Miracle-dz/UniFAR-FTUs huggingface dataset:
Polarity shift detection approaches in sentiment analysis: A survey

Sentiment analysis is a process of identifying and categorizing opinions expressed in a piece of text. It classifies the text into positive, negative or neutral. Lexicon-based and Supervised Machine Learning-based are the two main approaches in sentiment analysis. Bag-of-words model is used to represent the text as a vector of independent words and machine learning algorithms are used for classification. Polarity shift is the major problem in the Bag-of-words model. Polarity shift is a sentiment classification problem. It can reverse the sentiment polarity of the text. Classification performance of machine learning based systems can get affected by polarity shift. Negation is the type of polarity shift. Negative words can change the polarity of the sentimental words. Polarity shift detection methods are used to detect the polarity shift in the sentences. It helps to improve the performance of machine learning classification algorithms. Natural Language Processing can be used for feature extraction and classification. Sentiment analysis uses Natural Language Processing for extraction of opinion words from the text. Sentiment analysis plays an important role in identifying the opinion of the people about a specific topic or entity. This survey paper reviews the sentiment analysis approaches and highlight the need to address polarity shift problem in sentiment analysis. The different polarity shift detection techniques are discussed in this paper.
Targeting renin-angiotensin system in malignant hypertension in atypical hemolytic uremic syndrome

Hypertension is common in hemolytic uremic syndrome (HUS) and often difficult to control. Local renin-angiotensin activation is believed to be an important part of thrombotic microangiopathy, leading to a vicious cycle of progressive renal injury and intractable hypertension. This has been demonstrated in vitro via enhanced tissue factor expression on glomerular endothelial cells which is enhanced by angiotensin II. We report two pediatric cases of atypical HUS with severe refractory malignant hypertension, in which we targeted the renin-angiotensin system by using intravenous (IV) enalaprilat, oral aliskiren, and oral enalapril with quick and dramatic response of blood pressure. Both drugs, aliskiren and IV enalaprilat, were effective in controlling hypertension refractory to multiple antihypertensive medications. These appear to be promising alternatives in the treatment of severe atypical HUS-induced hypertension and hypertensive emergency.
Cutting Edge: Effector Memory CD8+ T Cells Play a Prominent Role in Recall Responses to Secondary Viral Infection in the Lung1

The relative contributions of CD62Lhigh (central) memory and CD62Llow (effector) memory T cell populations to recall responses are poorly understood, especially in the respiratory tract. In this study, we took advantage of a dual-adoptive transfer system in the mouse to simultaneously follow the recall response of effector and central memory subpopulations to intranasal parainfluenza virus infection. Using MHC class I and class II multimers, we tracked the responses of Ag-specific CD8+ and CD4+ memory T cells in the same animals. The data show that effector memory T cells mounted recall responses that were equal to, or greater than, those mounted by central memory T cells. Moreover, effector memory T cells were more efficient at subsequently establishing a second generation of memory T cells. These data contrast with other studies indicating that central memory CD8+ T cells are the prominent contributors to systemic virus infections.
A Strongly Consistent Criterion to Decide Between I(1) and I(0) Processes Based on Different Convergence Rates

The usual procedure to determine whether a univariate time series is stationary or first-difference stationary is to perform some unit root test. In this article, an alternative methodology is presented that leads to a strongly consistent two-step criterion to estimate the number of unit roots. The criterion is based on estimating some autoregressive polynomials using regression procedures and exploiting the fact that the nonstationary roots converge at a faster rate than the stationary ones. The proposed procedure requires at most four regressions and is easy to implement. A simulation study demonstrates that it can perform significantly better in practice than the Dickey–Fuller and the generalized least squares (GLS)-detrended Dickey–Fuller tests.
Threshold‐free estimation of functional antibody titers of a group B streptococcus opsonophagocytic killing assay

Opsonophagocytic killing assays (OPKA) are routinely used for the quantification of bactericidal antibodies in blood serum samples. Quantification of the OPKA readout, the titer, provides the basis for the statistical analysis of vaccine clinical trials having functional immune response endpoints. Traditional OPKA titers are defined as the maximum serum dilution yielding a predefined bacterial killing threshold value, and they are estimated by fitting a dose‐response model to the dilution‐killing curve. This paper illustrates a novel definition of titer, the threshold‐free titer, which preserves biological interpretability while not depending on any killing threshold or on a postulated shape of the dose‐response curve. These titers are shown to be more precise than the traditional threshold‐based titers when using simulated and experimental group B streptococcus OPKA experimental data. Also, titer linearity is shown to be not measurable when using threshold‐based titers, whereas it becomes measurable using threshold‐free titers. The biological interpretability and operational characteristics demonstrated here indicate that threshold‐free titers are an appropriate tool for the routine analysis of OPKA data. Copyright © 2015 John Wiley & Sons, Ltd.
Mapping the Wolf-Hirschhorn syndrome phenotype outside the currently accepted WHS critical region and defining a new critical region, WHSCR-2.

In an attempt to define the distinctive Wolf-Hirschhorn syndrome (WHS) phenotype, and to map its specific clinical manifestations, a total of eight patients carrying a 4p16.3 microdeletion were analyzed for their clinical phenotype and their respective genotypes. The extent of each individual deletion was established by fluorescence in situ hybridization, with a cosmid contig spanning the genomic region from MSX1 (distal half of 4p16.1) to the subtelomeric locus D4S3359. The deletions were 1.9-3.5 Mb, and all were terminal. All the patients presented with a mild phenotype, in which major malformations were usually absent. It is worth noting that head circumference was normal for height in two patients (those with the smallest deletions [1.9 and 2.2 Mb]). The currently accepted WHS critical region (WHSCR) was fully preserved in the patient with the 1.9-Mb deletion, in spite of a typical WHS phenotype. The deletion in this patient spanned the chromosome region from D4S3327 (190 b4 cosmid clone included) to the telomere. From a clinical point of view, the distinctive WHS phenotype is defined by the presence of typical facial appearance, mental retardation, growth delay, congenital hypotonia, and seizures. These signs represent the minimal diagnostic criteria for WHS. This basic phenotype maps distal to the currently accepted WHSCR. Here, we propose a new critical region for WHS, and we refer to this region as "WHSCR-2. " It falls within a 300-600-kb interval in 4p16.3, between the loci D4S3327 and D4S98-D4S168. Among the candidate genes already described for WHS, LETM1 (leucine zipper/EF-hand-containing transmembrane) is likely to be pathogenetically involved in seizures. On the basis of genotype-phenotype correlation analysis, dividing the WHS phenotype into two distinct clinical entities, a "classical" and a "mild" form, is recommended for the purpose of proper genetic counseling.
Parasites: evolution’s neurobiologists

Summary For millions of years, parasites have altered the behaviour of their hosts. Parasites can affect host behaviour by: (1) interfering with the host’s normal immune–neural communication, (2) secreting substances that directly alter neuronal activity via non-genomic mechanisms and (3) inducing genomic- and/or proteomic-based changes in the brain of the host. Changes in host behaviour are often restricted to particular behaviours, with many other behaviours remaining unaffected. Neuroscientists can produce this degree of selectivity by targeting specific brain areas. Parasites, however, do not selectively attack discrete brain areas. Parasites typically induce a variety of effects in several parts of the brain. Parasitic manipulation of host behaviour evolved within the context of the manipulation of other host physiological systems (especially the immune system) that was required for a parasite’s survival. This starting point, coupled with the fortuitous nature of evolutionary innovation and evolutionary pressures to minimize the costs of parasitic manipulation, likely contributed to the complex and indirect nature of the mechanisms involved in host behavioural control. Because parasites and neuroscientists use different tactics to control behaviour, studying the methods used by parasites can provide novel insights into how nervous systems generate and regulate behaviour. Studying how parasites influence host behaviour will also help us integrate genomic, proteomic and neurophysiological perspectives on behaviour.
Human Papillomavirus Type 16 E5 Protein Induces Expression of Beta Interferon through Interferon Regulatory Factor 1 in Human Keratinocytes

ABSTRACT Crucial steps in high-risk human papillomavirus (HR-HPV)-related carcinogenesis are the integration of HR-HPV into the host genome and loss of viral episomes. The mechanisms that promote cervical neoplastic progression are, however, not clearly understood. During HR-HPV infection, the HPV E5 protein is expressed in precancerous stages but not after viral integration. Given that it has been reported that loss of HPV16 episomes and cervical tumor progression are associated with increased expression of antiviral genes that are inducible by type I interferon (IFN), we asked whether E5, expressed in early phases of cervical carcinogenesis, affects IFN-β signaling. We show that the HPV type 16 (HPV16) E5 protein expression per se stimulates IFN-β expression. This stimulation is specifically mediated by the induction of interferon regulatory factor 1 (IRF-1) which, in turn, induces transcriptional activation of IRF-1-targeted interferon-stimulated genes (ISGs) as double-stranded RNA-dependent protein kinase R (PKR) and caspase 8. Our data show a new and unexpected role for HR-HPV E5 protein and indicate that HPV16 E5 may contribute to the mechanisms responsible for cervical carcinogenesis in part via stimulation of IFN-β and an IFN signature, with IRF-1 playing a pivotal role. HPV16 E5 and IRF-1 may thus serve as potential therapeutic targets in HPV-associated premalignant lesions.
NOS3 tagSNPs does not modify the chronic kidney disease progression in autosomal dominant polycystic kidney disease

Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary and progressive renal disorder. It is also recognised as the most frequent genetic cause of chronic kidney diseases (CKD). In the present study, four tagging SNPs and two more well studied polymorphisms (Intron 4 VNTR and Glu298Asp) the NOS3 gene were investigated to unravel the potential modifier effect of NOS3 gene on the progression of CKD in ADPKD.
A meta-analysis of empirical e-government research and its future research implications

The desired e-government potentials and its shortcomings in reality are key reasons why e-government has become a major topic of interest to academics and practitioners, leading to an extensive body of knowledge. However, the literature still demands further quantitative empirical research to substantiate theory development. This situation calls for a specific review of the literature that arranges relevant knowledge and provides a solid foundation for future research. However, available meta-analyses do not deliver the particular insights to appropriately address the shortage of quantitative empirical e-government research. Therefore, this study explicitly focuses on this specific field to systematically uncover areas requiring further exploration, and defines promising research directions for a solid foundation for future investigations. Key findings of the meta-analysis are: the existence of a systematic divide of existing quantitative empirical e-government studies into 12 research subtopics, which are assessed according to different classification criteria for scientific research gap-spotting; the identification of emerging subtopics that carry innovative research potential; and that e-government is expected to be an ongoing, open-ended research environment that still provides manifold investigative opportunities. Based on these findings, straightforward suggestions for future research are provided. Points for practitioners Beyond providing insights into the current state of quantitative empirical research for scientific researchers, this article also delivers value for professionals working in public management and administration. First, the study provides a comprehensive overview of e-government-related meta-analyses, which allows us to quickly identify the literature in order to tackle particular e-government management issues. Second, the article classifies existing quantitative empirical studies, defines specific subject areas and arranges relevant knowledge, which eases the processes of confining and labelling e-government activities. Last, since these deliverables are based on empirical studies that draw their conclusions from perceptions of reality, the summaries and classifications are thus regarded to be of special importance for public managers.
Incentive cooperative caching for localized information-centric networks

In-network caching has the potential to improve network efficiency and content distribution performance by satisfying user requests with cached content in Information-Centric Networking (ICN). Due to the fact that users in the same network domain can easily share their cached content with each other via home network devices, to reduce the transmission cost for obtaining content from the core network, caching cooperation home networks are constructed. Derived from the analysis of the economic relations among ICN entities, we propose an efficient incentive cooperative caching mechanism for content retrieval in localized ICNs in this paper. Particularly, access networks give rebates to those users who provide locally cached content for content retrieval in cache cooperation. To minimize the cost (including rebate and transmission cost) of obtaining a piece of content in the proposed caching framework, we also formulate an optimal caching problem as a multiple-choice knapsack problem. Furthermore, a sub-optimal caching scheme is proposed to handle the optimal content placement problem efficiently. Simulation results verify the superiority and efficiency of the proposed sub-optimal caching scheme compared with random caching.
Proteomic profiling reveals that Th2‐inducing dendritic cells stimulated with helminth antigens have a ‘limited maturation’ phenotype

Dendritic cells (DCs) are important in the initiation of primary immune responses against pathogens. To aid understanding of how DCs guide T helper (Th)2‐type responses, we employed 2‐DE in association with MS/MS to identify proteins which characterise pro‐Th2 DCs (matured with zero‐to‐three hours released proteins (0–3hRP), released by Schistosoma mansoni cercariae) versus pro‐Th1 DCs (matured with lipopolysaccharide, LPS) and immature DCs. Software analysis of average 2‐DE gels (three replicates per DC type) showed many similarities in the pattern of spots between the three groups of DCs but also marked changes. The major and significant changes in protein expression mainly affected cytoskeletal proteins. Other differences included chaperone proteins and enzymes involved in protein folding, S100 calcium‐binding proteins, peroxiredoxin 1, superoxide dismutase 1, several annexins and arginase 1. Our study demonstrates that pro‐Th2 DCs matured with 0–3hRP exhibit a proteome that is intermediate between that of immature DCs and pro‐Th1 DCs. Finally, the differential regulation of protein spots identified by MALDI‐MS/MS as having cytoskeletal and morphological functions was confirmed by contrast, confocal and scanning electron microscopy examination of DCs. Together, our results support the view that Th2 differentiation results from a ‘limited maturation’ of DCs.
The effect of host heterogeneity and parasite intragenomic interactions on parasite population structure

Understanding the processes that shape the genetic structure of parasite populations and the functional consequences of different parasite genotypes is critical for our ability to predict how an infection can spread through a host population and for the design of effective vaccines to combat infection and disease. Here, we examine how the genetic structure of parasite populations responds to host genetic heterogeneity. We consider the well-characterized molecular specificity of major histocompatibility complex binding of antigenic peptides to derive deterministic and stochastic models. We use these models to ask, firstly, what conditions favour the evolution of generalist parasite genotypes versus specialist parasite genotypes? Secondly, can parasite genotypes coexist in a population? We find that intragenomic interactions between parasite loci encoding antigenic peptides are pivotal in determining the outcome of evolution. Where parasite loci interact synergistically (i.e. the recognition of additional antigenic peptides has a disproportionately large effect on parasite fitness), generalist parasite genotypes are favoured. Where parasite loci act multiplicatively (have independent effects on fitness) or antagonistically (have diminishing effects on parasite fitness), specialist parasite genotypes are favoured. A key finding is that polymorphism is not stable and that, with respect to functionally important antigenic peptides, parasite populations are dominated by a single genotype.
Improved circulating half-life and efficacy of an antibody-interleukin 2 immunocytokine based on reduced intracellular proteolysis.

PURPOSE Previous studies showed that reducing the interaction of antibody-interleukin 2 immunocytokines with Fc receptors improved their circulating half-life in mice and increased their antitumor activity. We sought to modify sequences that would increase half-life but retain the ability to activate Fc receptor-mediated effector functions. EXPERIMENTAL DESIGN Modified immunocytokines were assessed in vitro for effector function and protease sensitivity and in vivo for pharmacokinetic and antitumor activities in an syngeneic tumor regression model. RESULTS Single amino acid changes in the junction sequence between the antibody and interleukin-2 components had dramatic effects on circulating half-life and antitumor activity. This effect was independent of Fc receptor binding to either Fcgamma receptors or the Fc protection receptor, but was associated with changes in susceptibility to intracellular proteases. CONCLUSIONS We have identified modifications that dramatically improve the circulating half-life of immunocytokines based on increased resistance to intracellular degradation and thus have demonstrated how these molecules can be recycled in and out of an intracellular compartment. Use of these improved immunocytokines with highly favorable pharmacokinetic properties and retained effector functions should lead to more effective treatment of epithelial cancers.
Analysis of Replication Kinetics of the Human Metapneumovirus in Different Cell Lines by Real-Time PCR

ABSTRACT Human metapneumovirus (hMPV) is associated with acute respiratory tract disease especially in young children. Using a quantitative real-time TaqMan PCR, we analyzed the replication kinetics of hMPV in different cell lines. Our results indicate that hMPV replicates slightly more efficiently in LLC-MK2 than in Vero cells and poorly in HEp-2 cells.
A Simple Modification of the Separation Method Reduces Heterogeneity of Adipose-Derived Stem Cells

High hopes are put into the use of mesenchymal stem cells (MSCs) in various approaches for tissue engineering and regenerative medicine. MSCs are derived from different tissues with only small differences in their phenotype or their differentiation potential, but higher differences in the cell yield. Since fat is easily accessible and contains a high amount of MSCs to be isolated, adipose-derived stem cells (ASCs) are very promising for clinical approaches. ASCs are not a completely homogeneous cell population. Our study was initiated to explore an easy and convenient method to reduce heterogeneity. We tested different isolation methods: (1) the standard isolation method for ASCs based on plastic attachment, (2) the standard method with an initial washing step after 60 min of adherence and (3) immunomagnetic isolation by 4 typical markers (CD49a, CD90, CD105 and CD271). Cells isolated by these methods were evaluated using quantitative PCR and flow cytometry as well as by their differentiation potential. Washing led to a significantly lower expression of desmin, smA and six2, and a higher expression of the stem cell markers nestin, oct-4 and sall-1, compared to standard isolated cells, while the immunomagnetically isolated cells showed no significant changes. All cells independent of the isolation method could be induced to differentiate into adipocytes and osteoblasts. Our study demonstrates that a simple washing step reduces heterogeneity of cultured ASCs according to PCR analysis, whereas the immunomagnetic isolation only showed minor advantages compared to the standard method, but the disadvantage of significantly lower cell yields in the primary isolates.
Comparative Pathology of Neurovirulent Lineage 1 (NY99/385) and Lineage 2 (SPU93/01) West Nile Virus Infections in BALBc Mice

The pathology in mice infected with neurovirulent South African lineage 2 West Nile virus (WNV) strains has not previously been described. Three- to 4-month-old male BALBc mice were infected with South African neurovirulent lineage 2 (SPU93/01) or lineage 1 (NY385/99) WNV strains and the gross and microscopic central nervous system (CNS) and extra-CNS pathology of both investigated and compared. Mice infected with both lineages showed similar illness, paralysis, and death from days 7 to 11 postinfection (PI). Two survivors of each lineage were euthanized on day 21 PI. WNV infection was confirmed by nested real-time reverse transcription polymerase chain reaction of tissues, mostly brain, in the majority of mice euthanized sick or that died and in 1 healthy lineage 2 survivor. Gross lesions caused by both lineages were identical and included marked gastric and proximal small intestinal fluid distension as described in a previous mouse study, but intestinal microscopic lesions differed. CNS lesions were subtle. Immunohistochemical (IHC)–positive labeling for WNV E protein was found in neurons multifocally in the brain of 3 lineage 1–infected and 3 lineage 2–infected mice from days 9 to 11 PI, 4 of these including brainstem neurons, and of cecal myenteric ganglion neurons in 1 lineage 2–infected day 8 PI mouse. Findings supported hypotheses in hamsters that gastrointestinal lesions are likely of brainstem origin. Ultrastructurally, virus-associated cytoplasmic vesicular or crystalline structures, or amorphous structures, were found to label IHC positive in control-positive avian cardiomyocytes and mouse thalamic neurons, respectively, and WNV-like 50-nm particles, which were scarce, did not label.