a long time in the immune system. Here we show that oral immunization of mice by the use of papillomavirus pseudoviruses encoding Gag generated mucosal and systemic Gag-specific cytotoxic T lymphocytes that effectively lysed Gag-expressing target cells. Furthermore, the pseudoviruses generated Gag-specific gamma interferon-producing T cells and serum immunoglobulin G (IgG) and mucosal IgA. In contrast, oral immunization with plasmid DNA encoding HIV-1 Gag did not induce specific immune responses. Importantly, oral immunization with the pseudoviruses induced Gag-specific memory cytotoxic T lymphocytes and protected mice against a rectal mucosal challenge with a recombinant vaccinia virus expressing HIV-1 Gag. Thus, papillomavirus pseudoviruses encoding Gag are a promising mucosal vaccine against AIDS.
Cloning of the Pseudomonas aeruginosa outer membrane porin protein P gene: evidence for a linked region of DNA homology

The gene encoding the outer membrane phosphate-selective porin protein P from Pseudomonas aeruginosa was cloned into Escherichia coli. The protein product was expressed and transported to the outer membrane of an E. coli phoE mutant and assembled into functional trimers. Expression of a product of the correct molecular weight was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot (immunoblot) analysis, using polyclonal antibodies to protein P monomer and trimer forms. Protein P trimers were partially purified from the E. coli clone and shown to form channels with the same conductance as those formed by protein P from P. aeruginosa. The location and orientation of the protein P-encoding (oprP) gene on the cloned DNA was identified by three methods: (i) mapping the insertion point of transposon Tn501 in a previously isolated P. aeruginosa protein P-deficient mutant; (ii) hybridization of restriction fragments from the cloned DNA to an oligonucleotide pool synthesized on the basis of the amino-terminal protein sequence of protein P; and (iii) fusion of a PstI fragment of the cloned DNA to the amino terminus of the beta-galactosidase gene of pUC8, producing a fusion protein that contained protein P-antigenic epitopes. Structural analysis of the cloned DNA and P. aeruginosa chromosomal DNA revealed the presence of two adjacent PstI fragments which cross-hybridized, suggesting a possible gene duplication. The P-related (PR) region hybridized to the oligonucleotide pool described above. When the PstI fragment which contained the PR region was fused to the beta-galactosidase gene of pUC8, a fusion protein was produced which reacted with a protein P-specific antiserum. However, the restriction endonuclease patterns of the PR region and the oprP gene differed significantly beyond the amino-terminal one-third of the two genes.
The Efficacy of Antifibrinolytic Drugs in Children Undergoing Noncardiac Surgery: A Systematic Review of the Literature

Children undergoing major surgery are frequently exposed to a high risk of blood loss often requiring transfusion. Although the risks associated with blood product transfusion have considerably decreased over the last decade, transfusion is still associated with significant morbidity and mortality. Thus, rigorous efforts should be made to decrease surgical bleeding and the need for blood product transfusion. Antifibrinolytic drugs have been shown to be effective when used in both adult and pediatric surgical patients. While there are data in adults to support safety, data remain limited for pediatric patients. Since the restriction of aprotinin use in 2008, the most commonly used antifibrinolytic drugs have been the lysine analogs, tranexamic acid (TXA), and &egr;-aminocaproic acid, which inhibit the conversion of plasminogen to plasmin and decrease the degree of fibrinolysis. We performed a systematic review of the literature pertaining to the efficacy of antifibrinolytic drugs in children undergoing noncardiac surgery. During spine surgery, both TXA and &egr;-aminocaproic acid decrease blood loss and transfusion requirements; however, this information comes from small, mainly retrospective trials. Two prospective, randomized, controlled trials have tested the efficacy of TXA in children undergoing craniofacial surgery and have reported that TXA decreases transfusion requirements. Two pharmacokinetic trials were also recently published and are summarized in this review. No data have been published regarding the efficacy of TXA administration in the pediatric trauma population. Further data are still needed in this field of study, and we discuss some perspectives for future research.
ML Parameter Generation with a Reformulated MGE Training Criterion - Participation in the Voice Conversion Challenge 2016

This paper describes our entry to the Voice Conversion Challenge 2016. Based on the maximum likelihood parameter generation algorithm, the method is a reformulation of the minimum generation error training criterion. It uses a GMM for soft classification, a Mel-cepstral vocoder for acoustic analysis and an improved dynamic time warping procedure for source-target alignment. To compensate the oversmoothing effect, the generated parameters are filtered through a speaker-independent postfilter implemented as a linear transform in cepstral domain. The process is completed with mean and variance adaptation of the logfundamental frequency and duration modification by a constant factor. The results of the evaluation show that the proposed system achieves a high conversion accuracy in comparison with other systems, while its naturalness scores are intermediate.
Three-phase three-level shunt active power filter with simplified synchronous reference frame

Shunt active power filter (SAPF) is the most effective solution to current harmonics. In its controller, Synchronous Reference Frame (SRF) principle has widely been applied in current harmonics extraction algorithm due to its simple implementation features. However, the conventional SRF algorithm performs with serious time delay due to strong reliance on sluggish numerical filters. Moreover, the algorithm is still considered to possess unnecessary features which impose excessive computational burden to the designed controller. Therefore, this paper presents a simplified SRF algorithm with improved performance for the purpose of current harmonics extraction in three-phase three-level neutral-point diode clamped (NPC) inverter-based SAPF. Two potential modifications are implemented which include replacement of numerical filter with mathematical based average identifier to improve mitigation performance and removal of redundant features to reduce algorithm complexity. The proposed algorithm is developed and evaluated in MATLAB / Simulink. Simulation results have confirmed the improvement achieved by the proposed algorithm in comparison to the conventional algorithm.
Locality aware P2P overlay architecture for live video streaming

Recently, using Peer-to-Peer (P2P) overlay architectures have become a popular approach for live video streaming over the Internet. Since the peers in these systems are geographically distributed, the communication between them imposes huge redundant traffic into the Internet. One solution to address this problem is utilizing the locality aware algorithms to optimize the neighbor selection policy. However, for real-time applications like live video streaming we need to consider the trade-off between localizing the traffic and service quality. In this paper, we propose a novel pure P2P framework through two phases; (1) Local tracker selection, and (2) Overlay mesh construction. We introduce different locality metrics for neighbor selection. This framework adapts itself to the number of participant peers in the network to guarantee scalability. To the best of our knowledge, this is the first work on the locality in live video streaming over P2P networks. Our comprehensive simulation results show that selecting the neighbors by considering locality concepts reduces (85% in average) the cross Autonomous System (AS) border traffics, compared to existing classic locality aware P2P systems. Moreover, the proposed framework decreases end-to-end delay and distortion (50% and 58% in average, respectively).