Sentiment Analysis in Digital Spaces: An Overview of Reviews

Sentiment analysis (SA) is commonly applied to digital textual data, revealing insight into opinions and feelings. Many systematic reviews have summarized existing work, but often overlook discussions of validity and scientific practices. Here, we present an overview of reviews, synthesizing 38 systematic reviews, containing 2,275 primary studies. We devise a bespoke quality assessment framework designed to assess the rigor and quality of systematic review methodologies and reporting standards. Our findings show diverse applications and methods, limited reporting rigor, and challenges over time. We discuss how future research and practitioners can address these issues and highlight their importance across numerous applications.Comment: 44 pages, 4 figures, 6 tables, 3 appendice

Principles and mechanisms of ultraviolet light emitting diode technology for food industry applications

peer-reviewedThe application of ultraviolet (UV) light to water, food contact surfaces and medical equipment for microbial inactivation is widely employed. To date, UV disinfection sources employed are primarily low-pressure and medium-pressure mercury lamps; emitting monochromatic and polychromatic light, respectively. Despite the widespread use of mercury lamps, there are multiple drawbacks associated with their use including; high energy consumption, large size which limits reactor design, high heat emission and the presence of mercury. Light emitting diodes (LEDs) have potential for use as a highly efficient UV decontamination technology. Recent advances in semiconductor development have resulted in UV-LEDs becoming more widely available. UV-LEDs emit monochromatic light, which enables customised UV-LED disinfection systems at specific wavelengths to be developed. The application of UV-LEDs for disinfection purposes has been studied in recent years, particularly with respect to water disinfections systems. In this review, studies relating to UV-LED food applications are discussed. Furthermore, the chemical changes induced in foods, as a result of UV treatment, together with advantages and limitations of the technology are outlined

Effectiveness of a novel UV light emitting diode based technology for the microbial inactivation of Bacillus subtilis in model food systems.

peer-reviewedThe objective of this study was to assess the effectiveness of a novel UV multiwavelength light emitting diode (LED) based technology for the inactivation of B. subtilis in two model food systems. The LED based system was used to treat B. subtilis bacterial cultures using various combinations of UV wavelengths (285, 365, 405, 285/365, 285/405, 365/405, 285/365/405 nm) for different treatment durations (5 & 10 min). Bacterial enumerations, post-treatment analysis and SEM imaging were carried out. UV treatment at 285 nm was found to be the most efficient individual wavelength for inactivation resulting in > 6 log10 reductions. Treatments at other wavelengths investigated also resulted in bacteriostatic effects. Synergistic effects were observed for treatment at a 285/405 nm combination in one model system. Growth kinetics were carried out using a modified Gompertz model and model fit was assessed by root mean squared error, accuracy factor and bias factor. Experimental data showed good fit with model employed with RMSE values ranging from 0.01 x 10-2 to 1.367 x 10-2 for 5 min treatment, and 0.01 x 10-2 to 0.210 x 10-2 for 10 min treatment. Multivariate analysis was also carried out using principal component analysis and explained 100% of the variation observed for 3 principal components. This study shows that UV-LED technology is effective as bactericidal and bacteriostatic technology, depending on wavelength used

Antimicrobial effects of airborne acoustic ultrasound and plasma activated water from cold and thermal plasma systems on biofilms

peer-reviewedBacterial bioflms are difcult to inactivate due to their high antimicrobial resistance. Therefore, new approaches are required for more efective bacterial bioflm inactivation. Airborne acoustic ultrasound improves bactericidal or bacteriostatic activity which is safe and environmentally friendly. While, plasma activated water (PAW) is attracting increasing attention due to its strong antimicrobial properties. This study determined efcacy of combined airborne acoustic ultrasound and plasma activated water from both cold and thermal plasma systems in inactivating Escherichia coli K12 bioflms. The application of airborne acoustic ultrasound (15 min) alone was signifcantly more efective in reducing E. coli counts in 48 and 72 h bioflms compared to 30 min treatment with PAW. The efect of airborne acoustic ultrasound was more pronounced when used in combination with PAW. Airborne acoustic ultrasound treatment for 15 min of the E. coli bioflm followed by treatment with PAW signifcantly reduced the bacterial count by 2.2—2.62 Log10 CFU/mL when compared to control bioflm treated with distilled water. This study demonstrates that the synergistic efects of airborne acoustic ultrasound and PAW for enhanced antimicrobial efects. These technologies have the potential to prevent and control bioflm formation in food and bio-medical applications.Science Foundation Irelan

Effect of non-thermal plasma technology on microbial inactivation and total phenolic content of model liquid food and black pepper grains

pre-printThe objectives of this study were to investigate the effects of cold plasma technology on the growth and survival rates of vegetative cells and spores, and total phenolic content of black pepper grains. Plasma treatment was carried out using a non-thermal plasma jet system operating at 20 kHz using atmospheric air at a flow of 11 L/min. Two matrices were used, a model liquid food system and black pepper grains, both inoculated with Bacillus subtilis vegetative cells and spores. The samples were treated at 15 and 30 kV for 3–20 min. The plate count method was used to observe the colony-forming units at selected storage times i.e. at 1, 24 and 48 h post treatment at 4 °C. The highest log reduction was observed at 24 h post treatment, i.e. 2.92 log reduction. A 1 log reduction was achieved in the case of black pepper inoculated with spores for all selected storage times. No significant differences in total phenolic content were observed between treated and non-treated samples (p > 0.05). Optical emission spectroscopy was used to detect reactive species which could be responsible for cell death. Atomic oxygen, atomic nitrogen, hydroxyl radicals, nitrite oxide and nitrate were detected in light emitted from the plasma. Cell membrane damage caused by non-thermal plasma technology was observed using scanning electron microscopy. This study concludes that cold plasma technology has potential for industry application in food processing to reduce microbial loads in dried foods with limited impacts on food quality

RNAseq Analyses Identify Tumor Necrosis Factor-Mediated Inflammation as a Major Abnormality in ALS Spinal Cord

ALS is a rapidly progressive, devastating neurodegenerative illness of adults that produces disabling weakness and spasticity arising from death of lower and upper motor neurons. No meaningful therapies exist to slow ALS progression, and molecular insights into pathogenesis and progression are sorely needed. In that context, we used high-depth, next generation RNA sequencing (RNAseq, Illumina) to define gene network abnormalities in RNA samples depleted of rRNA and isolated from cervical spinal cord sections of 7 ALS and 8 CTL samples. We aligned \u3e50 million 2X150 bp paired-end sequences/sample to the hg19 human genome and applied three different algorithms (Cuffdiff2, DEseq2, EdgeR) for identification of differentially expressed genes (DEG’s). Ingenuity Pathways Analysis (IPA) and Weighted Gene Co-expression Network Analysis (WGCNA) identified inflammatory processes as significantly elevated in our ALS samples, with tumor necrosis factor (TNF) found to be a major pathway regulator (IPA) and TNFα-induced protein 2 (TNFAIP2) as a major network “hub” gene (WGCNA). Using the oPOSSUM algorithm, we analyzed transcription factors (TF) controlling expression of the nine DEG/hub genes in the ALS samples and identified TF’s involved in inflammation (NFkB, REL, NFkB1) and macrophage function (NR1H2::RXRA heterodimer). Transient expression in human iPSC-derived motor neurons of TNFAIP2 (also a DEG identified by all three algorithms) reduced cell viability and induced caspase 3/7 activation. Using high-density RNAseq, multiple algorithms for DEG identification, and an unsupervised gene co-expression network approach, we identified significant elevation of inflammatory processes in ALS spinal cord with TNF as a major regulatory molecule. Overexpression of the DEG TNFAIP2 in human motor neurons, the population most vulnerable to die in ALS, increased cell death and caspase 3/7 activation. We propose that therapies targeted to reduce inflammatory TNFα signaling may be helpful in ALS patients

Allelic spectrum of the natural variation in CRP

With the recent completion of the International HapMap Project, many tools are in hand for genetic association studies seeking to test the common variant/common disease hypothesis. In contrast, very few tools and resources are in place for genotype–phenotype studies hypothesizing that rare variation has a large impact on the phenotype of interest. To create these tools for rare variant/common disease studies, much interest is being generated towards investing in re-sequencing either large sample sizes of random chromosomes or smaller sample sizes of patients with extreme phenotypes. As a case study for rare variant discovery in random chromosomes, we have re-sequenced ~1,000 chromosomes representing diverse populations for the gene C-reactive protein (CRP). CRP is an important gene in the fields of cardiovascular and inflammation genetics, and its size (~2 kb) makes it particularly amenable medical or deep re-sequencing. With these data, we explore several issues related to the present-day candidate gene association study including the benefits of complete SNP discovery, the effects of tagSNP selection across diverse populations, and completeness of dbSNP for CRP. Also, we show that while deep re-sequencing uncovers potentially medically relevant coding SNPs, these SNPs are fleetingly rare when genotyped in a population-based survey of 7,000 Americans (NHANES III). Collectively, these data suggest that several different types re-sequencing and genotyping approaches may be required to fully understand the complete spectrum of alleles that impact human phenotypes. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at http://dx.doi.org/10.1007/s00439-006-0160-y and is accessible for authorized users

Analysis of meiotic recombination in 22q11.2, a region that frequently undergoes deletions and duplications

BACKGROUND: The 22q11.2 deletion syndrome is the most frequent genomic disorder with an estimated frequency of 1/4000 live births. The majority of patients (90%) have the same deletion of 3 Mb (Typically Deleted Region, TDR) that results from aberrant recombination at meiosis between region specific low-copy repeats (LCRs). METHODS: As a first step towards the characterization of recombination rates and breakpoints within the 22q11.2 region we have constructed a high resolution recombination breakpoint map based on pedigree analysis and a population-based historical recombination map based on LD analysis. RESULTS: Our pedigree map allows the location of recombination breakpoints with a high resolution (potential recombination hotspots), and this approach has led to the identification of 5 breakpoint segments of 50 kb or less (8.6 kb the smallest), that coincide with historical hotspots. It has been suggested that aberrant recombination leading to deletion (and duplication) is caused by low rates of Allelic Homologous Recombination (AHR) within the affected region. However, recombination rate estimates for 22q11.2 region show that neither average recombination rates in the 22q11.2 region or within LCR22-2 (the LCR implicated in most deletions and duplications), are significantly below chromosome 22 averages. Furthermore, LCR22-2, the repeat most frequently implicated in rearrangements, is also the LCR22 with the highest levels of AHR. In addition, we find recombination events in the 22q11.2 region to cluster within families. Within this context, the same chromosome recombines twice in one family; first by AHR and in the next generation by NAHR resulting in an individual affected with the del22q11.2 syndrome. CONCLUSION: We show in the context of a first high resolution pedigree map of the 22q11.2 region that NAHR within LCR22 leading to duplications and deletions cannot be explained exclusively under a hypothesis of low AHR rates. In addition, we find that AHR recombination events cluster within families. If normal and aberrant recombination are mechanistically related, the fact that LCR22s undergo frequent AHR and that we find familial differences in recombination rates within the 22q11.2 region would have obvious health-related implications

Array-CGH in patients with Kabuki-like phenotype: Identification of two patients with complex rearrangements including 2q37 deletions and no other recurrent aberration

Background: Kabuki syndrome (KS) is a multiple congenital anomaly syndrome characterized by specific facial features, mild to moderate mental retardation, postnatal growth delay, skeletal abnormalities, and unusual dermatoglyphic patterns with prominent fingertip pads. A 3.5 Mb duplication at 8p23.1-p22 was once reported as a specific alteration in KS but has not been confirmed in other patients. The molecular basis of KS remains unknown. Methods: We have studied 16 Spanish patients with a clinical diagnosis of KS or KS-like to search for genomic imbalances using genome-wide array technologies. All putative rearrangements were confirmed by FISH, microsatellite markers and/or MLPA assays, which also determined whether the imbalance was de novo or inherited. Results: No duplication at 8p23.1-p22 was observed in our patients. We detected complex rearrangements involving 2q in two patients with Kabuki-like features: 1) a de novo inverted duplication of 11 Mb with a 4.5 Mb terminal deletion, and 2) a de novo 7.2 Mb-terminal deletion in a patient with an additional de novo 0.5 Mb interstitial deletion in 16p. Additional copy number variations (CNV), either inherited or reported in normal controls, were identified and interpreted as polymorphic variants. No specific CNV was significantly increased in the KS group. Conclusion: Our results further confirmed that genomic duplications of 8p23 region are not a common cause of KS and failed to detect other recurrent rearrangement causing this disorder. The detection of two patients with 2q37 deletions suggests that there is a phenotypic overlap between the two conditions, and screening this region in the Kabuki-like patients should be considered.This work was funded by grants from the Spanish Ministry of Health (FIS PI042063), Genome Spain and the European Commission (FP6-2005-037627). IC was supported by a Juan de la Cierva Postdoctoral fellowship